diff --git a/.badgery.yaml b/.badgery.yaml
new file mode 100644
index 0000000..99bcdc1
--- /dev/null
+++ b/.badgery.yaml
@@ -0,0 +1,72 @@
+default_branch: master
+develop_branch: develop
+
+cards:
+  - group: Tests
+    type: gh_action
+    title: Code/package tests (GitHub)
+    file: test.yml
+    enabled: true
+  - group: Tests
+    type: gh_action
+    title: Tutorial tests (GitHub)
+    file: tutorial-tests.yml
+    enabled: true
+
+  - group: Tests
+    type: gh_action
+    title: Package tests (PyPI)
+    file: pypi-test.yml
+    enabled: true
+
+  - group: Code Quality
+    type: codefactor
+    title: Code quality (CodeFactor)
+    enabled: true
+
+  - group: Code Quality
+    type: radon_mi
+    title: Maintainability index (radon)
+    report: reports/{branch}/maintainability-index.json
+    enabled: true
+
+  - group: Code Quality
+    type: radon_cc
+    title: Cyclomatic complexity (radon)
+    report: reports/{branch}/cyclomatic-complexity.json
+    enabled: true
+
+  - group: Size
+    type: radon_loc
+    title: Source/Logical lines of code (radon)
+    report: reports/{branch}/raw-metrics.json
+    enabled: true
+
+  - group: Size
+    type: radon_ff
+    title: Functions/Files count (radon)
+    report: reports/{branch}/cyclomatic-complexity.json
+    enabled: true
+
+  - group: Coverage
+    type: codecov
+    title: Unit test coverage (Codecov)
+    flag: unittests
+    enabled: true
+
+  - group: Coverage
+    type: interrogate
+    title: Docstring coverage (interrogate)
+    report: reports/{branch}/coverage-docstring.txt
+    enabled: true
+  - group: Build & Release
+    type: gh_action
+    title: Publishing (PyPI)
+    workflow: pypi-publish.yml
+    enabled: true
+
+  - group: Build & Release
+    type: gh_action
+    title: Docs build/deployment
+    workflow: docs.yml
+    enabled: true
diff --git a/.codecov.yml b/.codecov.yml
new file mode 100644
index 0000000..40872be
--- /dev/null
+++ b/.codecov.yml
@@ -0,0 +1,27 @@
+# Codecov configuration
+# https://docs.codecov.com/docs/codecov-yaml
+
+github_checks:
+  annotations: true
+
+comment:
+  layout: 'reach, diff, flags, files'
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+
+coverage:
+  status:
+    project:
+      default:
+        target: 80%
+        threshold: 0%
+        # require project coverage, don't allow wiggle room.
+        informational: false
+    patch:
+      default:
+        target: 80%
+        threshold: 5%
+        # Make patch coverage informational (won't block PR)
+        informational: true
diff --git a/.copier-answers.yml b/.copier-answers.yml
index 01349b0..92b8e27 100644
--- a/.copier-answers.yml
+++ b/.copier-answers.yml
@@ -1,11 +1,27 @@
-# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: e4625c1
-_src_path: gh:/EasyScience/EasyProjectTemplate
-description: Python package for bragg-edge analysis
-max_python: '3.12'
-min_python: '3.9'
-orgname: EasyScience
-packagename: easyimaging
-prettyname: Easyimaging
-projectname: EasyImaging
-year: 2024
+# WARNING: Do not edit this file manually.
+# Any changes will be overwritten by Copier.
+_commit: v0.11.4
+_src_path: gh:easyscience/templates
+app_docs_url: https://easyscience.github.io/imaging-app
+app_doi: 10.5281/zenodo.18163581
+app_package_name: easyimaging_app
+app_python: '3.13'
+app_repo_name: imaging-app
+home_page_url: https://easyscience.github.io/imaging
+home_repo_name: imaging
+lib_docs_url: https://easyscience.github.io/imaging-lib
+lib_doi: 10.5281/zenodo.18163581
+lib_package_name: easyimaging
+lib_python_max: '3.13'
+lib_python_min: '3.11'
+lib_repo_name: imaging-lib
+project_contact_email: support@easyscience.org
+project_copyright_years: 2024-2026
+project_extended_description: A software for performing Bragg-edge calculations based
+    on a crystalliographic model and refining its parameters against experimental
+    data
+project_name: EasyImaging
+project_short_description: Neutron imaging data analysis
+project_shortcut: EI
+project_type: both
+template_type: lib
diff --git a/.github/actions/download-artifact/action.yml b/.github/actions/download-artifact/action.yml
new file mode 100644
index 0000000..d1fff1a
--- /dev/null
+++ b/.github/actions/download-artifact/action.yml
@@ -0,0 +1,50 @@
+name: 'Download artifact'
+description: 'Wrapper for actions/download-artifact'
+inputs:
+  name:
+    description: 'Name of the artifact to download'
+    required: true
+
+  path:
+    description: 'Destination path'
+    required: false
+    default: '.'
+
+  pattern:
+    description: 'Glob pattern to match artifact names (optional)'
+    required: false
+    default: ''
+
+  merge-multiple:
+    description: 'Merge multiple artifacts into the same directory'
+    required: false
+    default: 'false'
+
+  github-token:
+    description: 'GitHub token for cross-repo download (optional)'
+    required: false
+    default: ''
+
+  repository:
+    description: 'owner/repo for cross-repo download (optional)'
+    required: false
+    default: ''
+
+  run-id:
+    description: 'Workflow run ID for cross-run download (optional)'
+    required: false
+    default: ''
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Download artifact
+      uses: actions/download-artifact@v8
+      with:
+        name: ${{ inputs.name }}
+        path: ${{ inputs.path }}
+        pattern: ${{ inputs.pattern }}
+        merge-multiple: ${{ inputs.merge-multiple }}
+        github-token: ${{ inputs.github-token }}
+        repository: ${{ inputs.repository }}
+        run-id: ${{ inputs.run-id }}
diff --git a/.github/actions/github-script/action.yml b/.github/actions/github-script/action.yml
new file mode 100644
index 0000000..50de89b
--- /dev/null
+++ b/.github/actions/github-script/action.yml
@@ -0,0 +1,19 @@
+name: 'GitHub Script'
+description: 'Wrapper for actions/github-script'
+inputs:
+  script:
+    description: 'JavaScript to run'
+    required: true
+
+  github-token:
+    description: 'GitHub token (defaults to github.token)'
+    required: false
+    default: ${{ github.token }}
+
+runs:
+  using: 'composite'
+  steps:
+    - uses: actions/github-script@v9
+      with:
+        script: ${{ inputs.script }}
+        github-token: ${{ inputs.github-token }}
diff --git a/.github/actions/setup-easyscience-bot/action.yml b/.github/actions/setup-easyscience-bot/action.yml
new file mode 100644
index 0000000..e51eb01
--- /dev/null
+++ b/.github/actions/setup-easyscience-bot/action.yml
@@ -0,0 +1,40 @@
+name: 'Setup EasyScience bot for pushing'
+description: 'Create GitHub App token and configure git identity + origin remote'
+inputs:
+  app-id:
+    description: 'GitHub App ID'
+    required: true
+  private-key:
+    description: 'GitHub App private key (PEM)'
+    required: true
+  repositories:
+    description: 'Additional repositories to grant access to (newline-separated)'
+    required: false
+    default: ''
+
+outputs:
+  token:
+    description: 'Installation access token'
+    value: ${{ steps.app-token.outputs.token }}
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Create GitHub App installation token
+      id: app-token
+      uses: actions/create-github-app-token@v3
+      with:
+        client-id: ${{ inputs.app-id }}
+        private-key: ${{ inputs.private-key }}
+        repositories: ${{ inputs.repositories }}
+
+    - name: Configure git for pushing
+      shell: bash
+      run: |
+        git config user.name "easyscience[bot]"
+        git config user.email "${{ inputs.app-id }}+easyscience[bot]@users.noreply.github.com"
+
+    - name: Configure origin remote to use the bot token
+      shell: bash
+      run: |
+        git remote set-url origin https://x-access-token:${{ steps.app-token.outputs.token }}@github.com/${{ github.repository }}.git
diff --git a/.github/actions/setup-pixi/action.yml b/.github/actions/setup-pixi/action.yml
index 8c68f51..dc3232c 100644
--- a/.github/actions/setup-pixi/action.yml
+++ b/.github/actions/setup-pixi/action.yml
@@ -1,16 +1,24 @@
 name: 'Setup Pixi Environment'
-description: 'Sets up pixi with common configuration'
+description: 'Wrapper for prefix-dev/setup-pixi'
 inputs:
   environments:
     description: 'Pixi environments to setup'
     required: false
-    default: 'dev'
+    default: 'default'
   activate-environment:
     description: 'Environment to activate'
     required: false
-    default: 'dev'
+    default: 'default'
   run-install:
-    description: 'Whether to run install'
+    description: 'Whether to run pixi install'
+    required: false
+    default: 'true'
+  locked:
+    description: 'Whether to run pixi install --locked'
+    required: false
+    default: 'false'
+  frozen:
+    description: 'Whether to run pixi install --frozen'
     required: false
     default: 'true'
   cache:
@@ -25,10 +33,12 @@ inputs:
 runs:
   using: 'composite'
   steps:
-    - uses: prefix-dev/setup-pixi@v0.9.0
+    - uses: prefix-dev/setup-pixi@v0.9.5
       with:
         environments: ${{ inputs.environments }}
         activate-environment: ${{ inputs.activate-environment }}
         run-install: ${{ inputs.run-install }}
+        locked: ${{ inputs.locked }}
+        frozen: ${{ inputs.frozen }}
         cache: ${{ inputs.cache }}
-        post-cleanup: ${{ inputs.post-cleanup }}
\ No newline at end of file
+        post-cleanup: ${{ inputs.post-cleanup }}
diff --git a/.github/actions/upload-artifact/action.yml b/.github/actions/upload-artifact/action.yml
new file mode 100644
index 0000000..fe8e468
--- /dev/null
+++ b/.github/actions/upload-artifact/action.yml
@@ -0,0 +1,49 @@
+name: 'Upload artifact'
+description: 'Wrapper for actions/upload-artifact'
+inputs:
+  name:
+    description: 'Artifact name'
+    required: true
+
+  path:
+    description: 'File(s)/dir(s)/glob(s) to upload (newline-separated)'
+    required: true
+
+  include-hidden-files:
+    description: 'Include hidden files'
+    required: false
+    default: 'true'
+
+  if-no-files-found:
+    description: 'warn | error | ignore'
+    required: false
+    default: 'error'
+
+  compression-level:
+    description: '0-9 (0 = no compression)'
+    required: false
+    default: '0'
+
+  retention-days:
+    description: 'Retention in days (optional)'
+    required: false
+    default: ''
+
+  overwrite:
+    description: 'Overwrite an existing artifact with the same name'
+    required: false
+    default: 'false'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Upload artifact
+      uses: actions/upload-artifact@v7
+      with:
+        name: ${{ inputs.name }}
+        path: ${{ inputs.path }}
+        include-hidden-files: ${{ inputs.include-hidden-files }}
+        if-no-files-found: ${{ inputs.if-no-files-found }}
+        compression-level: ${{ inputs.compression-level }}
+        retention-days: ${{ inputs.retention-days }}
+        overwrite: ${{ inputs.overwrite }}
diff --git a/.github/actions/upload-codecov/action.yml b/.github/actions/upload-codecov/action.yml
new file mode 100644
index 0000000..0cb15d1
--- /dev/null
+++ b/.github/actions/upload-codecov/action.yml
@@ -0,0 +1,42 @@
+name: 'Upload coverage to Codecov'
+description: 'Wrapper for codecov/codecov-action'
+
+inputs:
+  name:
+    description: 'Codecov upload name'
+    required: true
+
+  flags:
+    description: 'Codecov flags'
+    required: false
+    default: ''
+
+  files:
+    description: 'Coverage report files'
+    required: true
+
+  fail_ci_if_error:
+    description: 'Fail CI if upload fails'
+    required: false
+    default: 'true'
+
+  verbose:
+    description: 'Enable verbose output'
+    required: false
+    default: 'true'
+
+  token:
+    description: 'Codecov token'
+    required: true
+
+runs:
+  using: composite
+  steps:
+    - uses: codecov/codecov-action@v6
+      with:
+        name: ${{ inputs.name }}
+        flags: ${{ inputs.flags }}
+        files: ${{ inputs.files }}
+        fail_ci_if_error: ${{ inputs.fail_ci_if_error }}
+        verbose: ${{ inputs.verbose }}
+        token: ${{ inputs.token }}
diff --git a/.github/configs/pages-deployment.json b/.github/configs/pages-deployment.json
new file mode 100644
index 0000000..c0d3fbe
--- /dev/null
+++ b/.github/configs/pages-deployment.json
@@ -0,0 +1,6 @@
+{
+  "source": {
+    "branch": "gh-pages",
+    "path": "/"
+  }
+}
diff --git a/.github/configs/rulesets-develop.json b/.github/configs/rulesets-develop.json
new file mode 100644
index 0000000..04489e5
--- /dev/null
+++ b/.github/configs/rulesets-develop.json
@@ -0,0 +1,37 @@
+{
+  "name": "develop branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/develop"],
+      "exclude": []
+    }
+  },
+  "bypass_actors": [
+    {
+      "actor_id": 2476259,
+      "actor_type": "Integration",
+      "bypass_mode": "always"
+    }
+  ],
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "allowed_merge_methods": ["squash"],
+        "dismiss_stale_reviews_on_push": false,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_approving_review_count": 0,
+        "required_review_thread_resolution": false
+      }
+    }
+  ]
+}
diff --git a/.github/configs/rulesets-gh-pages.json b/.github/configs/rulesets-gh-pages.json
new file mode 100644
index 0000000..ebf3892
--- /dev/null
+++ b/.github/configs/rulesets-gh-pages.json
@@ -0,0 +1,19 @@
+{
+  "name": "gh-pages branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/gh-pages"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    }
+  ]
+}
diff --git a/.github/configs/rulesets-master.json b/.github/configs/rulesets-master.json
new file mode 100644
index 0000000..f658a5c
--- /dev/null
+++ b/.github/configs/rulesets-master.json
@@ -0,0 +1,30 @@
+{
+  "name": "master branch",
+  "target": "branch",
+  "enforcement": "active",
+  "conditions": {
+    "ref_name": {
+      "include": ["~DEFAULT_BRANCH"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "allowed_merge_methods": ["merge"],
+        "dismiss_stale_reviews_on_push": false,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_approving_review_count": 0,
+        "required_review_thread_resolution": false
+      }
+    }
+  ]
+}
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
index a95ea8f..16c5c0d 100644
--- a/.github/release-drafter.yml
+++ b/.github/release-drafter.yml
@@ -2,30 +2,30 @@
 name-template: v$NEXT_PATCH_VERSION 🌈
 tag-template: v$NEXT_PATCH_VERSION
 categories:
-- title: 🚀 Features
-  labels:
-  - feature
-  - enhancement
-- title: 🐛 Bug Fixes
-  labels:
-  - fix
-  - bugfix
-  - bug
-- title: 🧰 Maintenance
-  labels:
-  - chore
-  - documentation
+  - title: 🚀 Features
+    labels:
+      - feature
+      - enhancement
+  - title: 🐛 Bug Fixes
+    labels:
+      - fix
+      - bugfix
+      - bug
+  - title: 🧰 Maintenance
+    labels:
+      - chore
+      - documentation
 change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
 version-resolver:
   major:
     labels:
-    - major
+      - major
   minor:
     labels:
-    - minor
+      - minor
   patch:
     labels:
-    - patch
+      - patch
   default: patch
 template: |
   ## Changes
diff --git a/.github/scripts/backmerge-conflict-issue.js b/.github/scripts/backmerge-conflict-issue.js
new file mode 100644
index 0000000..f6bd98b
--- /dev/null
+++ b/.github/scripts/backmerge-conflict-issue.js
@@ -0,0 +1,69 @@
+module.exports = async ({ github, context, core }) => {
+  // Repo context
+  const owner = context.repo.owner
+  const repo = context.repo.repo
+
+  // Link to the exact workflow run that detected the conflict
+  const runUrl = `${context.serverUrl}/${owner}/${repo}/actions/runs/${context.runId}`
+
+  // We use a *stable title* so we can find/reuse the same "conflict tracker" issue
+  // instead of creating a new issue on every failed run.
+  const title = 'Backmerge conflict: master → develop'
+
+  // Comment/issue body includes the run URL so maintainers can jump straight to logs.
+  const body = [
+    'Automatic backmerge failed due to merge conflicts.',
+    '',
+    `Workflow run: ${runUrl}`,
+    '',
+    'Manual resolution required.',
+  ].join('\n')
+
+  // Label applied to the tracker issue (assumed to already exist in the repo).
+  const label = '[bot] backmerge'
+
+  // Search issues by title across *open and closed* issues.
+  // Why: if the conflict was resolved previously and the issue was closed,
+  // we prefer to reopen it and append a new comment instead of creating duplicates.
+  const q = `repo:${owner}/${repo} is:issue in:title "${title}"`
+  const search = await github.rest.search.issuesAndPullRequests({
+    q,
+    per_page: 10,
+  })
+
+  // Pick the first exact-title match (search can return partial matches).
+  const existing = search.data.items.find((i) => i.title === title)
+
+  if (existing) {
+    // If a tracker issue exists, reuse it:
+    // - reopen it if needed
+    // - add a comment with the new run URL
+    if (existing.state === 'closed') {
+      await github.rest.issues.update({
+        owner,
+        repo,
+        issue_number: existing.number,
+        state: 'open',
+      })
+    }
+
+    await github.rest.issues.createComment({
+      owner,
+      repo,
+      issue_number: existing.number,
+      body,
+    })
+
+    core.notice(`Conflict issue updated: #${existing.number}`)
+    return
+  }
+
+  // No tracker issue exists yet -> create the first one.
+  await github.rest.issues.create({
+    owner,
+    repo,
+    title,
+    body,
+    labels: [label],
+  })
+}
diff --git a/.github/scripts/publish-dashboard.sh b/.github/scripts/publish-dashboard.sh
new file mode 100644
index 0000000..dcbd0b3
--- /dev/null
+++ b/.github/scripts/publish-dashboard.sh
@@ -0,0 +1,77 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+remote_repository="${DASHBOARD_REMOTE_REPOSITORY:?}"
+publish_branch="${DASHBOARD_PUBLISH_BRANCH:-master}"
+source_dir="${DASHBOARD_SOURCE_DIR:?}"
+token="${DASHBOARD_TOKEN:?}"
+git_user_name="${DASHBOARD_GIT_USER_NAME:-easyscience[bot]}"
+git_user_email="${DASHBOARD_GIT_USER_EMAIL:?}"
+commit_message="${DASHBOARD_COMMIT_MESSAGE:?}"
+max_attempts="${DASHBOARD_PUSH_ATTEMPTS:-3}"
+delay_seconds="${DASHBOARD_PUSH_DELAY_SECONDS:-15}"
+
+workspace_dir="$(mktemp -d)"
+repo_dir="${workspace_dir}/dashboard"
+remote_url="https://x-access-token:${token}@github.com/${remote_repository}.git"
+
+cleanup() {
+  rm -rf "${workspace_dir}"
+}
+
+prepare_worktree() {
+  if [[ ! -d "${repo_dir}/.git" ]]; then
+    git clone --branch "${publish_branch}" --depth 1 "${remote_url}" "${repo_dir}"
+  else
+    git -C "${repo_dir}" fetch origin "${publish_branch}"
+    git -C "${repo_dir}" checkout "${publish_branch}"
+    git -C "${repo_dir}" reset --hard "origin/${publish_branch}"
+    git -C "${repo_dir}" clean -fd
+  fi
+
+  git -C "${repo_dir}" config user.name "${git_user_name}"
+  git -C "${repo_dir}" config user.email "${git_user_email}"
+}
+
+sync_publish_dir() {
+  cp -R "${source_dir}/." "${repo_dir}/"
+  git -C "${repo_dir}" add .
+
+  if git -C "${repo_dir}" diff --cached --quiet; then
+    return 1
+  fi
+
+  git -C "${repo_dir}" commit -m "${commit_message}"
+}
+
+trap cleanup EXIT
+
+prepare_worktree
+
+if ! sync_publish_dir; then
+  echo "No dashboard changes to publish."
+  exit 0
+fi
+
+for ((attempt = 1; attempt <= max_attempts; attempt += 1)); do
+  if git -C "${repo_dir}" push origin "HEAD:${publish_branch}"; then
+    echo "Dashboard published on attempt ${attempt}."
+    exit 0
+  fi
+
+  if ((attempt == max_attempts)); then
+    echo "Dashboard publish failed after ${max_attempts} attempts." >&2
+    exit 1
+  fi
+
+  echo "Dashboard push attempt ${attempt} failed. Retrying in ${delay_seconds}s." >&2
+  sleep "${delay_seconds}"
+
+  prepare_worktree
+
+  if ! sync_publish_dir; then
+    echo "Dashboard changes already exist in the target repository."
+    exit 0
+  fi
+done
\ No newline at end of file
diff --git a/.github/workflows/backmerge.yml b/.github/workflows/backmerge.yml
new file mode 100644
index 0000000..36ce6f5
--- /dev/null
+++ b/.github/workflows/backmerge.yml
@@ -0,0 +1,109 @@
+# This workflow automatically merges `master` into `develop` whenever a
+# new version release with a tag is published. It can also be triggered
+# manually via workflow_dispatch for cases where an automatic backmerge
+# is needed outside of the standard release process.
+# If a merge conflict occurs, the workflow creates an issue to notify
+# maintainers for manual resolution.
+
+name: Backmerge (master → develop)
+
+on:
+  release:
+    types: [published, prereleased]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  issues: write
+
+concurrency:
+  group: backmerge-master-into-develop
+  cancel-in-progress: false
+
+jobs:
+  backmerge:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - name: Checkout repository (for local actions)
+        uses: actions/checkout@v6
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+          repositories: ${{ github.event.repository.name }}
+
+      - name: Checkout repository (with bot token)
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          token: ${{ steps.bot.outputs.token }}
+
+      - name: Configure git identity
+        run: |
+          git config user.name "easyscience[bot]"
+          git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com"
+
+      - name: Set merge message
+        run: |
+          if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then
+            MESSAGE="Backmerge: master into develop (manual) [skip ci]"
+          else
+            TAG="${{ github.event.release.tag_name }}"
+            MESSAGE="Backmerge: master (${TAG}) into develop [skip ci]"
+          fi
+
+          echo "MESSAGE=$MESSAGE" >> "$GITHUB_ENV"
+          echo "message=$MESSAGE" >> "$GITHUB_OUTPUT"
+          echo "📝 Merge message: $MESSAGE" | tee -a "$GITHUB_STEP_SUMMARY"
+
+      - name: Prepare branches
+        run: |
+          git fetch origin master develop
+          git checkout -B develop origin/develop
+
+      - name: Check if develop is already up-to-date
+        id: up_to_date
+        run: |
+          if git merge-base --is-ancestor origin/master develop; then
+            echo "value=true" >> "$GITHUB_OUTPUT"
+            echo "ℹ️ Develop is already up-to-date with master" | tee -a "$GITHUB_STEP_SUMMARY"
+          else
+            echo "value=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Try merge master into develop
+        id: merge
+        if: steps.up_to_date.outputs.value == 'false'
+        continue-on-error: true
+        run: |
+          if ! git merge origin/master --no-ff -m "${MESSAGE}"; then
+            echo "conflict=true" >> "$GITHUB_OUTPUT"
+            echo "❌ Backmerge conflict detected." | tee -a "$GITHUB_STEP_SUMMARY"
+            git status --porcelain || true
+            exit 0
+          fi
+
+          echo "conflict=false" >> "$GITHUB_OUTPUT"
+          echo "✅ Merge commit created." | tee -a "$GITHUB_STEP_SUMMARY"
+
+      - name: Push to develop (if merge succeeded)
+        if:
+          steps.up_to_date.outputs.value == 'false' && steps.merge.outputs.conflict ==
+          'false'
+        run: |
+          git push origin develop
+          echo "🚀 Backmerge successful: master → develop" | tee -a "$GITHUB_STEP_SUMMARY"
+
+      - name: Create issue (if merge failed with conflicts)
+        if: steps.merge.outputs.conflict == 'true'
+        uses: ./.github/actions/github-script
+        with:
+          github-token: ${{ steps.bot.outputs.token }}
+          script: |
+            const run = require('./.github/scripts/backmerge-conflict-issue.js')
+            await run({ github, context, core })
diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml
new file mode 100644
index 0000000..21c72b3
--- /dev/null
+++ b/.github/workflows/cleanup.yml
@@ -0,0 +1,84 @@
+# This workflow will delete old workflow runs based on the input
+# parameters.
+# https://github.com/Mattraks/delete-workflow-runs
+
+name: Old workflow runs cleanup
+
+on:
+  # Run monthly, at 00:00 on the 1st day of month.
+  schedule:
+    - cron: '0 0 1 * *'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      days:
+        description: 'Number of days.'
+        required: true
+        default: '30'
+      minimum_runs:
+        description: 'The minimum runs to keep for each workflow.'
+        required: true
+        default: '6'
+      delete_workflow_pattern:
+        description:
+          'The name or filename of the workflow. if not set then it will target all
+          workflows.'
+        required: false
+      delete_workflow_by_state_pattern:
+        description:
+          'Remove workflow by state: active, deleted, disabled_fork,
+          disabled_inactivity, disabled_manually'
+        required: true
+        default: 'All'
+        type: choice
+        options:
+          - 'All'
+          - active
+          - deleted
+          - disabled_inactivity
+          - disabled_manually
+      delete_run_by_conclusion_pattern:
+        description:
+          'Remove workflow by conclusion: action_required, cancelled, failure, skipped,
+          success'
+        required: true
+        default: 'All'
+        type: choice
+        options:
+          - 'All'
+          - action_required
+          - cancelled
+          - failure
+          - skipped
+          - success
+      dry_run:
+        description: 'Only log actions, do not perform any delete operations (dry run).'
+        required: false
+        default: 'false'
+        type: choice
+        options:
+          - 'false'
+          - 'true'
+
+jobs:
+  del-runs:
+    runs-on: ubuntu-latest
+
+    permissions:
+      actions: write
+
+    steps:
+      - name: Delete workflow runs
+        uses: Mattraks/delete-workflow-runs@v2
+        with:
+          token: ${{ github.token }}
+          repository: ${{ github.repository }}
+          retain_days: ${{ github.event.inputs.days }}
+          keep_minimum_runs: ${{ github.event.inputs.minimum_runs }}
+          delete_workflow_pattern: ${{ github.event.inputs.delete_workflow_pattern }}
+          delete_workflow_by_state_pattern:
+            ${{ github.event.inputs.delete_workflow_by_state_pattern }}
+          delete_run_by_conclusion_pattern:
+            ${{ github.event.inputs.delete_run_by_conclusion_pattern }}
+          dry_run: ${{ github.event.inputs.dry_run }}
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
deleted file mode 100644
index 42eee5b..0000000
--- a/.github/workflows/codeql-analysis.yml
+++ /dev/null
@@ -1,71 +0,0 @@
-# CodeQL is the code analysis engine developed by GitHub to automate security checks.
-#
-# For more information see: https://docs.github.com/en/code-security/code-scanning/introduction-to-code-scanning/about-code-scanning-with-codeql
-
-
-name: "CodeQL"
-
-on:
-  push:
-    branches: [ master, pre-release, develop ]
-  pull_request:
-    # The branches below must be a subset of the branches above
-    branches: [ master ]
-  schedule:
-    - cron: '0 16 * * 5'
-
-jobs:
-  analyze:
-    name: Analyze
-    runs-on: ubuntu-latest
-
-    strategy:
-      fail-fast: false
-      matrix:
-        # Override automatic language detection by changing the below list
-        # Supported options are ['csharp', 'cpp', 'go', 'java', 'javascript', 'python']
-        language: ['python']
-        # Learn more...
-        # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        # We must fetch at least the immediate parents so that if this is
-        # a pull request then we can checkout the head.
-        fetch-depth: 2
-
-    # If this run was triggered by a pull request event, then checkout
-    # the head of the pull request instead of the merge commit.
-    - run: git checkout HEAD^2
-      if: ${{ github.event_name == 'pull_request' }}
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@master
-
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
-
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
-
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
-
-    #- run: |
-    #   make bootstrap
-    #   make release
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
\ No newline at end of file
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
new file mode 100644
index 0000000..5208a33
--- /dev/null
+++ b/.github/workflows/coverage.yml
@@ -0,0 +1,70 @@
+name: Coverage checks
+
+on:
+  # Trigger the workflow on push to develop
+  push:
+    branches:
+      - develop
+  # Trigger the workflow on pull request
+  pull_request:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Need permissions to trigger the dashboard build workflow
+permissions:
+  actions: write
+  contents: read
+
+# Allow only one concurrent workflow per PR or branch ref.
+# Cancel in-progress runs only for pull requests, but let branch push runs finish.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+
+jobs:
+  # Job 1: Run docstring coverage
+  docstring-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v6
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      - name: Run docstring coverage
+        run: pixi run docstring-coverage
+
+  # Job 2: Run unit tests with coverage and upload to Codecov
+  unit-tests-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v6
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      - name: Run unit tests with coverage
+        run: pixi run unit-tests-coverage --cov-report=xml:coverage-unit.xml
+
+      - name: Upload unit tests coverage to Codecov
+        if: ${{ !cancelled() }}
+        uses: ./.github/actions/upload-codecov
+        with:
+          name: unit-tests-job
+          flags: unittests
+          files: ./coverage-unit.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  # Job 4: Build and publish dashboard (reusable workflow)
+  run-reusable-workflows:
+    needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs
+    uses: ./.github/workflows/dashboard.yml
+    secrets: inherit
diff --git a/.github/workflows/dashboard.yml b/.github/workflows/dashboard.yml
new file mode 100644
index 0000000..573e308
--- /dev/null
+++ b/.github/workflows/dashboard.yml
@@ -0,0 +1,115 @@
+name: Dashboard build and publish
+
+on:
+  workflow_dispatch:
+  workflow_call:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: dashboard-publish-${{ github.repository }}
+  cancel-in-progress: false
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+  DEVELOP_BRANCH: develop
+  REPO_OWNER: ${{ github.repository_owner }}
+  REPO_NAME: ${{ github.event.repository.name }}
+
+jobs:
+  dashboard:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      # Install badgery into the active Pixi environment without modifying
+      # pixi.toml/pixi.lock. Using `pixi add` here re-solves the whole project
+      # and rebuilds the local editable package, which can cause intermittent
+      # Linux CI failures (`Text file busy`, os error 26).
+      - name: Install badgery
+        shell: bash
+        run: pixi run python -m pip install git+https://github.com/enhantica/badgery
+
+      - name: Run docstring coverage and code complexity/maintainability checks
+        run: |
+          for BRANCH in $DEFAULT_BRANCH $DEVELOP_BRANCH $CI_BRANCH; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Processing branch $BRANCH 🔹🔸🔹🔸🔹"
+            if [ -d "../$BRANCH" ]; then
+              echo "Branch $BRANCH already processed, skipping"
+              continue
+            fi
+
+            git worktree add ../$BRANCH origin/$BRANCH
+            mkdir -p reports/$BRANCH
+
+            echo "Docstring coverage for branch $BRANCH"
+            pixi run interrogate -c pyproject.toml --fail-under=0 ../$BRANCH/src > reports/$BRANCH/coverage-docstring.txt
+
+            echo "Cyclomatic complexity for branch $BRANCH"
+            pixi run radon cc -s -j ../$BRANCH/src > reports/$BRANCH/cyclomatic-complexity.json
+
+            echo "Maintainability index for branch $BRANCH"
+            pixi run radon mi -j ../$BRANCH/src > reports/$BRANCH/maintainability-index.json
+
+            echo "Raw metrics for branch $BRANCH"
+            pixi run radon raw -s -j ../$BRANCH/src > reports/$BRANCH/raw-metrics.json
+          done
+
+      - name: Generate dashboard HTML
+        run: >
+          pixi run python -m badgery --config .badgery.yaml --repo ${{ github.repository
+          }} --branch ${{ env.CI_BRANCH }} --output index.html
+
+      - name: Prepare publish directory
+        run: |
+          mkdir -p _dashboard_publish/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }}
+          cp index.html _dashboard_publish/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }}
+
+      # Create GitHub App token for pushing to external dashboard repo.
+      # The 'repositories' parameter is required to grant access to repos
+      # other than the one where the workflow is running.
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+          repositories: |
+            ${{ github.event.repository.name }}
+            dashboard
+
+      # Push to external dashboard repository with retry logic.
+      # Retry is needed to handle transient GitHub API/authentication issues
+      # that occasionally cause 403 errors when multiple workflows push concurrently.
+      # Uses personal_token (not github_token) as GITHUB_TOKEN cannot access external repos.
+      - name:
+          Push to ${{ env.REPO_OWNER }}/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH
+          }}
+        shell: bash
+        env:
+          DASHBOARD_COMMIT_MESSAGE: ${{ env.CI_BRANCH }}
+          DASHBOARD_GIT_USER_EMAIL:
+            ${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com
+          DASHBOARD_PUSH_ATTEMPTS: '3'
+          DASHBOARD_PUSH_DELAY_SECONDS: '15'
+          DASHBOARD_PUBLISH_BRANCH: master
+          DASHBOARD_REMOTE_REPOSITORY: ${{ env.REPO_OWNER }}/dashboard
+          DASHBOARD_SOURCE_DIR: ./_dashboard_publish
+          DASHBOARD_TOKEN: ${{ steps.bot.outputs.token }}
+        run: bash ./.github/scripts/publish-dashboard.sh
+
+      - name: Add dashboard link to summary
+        run: |
+          URL="https://${{ env.REPO_OWNER }}.github.io/dashboard/${{ env.REPO_NAME }}/${{ env.CI_BRANCH }}"
+          echo "Dashboard link: [$URL]($URL)" >> $GITHUB_STEP_SUMMARY
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 0000000..6b6db79
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,188 @@
+# This workflow builds and deploys documentation for the project.
+#
+# Overview:
+#  - Converts tutorial Python scripts to Jupyter notebooks and executes them.
+#  - Builds the documentation site using MkDocs with the Material theme.
+#  - Uploads the built site as an artifact for local inspection.
+#  - Deploys versioned documentation to the gh-pages branch using Mike:
+#    - For release tags (v*): deploys to a versioned folder (e.g., /0.9.1/) and updates /latest/.
+#    - For branches: deploys to /dev/.
+#
+# The action summary page will contain a link to the built artifact for downloading
+# and inspecting, as well as a link to the deployed documentation site.
+
+name: Docs build and deployment
+
+on:
+  # Trigger the workflow on push
+  push:
+    # Selected branches
+    branches: [develop] # master and main are already verified in PR
+    # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
+    tags: ['v*']
+  # Trigger the workflow on pull request
+  pull_request:
+    # Selected branches
+    branches: [master, main, develop]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# - Non-tagged pushes and pull requests all use `docs-dev` group, so
+#   they cancel each other.
+# - Tagged pushes use their own group like docs-v1.2.3, so they do not
+#   cancel non-tagged runs, and non-tagged runs do not cancel them.
+concurrency:
+  group: >-
+    ${{ startsWith(github.ref, 'refs/tags/v')
+      && format('docs-{0}', github.ref_name)
+      || 'docs-dev' }}
+  cancel-in-progress: true
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  # CI_BRANCH - the branch name (used in mkdocs.yml)
+  # For PRs: github.head_ref is the source branch
+  # For pushes: github.ref_name is the branch
+  # For tags: github.ref_name is the tag name
+  # GITHUB_REPOSITORY - the repository name (used in mkdocs.yml)
+  # NOTEBOOKS_DIR - the directory containing the Jupyter notebooks (used in mkdocs.yml)
+  DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+  DEVELOP_BRANCH: develop
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }}
+  GITHUB_REPOSITORY: ${{ github.repository }}
+  NOTEBOOKS_DIR: tutorials
+
+jobs:
+  # Single job that builds and deploys documentation.
+  # Uses macOS runner for consistent Plotly chart rendering.
+  build-deploy-docs:
+    runs-on: ubuntu-latest # macos-latest
+
+    permissions:
+      contents: write # Required for pushing to the gh-pages branch
+
+    steps:
+      # Setting DOCS_VERSION to be used in mkdocs.yml, and then in the
+      # main.html template. It defines the versioned docs subfolder name
+      # in the gh-pages branch. If it's a release tag, use the version
+      # number without the 'v' prefix, otherwise use 'dev'.
+      # Setting RELEASE_VERSION to be used in mkdocs.yml to show
+      # the latest release version in the index.md file. If it's a
+      # release tag, use the tag name, otherwise use the branch name
+      # for development builds.
+      - name: Set extra env variables
+        shell: bash
+        run: |
+          if [[ "${IS_RELEASE_TAG}" == "true" ]]; then
+            RELEASE_VERSION="${GITHUB_REF_NAME}"
+            DOCS_VERSION="${RELEASE_VERSION#v}"
+          else
+            RELEASE_VERSION="${CI_BRANCH}"
+            DOCS_VERSION="dev"
+          fi
+          echo "RELEASE_VERSION=${RELEASE_VERSION}" >> "$GITHUB_ENV"
+          echo "DOCS_VERSION=${DOCS_VERSION}" >> "$GITHUB_ENV"
+
+      # Check out the repository source code.
+      # Note: The gh-pages branch is fetched separately later for mike deployment.
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      # Activate dark mode to create documentation with Plotly charts in dark mode
+      # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher
+      # Something similar to mkdocs_plotly_plugin https://haoda-li.github.io/mkdocs-plotly-plugin/,
+      # but for generating documentation from notepads
+      #- name: Activate dark mode
+      #  run: |
+      #    brew install dark-mode
+      #    dark-mode status
+      #    dark-mode on
+      #    dark-mode status
+
+      # Set up the pixi package manager and install dependencies from pixi.toml.
+      # Uses frozen lockfile to ensure reproducible builds.
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+      # Pre-import the main package to exclude info messages from the docs
+      # E.g., Matplotlib may print messages to stdout/stderr when first
+      # imported. This step allows to avoid "Matplotlib is building the font
+      # cache" messages during notebook execution.
+      - name: Pre-build site step
+        run: pixi run python -c "import easyimaging"
+
+      # Prepare the Jupyter notebooks for documentation (strip output, etc.).
+      - name: Prepare notebooks
+        run: pixi run notebook-prepare
+
+      # Execute all Jupyter notebooks to generate output cells (plots, tables, etc.).
+      # Uses multiple cores for parallel execution to speed up the process.
+      - name: Run notebooks
+        # if: false # Temporarily disabled to speed up the docs build
+        run: pixi run notebook-exec
+
+      # Build the static files for the documentation site for local inspection
+      # Input: docs/ directory containing the Markdown files
+      # Output: site/ directory containing the generated HTML files
+      - name: Build site for local check
+        run: pixi run docs-build-local
+
+      # Upload the static files from the site/ directory to be used for
+      # local check
+      - name: Upload built site as artifact
+        uses: ./.github/actions/upload-artifact
+        with:
+          name: site-local_easyimaging-lib-${{ env.RELEASE_VERSION }}
+          path: docs/site/
+
+      # Create GitHub App token for pushing to gh-pages as easyscience[bot].
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      # Configure git identity and remote URL so mike pushes as easyscience[bot].
+      - name: Configure git for pushing
+        run: |
+          set -euo pipefail
+          git config user.name "easyscience[bot]"
+          git config user.email "${{ vars.EASYSCIENCE_APP_ID }}+easyscience[bot]@users.noreply.github.com"
+          git remote set-url origin "https://x-access-token:${{ steps.bot.outputs.token }}@github.com/${{ github.repository }}.git"
+
+      # Fetch the gh-pages branch to ensure mike has the latest remote state.
+      # This is required because the checkout step only fetches the source branch,
+      # not the gh-pages branch that mike needs to update.
+      - name: Fetch gh-pages branch
+        run: |
+          git fetch origin gh-pages:gh-pages 2>/dev/null || true
+
+      # Deploy versioned documentation using mike (MkDocs plugin for versioning).
+      # - For release tags (v*): deploys to versioned folder (e.g., /0.9.1/) and aliases to /latest/.
+      # - For branches: deploys to /dev/.
+      # The "${RELEASE_VERSION#v}" syntax strips the 'v' prefix (v0.9.1 -> 0.9.1).
+      # Also sets 'latest' as the default version for the version selector.
+      - name: Rebuild and deploy docs with mike
+        run: |
+          # Exit on error (-e), undefined vars (-u), and pipeline failures (pipefail)
+          set -euo pipefail
+
+          REPO_NAME="${{ github.event.repository.name }}"
+          BASE_URL="https://easyscience.github.io/${REPO_NAME}"
+
+          # Deploy the release version and update the "latest" alias
+          if [[ "${IS_RELEASE_TAG}" == "true" ]]; then
+            pixi run docs-deploy-pre "${RELEASE_VERSION#v}" latest
+            pixi run docs-set-default-pre latest
+            DEPLOYMENT_URL="${BASE_URL}/latest"
+
+          # Deploy/update the "dev" alias (or whatever your convention is)
+          else
+            pixi run docs-deploy-pre dev
+            DEPLOYMENT_URL="${BASE_URL}/dev"
+
+          fi
+
+          # Add links to the action summary page for easy access
+          echo "🔗 deployment url [${DEPLOYMENT_URL}](${DEPLOYMENT_URL})" >> "${GITHUB_STEP_SUMMARY}"
diff --git a/.github/workflows/documentation-build.yml b/.github/workflows/documentation-build.yml
deleted file mode 100644
index b238f74..0000000
--- a/.github/workflows/documentation-build.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-# This pipeline
-# - builds developer documentation
-# - pushes documentation to gh-pages branch of the same repository
-#
-# Deployment is handled by pages-build-deployment bot
-#
-# For more information see: https://docs.github.com/en/pages/getting-started-with-github-pages
-
-name: Build Documentation and Push to gh-pages Branch
-
-# Controls when the workflow will run
-on:
-  # Triggers the workflow on tag creation
-  push:
-    tags:
-      - 'v*'
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "build"
-  build_documentation:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v5
-      with:
-        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-
-    - name: Setup Pixi
-      uses: ./.github/actions/setup-pixi
-
-    - name: Build documentation
-      run: pixi run docs-build
-
-    - name: Build and Commit
-      uses: sphinx-notes/pages@master
-      with:
-        install_requirements: true
-        documentation_path: docs/src
-        
-    - name: Push changes
-      uses: ad-m/github-push-action@master
-      continue-on-error: true
-      with:
-        branch: gh-pages
\ No newline at end of file
diff --git a/.github/workflows/issues-labels.yml b/.github/workflows/issues-labels.yml
new file mode 100644
index 0000000..4fbf4fa
--- /dev/null
+++ b/.github/workflows/issues-labels.yml
@@ -0,0 +1,40 @@
+# Verifies if the current issue has at least one `[scope]` label and one
+# `[priority]` label. If either is missing, the workflow adds a reminder label.
+
+name: Issue labels check
+
+on:
+  issues:
+    types: [opened, labeled, unlabeled]
+
+permissions:
+  issues: write
+
+jobs:
+  check-labels:
+    runs-on: ubuntu-latest
+
+    concurrency:
+      group: issue-labels-${{ github.event.issue.number }}
+      cancel-in-progress: true
+
+    steps:
+      - name: Ensure [scope] label
+        uses: Rindrics/expect-label-prefix@v1.2.1
+        with:
+          repository_full_name: ${{ github.repository }}
+          token: ${{ github.token }}
+          label_prefix: '[scope]'
+          label_separator: ' '
+          add_label: 'true'
+          default_label: '[scope] ⚠️ label needed'
+
+      - name: Ensure [priority] label
+        uses: Rindrics/expect-label-prefix@v1.2.1
+        with:
+          repository_full_name: ${{ github.repository }}
+          token: ${{ github.token }}
+          label_prefix: '[priority]'
+          label_separator: ' '
+          add_label: 'true'
+          default_label: '[priority] ⚠️ label needed'
diff --git a/.github/workflows/lint-format.yml b/.github/workflows/lint-format.yml
new file mode 100644
index 0000000..16dd95c
--- /dev/null
+++ b/.github/workflows/lint-format.yml
@@ -0,0 +1,124 @@
+# The workflow checks
+#  - the validity of pyproject.toml,
+#  - the presence and correctness of SPDX license headers,
+#  - linting and formatting of Python code,
+#  - linting and formatting of docstrings in Python code,
+#  - formatting of non-Python files (like markdown and toml).
+#  - linting of Python code in Jupyter notebooks (for library template).
+#
+# A summary of the checks is added to the GitHub Actions summary.
+
+name: Lint and format checks
+
+on:
+  # Trigger the workflow on push
+  push:
+    branches-ignore: [master, main] # Already verified in PR
+    # Do not run this workflow on creating a new tag starting with
+    # 'v', e.g. 'v1.0.3' (see publish-pypi.yml)
+    tags-ignore: ['v*']
+  # Trigger the workflow on pull request
+  pull_request:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Allow only one concurrent workflow, skipping runs queued between the run
+# in-progress and latest queued. And cancel in-progress runs.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+
+jobs:
+  lint-format:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      - name: Run post-install developer steps
+        run: pixi run post-install
+
+      - name: Check validity of pyproject.toml
+        id: pyproject
+        continue-on-error: true
+        shell: bash
+        run: pixi run pyproject-check
+
+      - name: Check SPDX license headers
+        id: license_headers
+        continue-on-error: true
+        shell: bash
+        run: pixi run license-check
+
+      - name: Check linting of Python code
+        id: py_lint
+        continue-on-error: true
+        shell: bash
+        run: pixi run py-lint-check
+
+      - name: Check formatting of Python code
+        id: py_format
+        continue-on-error: true
+        shell: bash
+        run: pixi run py-format-check
+
+      - name: Check linting of docstrings in Python code
+        id: docstring_lint
+        continue-on-error: true
+        shell: bash
+        run: pixi run docstring-lint-check
+
+      - name: Check formatting of non-Python files (md, toml, etc.)
+        id: nonpy_format
+        continue-on-error: true
+        shell: bash
+        run: pixi run nonpy-format-check
+
+      - name: Check linting of Python code in Jupyter notebooks (ipynb)
+        id: notebook_lint
+        continue-on-error: true
+        shell: bash
+        run: pixi run notebook-lint-check
+
+      # Add summary
+      - name: Add quality checks summary
+        if: always()
+        shell: bash
+        run: |
+          {
+            echo "## 🧪 Checks Summary"
+            echo ""
+            echo "| Check | Status |"
+            echo "|-------|--------|"
+            echo "| pyproject.toml   | ${{ steps.pyproject.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| license headers  | ${{ steps.license_headers.outcome == 'success' && '✅'  || '❌' }} |"
+            echo "| py lint          | ${{ steps.py_lint.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| py format        | ${{ steps.py_format.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| docstring lint   | ${{ steps.docstring_lint.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| nonpy format     | ${{ steps.nonpy_format.outcome == 'success' && '✅' || '❌' }} |"
+            echo "| notebooks lint   | ${{ steps.notebook_lint.outcome == 'success' && '✅' || '❌' }} |"
+          } >> "$GITHUB_STEP_SUMMARY"
+
+      # Fail job if any check failed
+      - name: Fail job if any check failed
+        if: |
+          steps.pyproject.outcome == 'failure'
+          || steps.license_headers.outcome == 'failure'
+          || steps.py_lint.outcome == 'failure'
+          || steps.py_format.outcome == 'failure'
+          || steps.docstring_lint.outcome == 'failure'
+          || steps.nonpy_format.outcome == 'failure'
+          || steps.notebook_lint.outcome == 'failure'
+        shell: bash
+        run: exit 1
diff --git a/.github/workflows/nightly-check.yml b/.github/workflows/nightly-check.yml
deleted file mode 100644
index 133ba4d..0000000
--- a/.github/workflows/nightly-check.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-# Nightly Check - install dependencies and run tests after pixi update-lock
-name: Nightly Check
-on:
-  schedule:
-    - cron: '0 0 * * *'  # Runs every day at midnight UTC
-  workflow_dispatch:
-
-jobs:
-  nightly-check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Setup Pixi
-      uses: ./.github/actions/setup-pixi
-
-    - name: Update lock file
-      run: pixi run update-lock
-
-    - name: Build package
-      run: pixi run build
-
-    - name: Run tox tests
-      run: pixi run tox
diff --git a/.github/workflows/ossar-analysis.yml b/.github/workflows/ossar-analysis.yml
deleted file mode 100644
index 1b941b7..0000000
--- a/.github/workflows/ossar-analysis.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-# This workflow integrates a collection of open source static analysis tools
-# with GitHub code scanning.
-#
-# For more information see: https://github.com/github/ossar-action
-
-
-name: OSSAR
-
-on:
-  pull_request:
-
-jobs:
-  OSSAR-Scan:
-    # OSSAR runs on windows-latest.
-    # ubuntu-latest and macos-latest support coming soon
-    runs-on: windows-latest
-
-    steps:
-      # Checkout your code repository to scan
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        # We must fetch at least the immediate parents so that if this is
-        # a pull request then we can checkout the head.
-        fetch-depth: 2
-
-    # If this run was triggered by a pull request event, then checkout
-    # the head of the pull request instead of the merge commit.
-    - run: git checkout HEAD^2
-      if: ${{ github.event_name == 'pull_request' }}
-
-    # Ensure a compatible version of dotnet is installed.
-    # The [Microsoft Security Code Analysis CLI](https://aka.ms/mscadocs) is built with dotnet v3.1.201.
-    # A version greater than or equal to v3.1.201 of dotnet must be installed on the agent in order to run this action.
-    # Remote agents already have a compatible version of dotnet installed and this step may be skipped.
-    # For local agents, ensure dotnet version 3.1.201 or later is installed by including this action:
-    # - name: Install .NET
-    #   uses: actions/setup-dotnet@v1
-    #   with:
-    #     dotnet-version: '3.1.x'
-
-      # Run open source static analysis tools
-    - name: Run OSSAR
-      uses: github/ossar-action@v2.0.0
-      id: ossar
-
-      # Upload results to the Security tab
-    - name: Upload OSSAR results
-      uses: github/codeql-action/upload-sarif@v3
-      with:
-        sarif_file: ${{ steps.ossar.outputs.sarifFile }}
\ No newline at end of file
diff --git a/.github/workflows/pr-labels.yml b/.github/workflows/pr-labels.yml
new file mode 100644
index 0000000..fcb8a78
--- /dev/null
+++ b/.github/workflows/pr-labels.yml
@@ -0,0 +1,45 @@
+# Verifies if a pull request has at least one label from a set of valid
+# labels before it can be merged.
+#
+# The label validation is delegated to `mheap/github-action-required-labels`,
+# which checks the current PR labels via the GitHub API and can add or update a
+# PR comment when the required label set is missing.
+
+name: PR labels check
+
+on:
+  pull_request_target:
+    types: [opened, labeled, unlabeled, synchronize]
+
+permissions:
+  issues: write
+  pull-requests: write
+
+jobs:
+  check-labels:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      - uses: mheap/github-action-required-labels@v5
+        with:
+          token: ${{ steps.bot.outputs.token }}
+          add_comment: true
+          mode: minimum
+          count: 1
+          labels: |
+            [bot] release
+            [scope] bug
+            [scope] documentation
+            [scope] enhancement
+            [scope] maintenance
+            [scope] significant
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
new file mode 100644
index 0000000..cd47c82
--- /dev/null
+++ b/.github/workflows/pypi-publish.yml
@@ -0,0 +1,46 @@
+# Builds a Python package and publish it to PyPI when a new tag is
+# created.
+
+name: PyPI publishing
+
+on:
+  # Runs on creating a new tag starting with 'v', e.g. 'v1.0.3'
+  push:
+    tags: ['v*']
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  pypi-publish:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0 # full history with tags to get the version number by versioningit
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      # Build the Python package (to dist/ folder)
+      - name: Create Python package
+        run: pixi run default-build
+
+      # Publish the package to PyPI (from dist/ folder)
+      # Instead of publishing with personal access token, we use
+      # GitHub Actions OIDC to get a short-lived token from PyPI.
+      # New publisher must be previously configured in PyPI at
+      # https://pypi.org/manage/project/easyimaging/settings/publishing/
+      # Use the following data:
+      # Owner: easyscience
+      # Repository name: imaging-lib
+      # Workflow name: pypi-publish.yml
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: 'dist'
diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml
new file mode 100644
index 0000000..0ea822e
--- /dev/null
+++ b/.github/workflows/pypi-test.yml
@@ -0,0 +1,80 @@
+name: PyPI package tests
+
+on:
+  # Run daily, at 00:00.
+  schedule:
+    - cron: '0 0 * * *'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Allow only one concurrent workflow, skipping runs queued between the run
+# in-progress and latest queued. And cancel in-progress runs.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+
+jobs:
+  # Job 1: Test installation from PyPI on multiple OS
+  pypi-package-tests:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+        with:
+          environments: ''
+          activate-environment: ''
+          run-install: false
+          frozen: false
+
+      - name: Init pixi project
+        run: pixi init easyimaging
+
+      - name: Set the minimum system requirements
+        working-directory: easyimaging
+        run: pixi project system-requirements add macos 14.0
+
+      - name: Add Python 3.13 from Conda
+        working-directory: easyimaging
+        run: pixi add "python=3.13"
+
+      - name: Add other Conda dependencies
+        working-directory: easyimaging
+        run: pixi add gsl
+
+      - name: Add easyimaging (with dev dependencies) from PyPI
+        working-directory: easyimaging
+        run: pixi add --pypi "easyimaging[dev]"
+
+      - name: Run unit tests to verify the installation
+        working-directory: easyimaging
+        run: pixi run python -m pytest ../tests/unit/ --color=yes -v
+
+      # - name: Run functional tests to verify the installation
+      #   working-directory: easyimaging
+      #   run: pixi run python -m pytest ../tests/functional/ --color=yes -v
+
+      - name: Run integration tests to verify the installation
+        working-directory: easyimaging
+        run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto
+
+  # Job 2: Build and publish dashboard (reusable workflow)
+  run-reusable-workflows:
+    needs: pypi-package-tests # depend on previous job
+    uses: ./.github/workflows/dashboard.yml
+    secrets: inherit
diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
deleted file mode 100644
index 3fc3cfb..0000000
--- a/.github/workflows/python-ci.yml
+++ /dev/null
@@ -1,95 +0,0 @@
-# This workflow will for a variety of Python versions
-# - install the code base
-# - lint the code base
-# - test the code base
-# - upload the test coverage to codecov
-#
-# It will also
-# - build the package
-# - check the package
-#
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: CI using Pixi
-
-on: [push, pull_request]
-
-jobs:
-  Code_Consistency:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v5
-      - name: Setup Pixi
-        uses: ./.github/actions/setup-pixi
-      - name: Run linting
-        run: pixi run lint
-
-      - name: Suggestion to fix lint issues
-        if: ${{ failure() }}
-        run: |
-            echo "::notice::In project root run 'pixi run lint-fix' and commit changes to fix issues."
-            exit 1
-
-      - name: Run formatting
-        run: pixi run format-check
-
-      - name: Suggestion to fix format issues
-        if: ${{ failure() }}
-        run: |
-            echo "::notice::In project root run 'pixi run format' and commit changes to fix issues."
-            exit 1
-
-  Code_Testing:
-    strategy:
-      max-parallel: 4
-      matrix:
-        python-version: ['3.11', '3.12', '3.13']
-        os: [ubuntu-latest, macos-latest, macos-15-intel, windows-latest]
-
-    runs-on: ${{ matrix.os }}
-    if: "!contains(github.event.head_commit.message, '[ci skip]')"
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Setup Pixi
-      uses: prefix-dev/setup-pixi@v0.9.0
-      with:
-        run-install: false
-        cache: false
-        post-cleanup: false
-
-    - name: Set Python version
-      run: pixi add python=${{ matrix.python-version }}
-
-
-    - name: Install dependencies and run tests
-      run: pixi run -e dev test
-
-    - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v5
-      with:
-        name: unit-tests-job
-        flags: unittests
-        files: ./coverage-unit.xml
-        fail_ci_if_error: true
-        verbose: true
-        token: ${{ secrets.CODECOV_TOKEN }}
-        slug: EasyScience/imaging-lib
-
-  Package_Testing:
-
-    runs-on: ubuntu-latest
-    if: "!contains(github.event.head_commit.message, '[ci skip]')"
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Setup Pixi
-      uses: ./.github/actions/setup-pixi
-
-    - name: Build package
-      run: pixi run build
-
-    - name: Run tox tests
-      run: pixi run tox
\ No newline at end of file
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
deleted file mode 100644
index 1b4b1b8..0000000
--- a/.github/workflows/python-package.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-# This workflow will for a variety of Python versions
-# - build a python package
-# - run tests on the produced package
-# - upload the package as an artifact
-#
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Create Python Package
-
-on:
-  push:
-    branches: [ master, pre-release ]
-  pull_request:
-    branches: [ master, pre-release ]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.11', '3.12', '3.13']
-    if: "!contains(github.event.head_commit.message, '[ci skip]')"
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Setup Pixi
-      uses: ./.github/actions/setup-pixi
-
-    - name: Set Python version
-      run: pixi add python=${{ matrix.python-version }}
-
-    - name: Build package
-      run: pixi run build
-
-    - name: Run tests with tox
-      run: pixi run tox
-
-    - uses: actions/upload-artifact@v4
-      with:
-        name: EasyImaging - Python ${{ matrix.python-version }}
-        path: ${{ github.workspace }}/dist/*
-        overwrite: true
\ No newline at end of file
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
deleted file mode 100644
index d3775cb..0000000
--- a/.github/workflows/python-publish.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-# This workflow will
-# - build distribution package, pure python wheel
-# - publish produced distribution package to PyPI
-#
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-
-name: Publish Python Package
-
-# Controls when the workflow will run
-on:
-  # Triggers the workflow on tag creation
-  push:
-    tags:
-      - 'v*'
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-jobs:
-  deploy:
-
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Setup Pixi
-      uses: ./.github/actions/setup-pixi
-
-    - name: Build package
-      run: pixi run build
-
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_TOKEN_ES }}
\ No newline at end of file
diff --git a/.github/workflows/release-drafter-verify-pr-labels.yml b/.github/workflows/release-drafter-verify-pr-labels.yml
deleted file mode 100644
index b024955..0000000
--- a/.github/workflows/release-drafter-verify-pr-labels.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-# This workflow will
-# - verify that a PR has a known label before it can be merged.
-#
-# A PR is enforced to have one of the labels listed in the valid-labels input.
-#
-# For more information see: https://github.com/marketplace/actions/release-drafter
-
-
-name: Verify PR labels
-on:
-  pull_request_target:
-    types: [opened, labeled, unlabeled, synchronize]
-
-jobs:
-  check_pr_labels:
-    runs-on: ubuntu-latest
-    name: Verify that the PR has a valid label
-    steps:
-    - name: Verify PR label action
-      uses: jesusvasquez333/verify-pr-label-action@v1.4.0
-      id: verify-pr-label
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        valid-labels: chore, fix, bugfix, bug, enhancement, feature, dependencies, documentation
-        pull-request-number: ${{ github.event.pull_request.number }}
-        disable-reviews: false
diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml
deleted file mode 100644
index beb4813..0000000
--- a/.github/workflows/release-drafter.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-# This workflow will
-# - draft a new release the next time a release is tagged.
-#
-# Uses the release-drafter.yml configuration file in the .github directory.
-#
-# For more information see: https://github.com/marketplace/actions/release-drafter
-
-
-name: Release Drafter
-
-on:
-  push:
-    tags:
-      - 'v*'
-
-jobs:
-  update_release_draft:
-    runs-on: ubuntu-latest
-    steps:
-      # Drafts your next Release notes as Pull Requests are merged into "master"
-      - uses: release-drafter/release-drafter@v6
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml
new file mode 100644
index 0000000..1f32bd4
--- /dev/null
+++ b/.github/workflows/release-notes.yml
@@ -0,0 +1,71 @@
+# Drafts your next Release notes as pull requests are merged into
+# default branch
+
+name: Release draft update
+
+on:
+  # Runs on pushes targeting the default branch (updates the real draft release)
+  push:
+    branches: [master, main]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  draft-release-notes:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0 # full history with tags to get the version number
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      - name: Drafts the next release notes
+        id: draft
+        uses: enhantica/drafterino@v2
+        with:
+          config: |
+            title: 'easyimaging $COMPUTED_VERSION'
+            tag: 'v$COMPUTED_VERSION'
+            note-template: '- $PR_TITLE (#$PR_NUMBER)'
+
+            default-bump: post
+
+            major-bump-labels: ['[scope] significant']
+            minor-bump-labels: ['[scope] enhancement']
+            patch-bump-labels: ['[scope] bug', '[scope] maintenance']
+            post-bump-labels: ['[scope] documentation']
+
+            release-notes:
+              - title: 'Added'
+                labels: ['[scope] significant', '[scope] enhancement']
+              - title: 'Fixed'
+                labels: ['[scope] bug']
+              - title: 'Changed'
+                labels: ['[scope] maintenance', '[scope] documentation']
+        env:
+          GITHUB_TOKEN: ${{ steps.bot.outputs.token }}
+
+      - name: Create GitHub draft release
+        uses: softprops/action-gh-release@v3
+        with:
+          draft: true
+          tag_name: ${{ steps.draft.outputs.tag_name }}
+          name: ${{ steps.draft.outputs.release_name }}
+          body: ${{ steps.draft.outputs.release_notes }}
+        env:
+          GITHUB_TOKEN: ${{ steps.bot.outputs.token }}
diff --git a/.github/workflows/release-pr.yml b/.github/workflows/release-pr.yml
new file mode 100644
index 0000000..3fa073b
--- /dev/null
+++ b/.github/workflows/release-pr.yml
@@ -0,0 +1,55 @@
+# This workflow creates an automated release PR from a source branch into the default branch.
+#
+# Usage:
+#   - Triggered manually via workflow_dispatch.
+#   - Creates a PR titled "Release: merge <source> into <default>".
+#   - Adds the label "[bot] release" so it is excluded from changelogs.
+#   - The PR body makes clear that this is automation only (no review needed).
+
+name: 'Release PR (develop → master)'
+
+on:
+  workflow_dispatch:
+    inputs:
+      source_branch:
+        description: 'Source branch to create PR from'
+        required: false
+        default: 'develop'
+        type: string
+
+permissions:
+  contents: read
+  pull-requests: write
+
+env:
+  DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+  SOURCE_BRANCH: ${{ inputs.source_branch || 'develop' }}
+
+jobs:
+  create-pull-request:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout ${{ env.SOURCE_BRANCH }} branch
+        uses: actions/checkout@v6
+        with:
+          ref: ${{ env.SOURCE_BRANCH }}
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      - name: Create PR from ${{ env.SOURCE_BRANCH }} to ${{ env.DEFAULT_BRANCH }}
+        env:
+          GH_TOKEN: ${{ steps.bot.outputs.token }}
+        run: |
+          gh pr create \
+            --base ${{ env.DEFAULT_BRANCH }} \
+            --head ${{ env.SOURCE_BRANCH }} \
+            --title "🎉 Release: merge ${{ env.SOURCE_BRANCH }} into ${{ env.DEFAULT_BRANCH }}" \
+            --label "[bot] release" \
+            --body "This PR is created automatically to trigger the release pipeline. It merges the accumulated changes from \`${{ env.SOURCE_BRANCH }}\` into \`${{ env.DEFAULT_BRANCH }}\`.
+
+            ⚠️ It is labeled \`[bot] release\` and is excluded from release notes and version bump logic."
diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml
new file mode 100644
index 0000000..0f43db3
--- /dev/null
+++ b/.github/workflows/security.yml
@@ -0,0 +1,93 @@
+# Code scanning (CodeQL) for vulnerabilities and insecure coding patterns.
+#
+# What this workflow does
+# - Runs GitHub CodeQL analysis and uploads results to your repository's Security tab.
+# - Triggers on PRs (so findings appear as PR checks) and on pushes to `develop`.
+# - Runs on a weekly schedule.
+#
+# Where to find results on GitHub
+# - Repository → Security → Code scanning alerts
+#   (You can filter by tool = CodeQL and by branch.)
+#
+# Where to configure on GitHub
+# - Repository → Settings → Advanced Security
+#   Enable "GitHub Advanced Security" (if available) and configure CodeQL there.
+# - Repository → Security → Code scanning alerts
+#   This page shows findings produced by this workflow.
+#
+# Notes about the scheduled run
+# - Scheduled workflows are triggered from the repository's *default branch*.
+#   If your default branch is `master` but you want the scheduled scan to analyze
+#   `develop`, this workflow checks out `develop` explicitly for scheduled runs.
+#
+# References
+# - CodeQL Action: https://github.com/github/codeql-action
+# - Advanced setup docs: https://docs.github.com/en/code-security/code-scanning
+
+name: Security scans with CodeQL
+
+on:
+  # Run on pull requests so results show up as PR checks and code
+  # scanning alerts.
+  pull_request:
+    branches: [master, main, develop]
+
+  # Run on pushes (e.g., after merging PRs).
+  push:
+    branches: [master, main, develop]
+
+  # Run weekly. (Cron is in UTC.)
+  schedule:
+    - cron: '0 3 * * 1'
+
+permissions:
+  contents: read
+  security-events: write
+
+jobs:
+  codeql:
+    name: Code scanning
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        # Keep this list tight to avoid noise and speed up runs.
+        language: [python, actions]
+
+    steps:
+      # Scheduled workflows run from the default branch.
+      # We explicitly analyze `develop` on the schedule to keep the scan
+      # focused on the active dev branch.
+      - name: Checkout repository (scheduled → develop)
+        if: ${{ github.event_name == 'schedule' }}
+        uses: actions/checkout@v6
+        with:
+          ref: develop
+
+      - name: Checkout repository
+        if: ${{ github.event_name != 'schedule' }}
+        uses: actions/checkout@v6
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v4
+        with:
+          languages: ${{ matrix.language }}
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v4
+
+  print-link:
+    name: Print results link
+    runs-on: ubuntu-latest
+
+    needs: codeql
+    permissions: {} # no special perms needed just to print links
+
+    steps:
+      - name: Add Code Scanning link to job summary
+        run: |
+          echo "## 🔎 CodeQL Results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "View Code Scanning alerts here:" >> $GITHUB_STEP_SUMMARY
+          echo "${{ github.server_url }}/${{ github.repository }}/security/code-scanning" >> $GITHUB_STEP_SUMMARY
diff --git a/.github/workflows/test-trigger.yml b/.github/workflows/test-trigger.yml
new file mode 100644
index 0000000..440bae3
--- /dev/null
+++ b/.github/workflows/test-trigger.yml
@@ -0,0 +1,40 @@
+name: Scheduled code tests trigger
+
+on:
+  # Run daily, at 00:00.
+  schedule:
+    - cron: '0 0 * * *'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  code-tests-trigger:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout develop branch
+        uses: actions/checkout@v6
+        with:
+          ref: develop
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      - name: Dispatch code tests workflow
+        uses: ./.github/actions/github-script
+        with:
+          github-token: ${{ steps.bot.outputs.token }}
+          script: |
+            await github.rest.actions.createWorkflowDispatch({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              workflow_id: "test.yml",
+              ref: "develop"
+            });
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..ff7e4e9
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,302 @@
+# This is the main workflow for testing the code before and after
+# packaging it.
+# The workflow is divided into three jobs:
+# 1. env-prepare:
+#    - Prepare the environment for testing
+# 2. source-test:
+#    - Test the code base against the latest code in the repository
+#    - Create the Python package
+#    - Upload the Python package for the next job
+# 3. package-test:
+#    - Download the Python package (including extra files) from the previous job
+#    - Install the downloaded Python package
+#    - Test the code base against the installed package
+# 4. dashboard-build-trigger:
+#    - Trigger the dashboard build workflow to update the code quality
+#      metrics on the dashboard
+
+name: Code and package tests
+
+on:
+  # Trigger the workflow on push
+  push:
+    branches-ignore: [master, main] # Already verified in PR
+    # But do not run this workflow on creating a new tag starting with
+    # 'v', e.g. 'v1.0.3' (see publish-pypi.yml)
+    tags-ignore: ['v*']
+  # Trigger the workflow on pull request
+  pull_request:
+    branches: ['**']
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Need permissions to trigger the dashboard build workflow
+permissions:
+  actions: write
+  contents: read
+
+# Allow only one concurrent workflow, skipping runs queued between the run
+# in-progress and latest queued. And cancel in-progress runs.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  PY_VERSIONS: '3.11 3.13'
+  PIXI_ENVS: 'py-311-env py-313-env'
+
+jobs:
+  # Job 1: Set up environment variables
+  env-prepare:
+    runs-on: [ubuntu-latest]
+
+    outputs:
+      pytest-marks: ${{ steps.set-mark.outputs.pytest_marks }}
+
+    steps:
+      # Determine if integration tests should be run fully or only the fast ones
+      # (to save time on branches other than master and develop)
+      - name: Set mark for integration tests
+        id: set-mark
+        run: |
+          if [[ "${{ env.CI_BRANCH }}" == "master" || "${{ env.CI_BRANCH }}" == "develop" ]]; then
+            echo "pytest_marks=" >> $GITHUB_OUTPUT
+          else
+            echo "pytest_marks=-m fast" >> $GITHUB_OUTPUT
+          fi
+
+  # Job 2: Test code
+  source-test:
+    needs: env-prepare # depend on previous job
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-15, windows-2022]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+        with:
+          environments: ${{ env.PIXI_ENVS }}
+
+      - name: Run unit tests
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
+
+            echo "Running tests in environment: $env"
+            pixi run --environment $env unit-tests
+          done
+
+      # - name: Run functional tests
+      #   shell: bash
+      #   run: |
+      #     set -euo pipefail
+
+      #     for py_ver in $PY_VERSIONS; do
+      #       echo
+      #       echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+      #       env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
+
+      #       echo "Running tests in environment: $env"
+      #       pixi run --environment $env functional-tests
+      #     done
+
+      - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
+
+            echo "Running tests in environment: $env"
+            pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }}
+          done
+
+      # Delete all local tags when not on a tagged commit to force versioningit
+      # to fall back to the configured default-tag, which is '999.0.0' in our case.
+      # This is needed for testing the package in the next job, as its version
+      # must be higher than the PyPI version for pip to prefer the local version.
+      - name: Force using versioningit default tag (non tagged release)
+        if: startsWith(github.ref , 'refs/tags/v') != true
+        run: git tag --delete $(git tag)
+
+      - name: Build package wheels for all Python versions
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+
+            echo "Building wheel in environment: $env"
+            pixi run --environment $env dist-build
+
+            echo "Moving built wheel to dist/py$py_ver/"
+            pixi run mkdir -p dist/py$py_ver
+            pixi run mv dist/*.whl dist/py$py_ver/
+          done
+
+      - name: Remove Python cache files before uploading
+        shell: bash
+        run: pixi run clean-pycache
+
+      # More than one file/dir need to be specified in 'path', to preserve the
+      # structure of the dist/ directory, not only its contents.
+      - name: Upload package (incl. extras) for next job
+        uses: ./.github/actions/upload-artifact
+        with:
+          name: easyimaging_${{ matrix.os }}_${{ runner.arch }}
+          path: dist/
+
+  # Job 3: Test the package
+  package-test:
+    needs: source-test # depend on previous job
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-15, windows-2022]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Download package (incl. extras) from previous job
+        uses: ./.github/actions/download-artifact
+        with:
+          # name and path should be taken from the upload step of the previous job
+          name: easyimaging_${{ matrix.os }}_${{ runner.arch }}
+          path: dist/
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+        with:
+          environments: ''
+          activate-environment: ''
+          run-install: false
+          frozen: false
+
+      - name: Install easyimaging from the built wheel
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            echo "Initializing pixi project"
+            pixi init easyimaging_py$py_ver
+            cd easyimaging_py$py_ver
+
+            echo "Adding Python $py_ver"
+            pixi add "python=$py_ver"
+
+            echo "Setting macOS 14.0 as minimum required"
+            pixi project system-requirements add macos 14.0
+
+            echo "Looking for wheel in ../dist/py$py_ver/"
+            ls -l "../dist/py$py_ver/"
+
+            whl_path=(../dist/"py$py_ver"/*.whl)
+            if [[ ! -f "${whl_path[0]}" ]]; then
+              echo "❌ No wheel found in ../dist/py$py_ver/"
+              exit 1
+            fi
+
+            whl_abs_path="$(python -c 'import os,sys; print(os.path.abspath(sys.argv[1]))' "${whl_path[0]}")"
+
+            echo "Adding easyimaging from: $whl_abs_path"
+            pixi add --pypi "easyimaging[dev] @ ${whl_abs_path}"
+
+            echo "Exiting pixi project directory"
+            cd ..
+          done
+
+      - name: Run unit tests
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            echo "Entering pixi project directory easyimaging_py$py_ver"
+            cd easyimaging_py$py_ver
+
+            echo "Running tests"
+            pixi run python -m pytest ../tests/unit/ --color=yes -v
+
+            echo "Exiting pixi project directory"
+            cd ..
+          done
+
+      # - name: Run functional tests
+      #   shell: bash
+      #   run: |
+      #     set -euo pipefail
+
+      #     for py_ver in $PY_VERSIONS; do
+      #       echo
+      #       echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+      #       echo "Entering pixi project directory easyimaging_py$py_ver"
+      #       cd easyimaging_py$py_ver
+
+      #       echo "Running tests"
+      #       pixi run python -m pytest ../tests/functional/ --color=yes -v
+
+      #       echo "Exiting pixi project directory"
+      #       cd ..
+      #     done
+
+      - name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          for py_ver in $PY_VERSIONS; do
+            echo
+            echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+            echo "Entering pixi project directory easyimaging_py$py_ver"
+            cd easyimaging_py$py_ver
+
+            echo "Running tests"
+            pixi run python -m pytest ../tests/integration/ --color=yes -n auto -v ${{ needs.env-prepare.outputs.pytest-marks }}
+
+            echo "Exiting pixi project directory"
+            cd ..
+          done
+
+  # Job 4: Build and publish dashboard (reusable workflow)
+  run-reusable-workflows:
+    needs: package-test # depend on previous job
+    uses: ./.github/workflows/dashboard.yml
+    secrets: inherit
diff --git a/.github/workflows/tutorial-tests-trigger.yml b/.github/workflows/tutorial-tests-trigger.yml
new file mode 100644
index 0000000..4b160d8
--- /dev/null
+++ b/.github/workflows/tutorial-tests-trigger.yml
@@ -0,0 +1,40 @@
+name: Scheduled tutorial tests trigger
+
+on:
+  # Run daily, at 00:00.
+  schedule:
+    - cron: '0 0 * * *'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  tutorial-tests-trigger:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout develop branch
+        uses: actions/checkout@v6
+        with:
+          ref: develop
+
+      - name: Setup easyscience[bot]
+        id: bot
+        uses: ./.github/actions/setup-easyscience-bot
+        with:
+          app-id: ${{ vars.EASYSCIENCE_APP_ID }}
+          private-key: ${{ secrets.EASYSCIENCE_APP_KEY }}
+
+      - name: Dispatch tutorial tests workflow
+        uses: ./.github/actions/github-script
+        with:
+          github-token: ${{ steps.bot.outputs.token }}
+          script: |
+            await github.rest.actions.createWorkflowDispatch({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              workflow_id: "tutorial-tests.yml",
+              ref: "develop"
+            });
diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml
new file mode 100644
index 0000000..a4fc940
--- /dev/null
+++ b/.github/workflows/tutorial-tests.yml
@@ -0,0 +1,60 @@
+name: Tutorial tests
+
+on:
+  # Trigger the workflow on push
+  push:
+    # Selected branches
+    branches: [develop] # master and main are already verified in PR
+  # Trigger the workflow on pull request
+  pull_request:
+    branches: ['**']
+  # Trigger the workflow on workflow_call (to be called from other workflows)
+  # Needed, as standard schedule triggers the master branch only, but we want
+  # to run this workflow on develop branch.
+  workflow_call:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+# Allow only one concurrent workflow, skipping runs queued between the run
+# in-progress and latest queued. And cancel in-progress runs.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+# Set the environment variables to be used in all jobs defined in this workflow
+env:
+  CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+
+jobs:
+  # Job 1: Test tutorials as scripts and notebooks on multiple OS
+  tutorial-tests:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up pixi
+        uses: ./.github/actions/setup-pixi
+
+      - name: Prepare notebooks
+        shell: bash
+        run: pixi run notebook-prepare
+
+      - name: Test tutorials as notebooks
+        shell: bash
+        run: pixi run notebook-tests
+
+  # Job 2: Build and publish dashboard (reusable workflow)
+  run-reusable-workflows:
+    needs: tutorial-tests # depend on previous job
+    uses: ./.github/workflows/dashboard.yml
+    secrets: inherit
diff --git a/.github/workflows/verify_issue_labels.yml b/.github/workflows/verify_issue_labels.yml
deleted file mode 100644
index 69ec3a1..0000000
--- a/.github/workflows/verify_issue_labels.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-# This workflow will verify that all issues have at
-# least one of the [scope] labels and one of the [priority] labels
-
-name: Verify issue labels
-on:
-  issues:
-    types: [opened, labeled, unlabeled]
-
-jobs:
-  check_issue_labels:
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-    steps:
-      - name: Require [scope] label
-        uses: trstringer/require-label-prefix@v1
-        with:
-          secret: ${{ github.TOKEN }}
-          prefix: "[scope]"
-          addLabel: true
-          defaultLabel: "[scope] ⚠️ label needed"
-
-      - name: Require [priority] label
-        if: always()
-        uses: trstringer/require-label-prefix@v1
-        with:
-          secret: ${{ github.TOKEN }}
-          prefix: "[priority]"
-          addLabel: true
-          defaultLabel: "[priority] ⚠️ label needed"
-
diff --git a/.github/workflows/verify_pr_labels.yml b/.github/workflows/verify_pr_labels.yml
deleted file mode 100644
index e7eb0f5..0000000
--- a/.github/workflows/verify_pr_labels.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-# This workflow will verify that all PRs have at
-# least one of the [scope] labels before they can be merged.
-
-name: Verify PR labels
-on:
-  pull_request_target:
-    types: [opened, labeled, unlabeled, synchronize]
-
-jobs:
-  check_pr_label:
-    runs-on: ubuntu-latest
-    permissions:
-      pull-requests: write
-    name: Verify that the PR has a valid label
-    steps:
-    - name: Verify PR label action
-      uses: jesusvasquez333/verify-pr-label-action@v1.4.0
-      id: verify-pr-label
-      with:
-        github-token: ${{ github.TOKEN }}
-        valid-labels: '[scope] bug, [scope] enhancement, [scope] documentation, [scope] significant, [scope] maintenance'
-        pull-request-number: ${{ github.event.pull_request.number }}
-        disable-reviews: false
diff --git a/.gitignore b/.gitignore
index 772dbfe..5034033 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,48 +1,49 @@
-# QtCreator
-*.autosave
-
-# QtCreator Qml
-*.qmlproject.user
-*.qmlproject.user.*
-
-# QtCreator Python
-*.pyproject.user
-*.pyproject.user.*
-
-# QtCreator CMake
-CMakeLists.txt.user*
-
 # Python
-__pycache__
-.venv
+__pycache__/
+.venv/
 .coverage
 .pyc
 
-# Poetry
-dist
-poetry.lock
-*.egg-info
+# Pixi
+.pixi/
 
 # PyInstaller
-build
+dist/
+build/
 *.spec
 
-# Jupyter
+# MkDocs
+docs/site/
+
+# Jupyter Notebooks
 .ipynb_checkpoints
 
+# Node
+node_modules/
+
+# QtCreator
+*.autosave
+*.qmlproject.user
+*.qmlproject.user.*
+*.pyproject.user
+*.pyproject.user.*
+CMakeLists.txt.user*
+
+# PyCharm
+.idea/
+
+# VS Code
+.vscode/
+
 # macOS
 .DS_Store
 *.app
 *.dmg
 
-# Docs
-docs/_build
-
-# VSCode
-.vscode
-
-# Pixi
-.pixi/
+# Misc
+.cache/
+*.log
+*.zip
 
 # Large files
 *.hdf
@@ -50,11 +51,4 @@ docs/_build
 *sample.tiff
 *open_beam.tiff
 ProofOfConcept/sample_data/*.tiff
-ProofOfConcept/sample_data/*
-
-# Misc
-..*
-*.log
-*.zip
-.ci/
-.idea/
+ProofOfConcept/sample_data/*
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..9a3855f
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,61 @@
+repos:
+  - repo: local
+    hooks:
+      # -------------
+      # Manual checks
+      # -------------
+      - id: pixi-pyproject-check
+        name: pixi run pyproject-check
+        entry: pixi run pyproject-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+      - id: license-headers-check
+        name: pixi run license-check
+        entry: pixi run license-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+      - id: pixi-py-lint-check
+        name: pixi run py-lint-check
+        entry: pixi run py-lint-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+      - id: pixi-py-format-check
+        name: pixi run py-format-check
+        entry: pixi run py-format-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+      - id: pixi-docstring-lint-check
+        name: pixi run docstring-lint-check
+        entry: pixi run docstring-lint-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+      - id: pixi-nonpy-format-check
+        name: pixi run nonpy-format-check
+        entry: pixi run nonpy-format-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+      - id: pixi-notebook-lint-check
+        name: pixi run notebook-lint-check
+        entry: pixi run notebook-lint-check
+        language: system
+        pass_filenames: false
+        stages: [manual]
+
+      - id: pixi-unit-tests
+        name: pixi run unit-tests
+        entry: pixi run unit-tests
+        language: system
+        pass_filenames: false
+        stages: [manual]
diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 0000000..ec19b5e
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,35 @@
+# Git
+.git/
+
+# Copier
+.copier-answers*.yml
+
+# Pixi
+.pixi
+pixi.lock
+
+# MkDocs
+docs/overrides/
+docs/site/
+docs/docs/assets/
+
+# Python
+.pytest_cache/
+
+# MyPy
+.mypy_cache/
+
+# Ruff
+.ruff_cache/
+
+# Node
+node_modules
+
+# Tox
+.tox
+
+# Misc
+.benchmarks
+.cache
+deps/
+tmp/
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..49a61c0
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,448 @@
+# Contributing to EasyImaging
+
+Thank you for your interest in contributing to **EasyImaging**!
+
+This guide explains how you can:
+
+- Report issues
+- Contribute code
+- Improve documentation
+- Suggest enhancements
+- Interact with the EasyScience community
+
+Whether you are an experienced developer or contributing for the first
+time, this document walks you through the entire process step by step.
+
+Please make sure you follow the EasyScience organization-wide
+[Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md).
+
+---
+
+## Table of Contents
+
+- [How to Interact With This Project](#how-to-interact-with-this-project)
+- [1. Understanding the Development Model](#1-understanding-the-development-model)
+- [2. Getting the Code](#2-getting-the-code)
+- [3. Setting Up the Development Environment](#3-setting-up-the-development-environment)
+- [4. Creating a Branch](#4-creating-a-branch)
+- [5. Implementing Your Changes](#5-implementing-your-changes)
+- [6. Code Quality Checks](#6-code-quality-checks)
+- [7. Opening a Pull Request](#7-opening-a-pull-request)
+- [8. Continuous Integration (CI)](#8-continuous-integration-ci)
+- [9. Code Review](#9-code-review)
+- [10. Documentation Contributions](#10-documentation-contributions)
+- [11. Reporting Issues](#11-reporting-issues)
+- [12. Security Issues](#12-security-issues)
+- [13. Releases](#13-releases)
+
+---
+
+## How to Interact With This Project
+
+If you are not planning to contribute code, you may want to:
+
+- 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues)
+- 🛡 Report a security issue — see [Security Issues](#12-security-issues)
+- 💬 Ask a question or start a discussion at
+  [Project Discussions](https://github.com/easyscience/imaging-lib/discussions)
+
+If you plan to contribute code or documentation, continue below.
+
+---
+
+## 1. Understanding the Development Model
+
+Before you start coding, it is important to understand how development
+works in this project.
+
+### Branching Strategy
+
+We use the following branches:
+
+- `master` — stable releases only
+- `develop` — active development branch
+- Short-lived branches — feature or fix branches created for a single
+  contribution and deleted after merge
+
+> [!IMPORTANT]
+>
+> All normal contributions must target the `develop` branch.
+>
+> - Do **not** open Pull Requests against `master`
+> - Always create your branch from `develop`
+> - Always target `develop` when opening a Pull Request
+
+See ADR easyscience/.github#12 for more details on the branching
+strategy.
+
+---
+
+## 2. Getting the Code
+
+### 2.1. If You Are an External Contributor
+
+If you are not a core maintainer of this repository, follow these steps.
+
+1. Open the repository page: `https://github.com/easyscience/imaging-lib`
+
+2. Click the **Fork** button (top-right corner). This creates your own
+   copy of the repository.
+
+3. Clone your fork locally:
+
+   ```bash
+   git clone https://github.com/<your-username>/imaging-lib.git
+   cd imaging-lib
+   ```
+
+4. Add the original repository as `upstream`:
+
+   ```bash
+   git remote add upstream https://github.com/easyscience/imaging-lib.git
+   ```
+
+5. Switch to the `develop` branch and update it:
+
+   ```bash
+   git fetch upstream
+   git checkout develop
+   git pull upstream develop
+   ```
+
+If you have contributed before, make sure your local `develop` branch is
+up to date before starting new work. You can update it with:
+
+```bash
+git fetch upstream
+git pull upstream develop
+```
+
+This ensures you are working on the latest version of the project.
+
+### 2.2. If You Are a Core Team Member
+
+Core team members can create branches directly in this repository and
+therefore do not need to fork it, but the rest of the workflow remains
+the same.
+
+---
+
+## 3. Setting Up the Development Environment
+
+You need:
+
+- Git
+- Pixi
+
+EasyScience projects use **Pixi** to manage the development environment.
+
+To install Pixi, follow the official instructions:
+https://pixi.prefix.dev/latest/installation/
+
+You do **not** need to manually install Python. Pixi automatically:
+
+- Creates the correct Python environment
+- Installs all required dependencies
+- Installs development tools (linters, formatters, test tools)
+
+Set up the environment:
+
+```bash
+pixi install
+pixi run post-install  # Install additional tooling
+```
+
+After this step, your development environment is ready.
+
+See ADR easyscience/.github#63 for more details about using Pixi for
+development.
+
+---
+
+## 4. Creating a Branch
+
+Never work directly on `develop`.
+
+Create a new branch:
+
+```bash
+git checkout -b my-change develop
+```
+
+> [!IMPORTANT]
+>
+> Use a clear and descriptive name, for example:
+>
+> - `improve-solver-speed`
+> - `fix-boundary-condition`
+> - `add-tutorial-example`
+
+Clear branch names make reviews and history easier to understand.
+
+---
+
+## 5. Implementing Your Changes
+
+While developing, make small, logical commits with clear messages.
+
+Example:
+
+```bash
+git add .
+git commit -m "Improve performance of time integrator for large systems"
+```
+
+---
+
+## 6. Code Quality Checks
+
+> [!IMPORTANT]
+>
+> When adding new functionality or making changes, make sure to add or
+> update the following as needed:
+>
+> - 📘 docstrings
+> - 🧪 unit tests
+
+Before opening a Pull Request, always run:
+
+```bash
+pixi run check
+```
+
+This command:
+
+- Validates the pyproject.toml file
+- Checks for licence headers in code files
+- Identifies linting and formatting issues in Python code
+- Checks docstring linting and formatting issues in Python code
+- Detects formatting issues in non-Python files (MD, YAML, TOML etc.)
+- Checks linting issues in Jupyter notebooks (if applicable)
+- Runs unit tests
+
+A successful run should look like this:
+
+```bash
+pixi run pyproject-check.......................Passed
+pixi run license-check.........................Passed
+pixi run py-lint-check.........................Passed
+pixi run py-format-check.......................Passed
+pixi run docstring-lint-check..................Passed
+pixi run nonpy-format-check....................Passed
+pixi run notebook-lint-check...................Passed
+pixi run unit-tests............................Passed
+```
+
+If something fails, read the error message carefully and fix the issue.
+
+You can run individual checks, for example, to run only unit tests:
+
+```bash
+pixi run unit-tests
+```
+
+or to run only Python linting checks:
+
+```bash
+pixi run py-lint-check
+```
+
+To add missing license headers:
+
+```bash
+pixi run spdx-add
+```
+
+Some formatting issues can be fixed automatically:
+
+```bash
+pixi run fix
+```
+
+If everything is correctly formatted, you will see:
+
+```text
+✅ All auto-formatting steps completed successfully!
+```
+
+This indicates that the auto-formatting pipeline completed successfully.
+If you do not see this message and no error messages appear, try running
+the command again.
+
+If errors are reported, resolve them and re-run:
+
+```bash
+pixi run check
+```
+
+> [!IMPORTANT]
+>
+> All checks must pass before your Pull Request can be merged.
+
+If you are unsure how to fix an issue, ask for help in your Pull Request
+discussion.
+
+---
+
+## 7. Opening a Pull Request
+
+Push your branch:
+
+```bash
+git push origin my-change
+```
+
+On GitHub:
+
+- Click **Compare & Pull Request**
+- Ensure the base branch is `develop`
+- Write a clear and concise title
+- Add a description explaining what changed and why
+- Add the required `[scope]` label
+
+### Pull Request Title
+
+> [!IMPORTANT]
+>
+> The PR title appears in release notes and changelogs. It should be
+> concise and informative.
+
+Good examples:
+
+- Improve performance of time integrator for large systems
+- Fix incorrect boundary condition handling in solver
+- Add adaptive step-size control to ODE solver
+- Add tutorial for custom model configuration
+- Refactor solver API for improved readability
+
+### Required `[scope]` Label
+
+> [!IMPORTANT]
+>
+> Each Pull Request must include a `[scope]` label, which is used for
+> automatically suggesting version bumps when preparing a new release.
+
+The available scopes are:
+
+| Label                   | Description                                                             |
+| ----------------------- | ----------------------------------------------------------------------- |
+| `[scope] bug`           | Bug report or fix (major.minor.**PATCH**)                               |
+| `[scope] documentation` | Documentation-only changes (major.minor.patch.**POST**)                 |
+| `[scope] enhancement`   | Adds or improves features (major.**MINOR**.patch)                       |
+| `[scope] maintenance`   | Code/tooling cleanup without feature or bug fix (major.minor.**PATCH**) |
+| `[scope] significant`   | Breaking or major changes (**MAJOR**.minor.patch)                       |
+
+See ADR easyscience/.github#33 for more details on the standardized
+labeling scheme.
+
+---
+
+## 8. Continuous Integration (CI)
+
+After opening a Pull Request:
+
+- Automated checks run automatically
+- You will see green checkmarks or red crosses
+
+If checks fail:
+
+1. Open the failing check
+2. Read the logs
+3. Fix the issue locally
+4. Run `pixi run check`
+5. Push your changes
+
+The Pull Request updates automatically.
+
+---
+
+## 9. Code Review
+
+All Pull Requests are reviewed by at least one core team member.
+
+Code review is collaborative and aims to improve quality.
+
+Do not take comments personally — they are meant to help.
+
+To update your PR:
+
+```bash
+git add .
+git commit -m "Address review comments"
+git push
+```
+
+---
+
+## 10. Documentation Contributions
+
+> [!IMPORTANT]
+>
+> If your change affects user-facing functionality, update the project
+> documentation accordingly — specifically the `nav:` (navigation)
+> structure in `mkdocs.yml` and the relevant documentation Markdown files
+> in `docs/docs/`.
+>
+> ```text
+> 📁 docs
+> ├── 📁 docs        - Markdown files for documentation
+> │   └── ...
+> └── 📄 mkdocs.yml  - Configuration file (navigation, theme, etc.)
+> ```
+
+This may include:
+
+- API documentation
+- Examples
+- Tutorials
+- Jupyter notebooks
+
+Preview documentation locally:
+
+```bash
+pixi run docs-serve
+```
+
+Open the URL shown in the terminal to review your changes.
+
+---
+
+## 11. Reporting Issues
+
+If you find a bug but cannot work on a fix, please consider opening an
+issue.
+
+When reporting an issue, it helps to:
+
+- Search existing issues first.
+- Provide clear reproduction steps.
+- Include logs, screenshots, and environment details.
+
+Clear and detailed reports help maintainers investigate and resolve
+issues more effectively.
+
+---
+
+## 12. Security Issues
+
+> [!IMPORTANT]
+>
+> Please do **not** report security vulnerabilities publicly.
+
+If you discover a potential vulnerability, please contact the maintainers
+privately so the issue can be investigated and addressed responsibly.
+
+---
+
+## 13. Releases
+
+Once your contribution is merged into `develop`, it will eventually be
+included in the next stable release.
+
+When enough changes have accumulated in `develop`, core team members
+merge `develop` into `master` to prepare a new release. The release is
+then tagged and published on GitHub and PyPI.
+
+---
+
+Thank you for contributing to EasyImaging and the EasyScience ecosystem!
diff --git a/LICENSE b/LICENSE
index c1ee0cf..25f8a20 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,7 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2024, Easyscience contributors (https://github.com/EasyScience)
-All rights reserved.
+Copyright (c) 2024-2026 EasyScience contributors.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
diff --git a/README.md b/README.md
index 43830ef..3721732 100644
--- a/README.md
+++ b/README.md
@@ -2,14 +2,54 @@
 [![PyPI badge](http://img.shields.io/pypi/v/EasyImaging.svg)](https://pypi.python.org/pypi/EasyImaging)
 [![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](LICENSE)
 
-<img src="https://raw.githubusercontent.com/EasyScience/EasyImagingLib/master/resources/images/ei_logo.svg" height="65">
+<p>
+  <picture>
+    <!-- light mode logo -->
+    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easyimaging/logos/light.svg'>
+    <!-- dark mode logo -->
+    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easyimaging/logos/dark.svg'>
+    <!-- default logo == light mode logo -->
+    <img src='https://raw.githubusercontent.com/easyscience/assets-branding/refs/heads/master/easyimaging/logos/light.svg' alt='EasyImaging'>
+  </picture>
+</p>
 
-## About
+**EasyImaging** is a software for performing Bragg-edge calculations
+based on a crystalliographic model and refining its parameters against
+experimental data.
 
-Python package for bragg-edge analysis
+<!-- HOME REPOSITORY SECTION -->
 
-## Installation
+**EasyImaging** is developed both as a Python library and as a
+cross-platform desktop application.
 
-```sh
-python -m pip install easyimaging
-```
+Here, we focus on the Python library. For the graphical user interface
+(GUI), please see the corresponding
+[GUI resources](https://github.com/easyscience/imaging-app).
+
+License:
+[BSD 3-Clause](https://github.com/easyscience/imaging-lib/blob/master/LICENSE)
+
+## Useful Links
+
+### For Users
+
+- 📖 [Documentation](https://easyscience.github.io/imaging-lib/latest)
+- 🚀
+  [Getting Started](https://easyscience.github.io/imaging-lib/latest/introduction)
+- 🧪
+  [Tutorials](https://easyscience.github.io/imaging-lib/latest/tutorials)
+- 💬
+  [Get in Touch](https://easyscience.github.io/imaging-lib/latest/introduction/#get-in-touch)
+- 🧾
+  [Citation](https://easyscience.github.io/imaging-lib/latest/introduction/#citation)
+
+### For Contributors
+
+- 🧑‍💻 [Source Code](https://github.com/easyscience/imaging-lib)
+- 🐞 [Issue Tracker](https://github.com/easyscience/imaging-lib/issues)
+- 💡
+  [Discussions](https://github.com/easyscience/imaging-lib/discussions)
+- 🤝
+  [Contributing Guide](https://github.com/easyscience/imaging-lib/blob/master/CONTRIBUTING.md)
+- 🛡
+  [Code of Conduct](https://github.com/easyscience/.github/blob/master/CODE_OF_CONDUCT.md)
diff --git a/docs/docs/api-reference/index.md b/docs/docs/api-reference/index.md
new file mode 100644
index 0000000..c4a12ab
--- /dev/null
+++ b/docs/docs/api-reference/index.md
@@ -0,0 +1,15 @@
+---
+icon: material/code-braces-box
+---
+
+# :material-code-braces-box: API Reference
+
+This section contains the reference detailing the functions and modules
+available in EasyImaging.
+
+- [Measurement](measurement/measurement.md) - Loads and inspects
+  measurement data.
+- [regions_of_interest](regions_of_interest/index.md) - This module
+  contains all types of Regions Of Interests (ROIs) available:
+  - [RectangleROI](regions_of_interest/rectangle_roi.md) - A rectangular
+    ROI. The most basic and common type of ROI
diff --git a/docs/docs/api-reference/measurement/measurement.md b/docs/docs/api-reference/measurement/measurement.md
new file mode 100644
index 0000000..5ebe871
--- /dev/null
+++ b/docs/docs/api-reference/measurement/measurement.md
@@ -0,0 +1,5 @@
+---
+icon: fontawesome/solid/microscope
+---
+
+::: easyimaging.Measurement
diff --git a/docs/docs/api-reference/regions_of_interest/index.md b/docs/docs/api-reference/regions_of_interest/index.md
new file mode 100644
index 0000000..c1e959f
--- /dev/null
+++ b/docs/docs/api-reference/regions_of_interest/index.md
@@ -0,0 +1,11 @@
+---
+icon: fontawesome/solid/crop-simple
+---
+
+# :fontawesome-solid-crop-simple: Regions Of Interest (ROIs)
+
+This module contains the different kinds of Regions Of Interest (ROIs)
+available in EasyImaging. More will be added at a later date
+
+- [RectangleROI](rectangle_roi.md) - A rectangular ROI. The most basic
+  and common type of ROI
diff --git a/docs/docs/api-reference/regions_of_interest/rectangle_roi.md b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md
new file mode 100644
index 0000000..005f44b
--- /dev/null
+++ b/docs/docs/api-reference/regions_of_interest/rectangle_roi.md
@@ -0,0 +1 @@
+::: easyimaging.regions_of_interest.RectangleROI
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diff --git a/docs/docs/assets/images/vector-square_light.png b/docs/docs/assets/images/vector-square_light.png
new file mode 100644
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diff --git a/docs/docs/assets/javascripts/extra.js b/docs/docs/assets/javascripts/extra.js
new file mode 100644
index 0000000..9596ee0
--- /dev/null
+++ b/docs/docs/assets/javascripts/extra.js
@@ -0,0 +1,27 @@
+;(function () {
+  'use strict'
+
+  // Variables
+  const header = document.getElementsByTagName('header')[0]
+
+  console.log(window.pageYOffset)
+
+  // Hide-show header shadow
+  function toggleHeaderShadow() {
+    if (window.pageYOffset <= 0) {
+      header.classList.remove('md-header--shadow')
+    } else {
+      header.classList.add('md-header--shadow')
+    }
+  }
+
+  // Onload
+  window.onload = function () {
+    toggleHeaderShadow()
+  }
+
+  // Onscroll
+  window.onscroll = function () {
+    toggleHeaderShadow()
+  }
+})()
diff --git a/docs/docs/assets/javascripts/mathjax.js b/docs/docs/assets/javascripts/mathjax.js
new file mode 100644
index 0000000..333524e
--- /dev/null
+++ b/docs/docs/assets/javascripts/mathjax.js
@@ -0,0 +1,33 @@
+window.MathJax = {
+  tex: {
+    //inlineMath: [['\\(', '\\)']],
+    //displayMath: [['\\[', '\\]']],
+    // Add support for $...$ and \(...\) delimiters
+    inlineMath: [
+      ['$', '$'],
+      ['\\(', '\\)'],
+    ],
+    // Add support for $$...$$ and \[...]\ delimiters
+    displayMath: [
+      ['$$', '$$'],
+      ['\\[', '\\]'],
+    ],
+    processEscapes: true,
+    processEnvironments: true,
+  },
+  options: {
+    //ignoreHtmlClass: ".*|",
+    //processHtmlClass: "arithmatex"
+    // Skip code blocks only
+    skipHtmlTags: ['script', 'noscript', 'style', 'textarea', 'pre', 'code'],
+    // Only ignore explicit opt-out
+    ignoreHtmlClass: 'no-mathjax|tex2jax_ignore',
+  },
+}
+
+document$.subscribe(() => {
+  MathJax.startup.output.clearCache()
+  MathJax.typesetClear()
+  MathJax.texReset()
+  MathJax.typesetPromise()
+})
diff --git a/docs/docs/assets/stylesheets/extra.css b/docs/docs/assets/stylesheets/extra.css
new file mode 100644
index 0000000..5bc1db1
--- /dev/null
+++ b/docs/docs/assets/stylesheets/extra.css
@@ -0,0 +1,366 @@
+/*************/
+/* Variables */
+/*************/
+
+:root {
+  --sz-link-color--lightmode:             #0184c7;
+  --sz-hovered-link-color--lightmode:     #37bdf9;
+  --sz-body-background-color--lightmode:  #fafafa;
+  --sz-body-text-color--lightmode:        #525252;
+  --sz-body-heading-color--lightmode:     #434343;
+  --sz-code-background-color--lightmode:  #ececec;
+
+  --sz-link-color--darkmode:              #37bdf9;
+  --sz-hovered-link-color--darkmode:      #2890c0;
+  --sz-body-background-color--darkmode:   #262626;
+  --sz-body-text-color--darkmode:         #a3a3a3;
+  --sz-body-heading-color--darkmode:      #e5e5e5;
+  --sz-code-background-color--darkmode:   #212121;
+}
+
+/****************/
+/* Color styles */
+/****************/
+
+/* Default styles https://github.com/squidfunk/mkdocs-material/blob/master/src/assets/stylesheets/main/_typeset.scss */
+
+/* Light mode */
+
+/* Default light mode https://github.com/squidfunk/mkdocs-material/blob/master/src/assets/stylesheets/main/_colors.scss */
+
+[data-md-color-scheme="default"] {
+
+  /* Primary color shades */
+  --md-primary-fg-color:            var(--sz-body-background-color--lightmode);  /* Navigation background */
+  --md-primary-bg-color:            var(--sz-body-text-color--lightmode);        /* E.g., Header title and icons */
+  --md-primary-bg-color--light:     var(--sz-body-text-color--lightmode);        /* E.g., Header search */
+
+  /* Accent color shades */
+  --md-accent-fg-color:             var(--sz-hovered-link-color--lightmode);     /* E.g., Hovered `a` elements & copy icon in code */
+
+  /* Default color shades */
+  --md-default-fg-color:            var(--sz-body-text-color--lightmode);
+  --md-default-fg-color--light:     var(--sz-body-heading-color--lightmode);     /* E.g., `h1` color & TOC viewed items & `$` in code */
+  --md-default-fg-color--lighter:   var(--sz-body-text-color--lightmode);        /* E.g., `¶` sign near `h1-h8` */
+  --md-default-fg-color--lightest:  var(--sz-body-text-color--lightmode);        /* E.g., Copy icon in code */
+  --md-default-bg-color:            var(--sz-body-background-color--lightmode);
+
+  /* Code color shades */
+  --md-code-bg-color:               var(--sz-code-background-color--lightmode);
+
+  /* Typeset color shades */
+  --md-typeset-color:               var(--sz-body-text-color--lightmode);
+
+  /* Typeset `a` color shades */
+  --md-typeset-a-color:             var(--sz-link-color--lightmode);
+
+  /* Footer color shades */
+  --md-footer-fg-color:             var(--sz-body-text-color--lightmode);        /* E.g., Next -> */
+  --md-footer-fg-color--light:      var(--sz-body-text-color--lightmode);        /* E.g., © 2022 EasyDiffraction, Material for MkDocs */
+  --md-footer-fg-color--lighter:    var(--sz-body-text-color--lightmode);        /* E.g. Made with */
+  --md-footer-bg-color:             hsla(0, 0%, 0%, 0.0);                        /* Space with, e.g., Next -> */
+  --md-footer-bg-color--dark:       hsla(0, 0%, 0%, 0.0);                        /* Space with, e.g., © 2022 EasyDiffraction */
+
+  /* Custom colors */
+  --sz-red-color:                   #F44336;
+  --sz-blue-color:                  #03A9F4;
+  --sz-green-color:                 #4CAF50;
+  --sz-orange-color:                #FF9800;
+
+  /* Logo display */
+  --md-footer-logo-dark-mode:       none;
+  --md-footer-logo-light-mode:      block;
+}
+
+/* Dark mode */
+
+/* Default dark mode: https://github.com/squidfunk/mkdocs-material/blob/master/src/assets/stylesheets/palette/_scheme.scss */
+
+[data-md-color-scheme="slate"] {
+
+  /* Primary color shades */
+  --md-primary-fg-color:            var(--sz-body-background-color--darkmode);   /* Navigation background */
+  --md-primary-bg-color:            var(--sz-body-text-color--darkmode);         /* E.g., Header title and icons */
+  --md-primary-bg-color--light:     var(--sz-body-text-color--darkmode);         /* E.g., Header search */
+
+  /* Accent color shades */
+  --md-accent-fg-color:             var(--sz-hovered-link-color--darkmode);      /* E.g., Hovered `a` elements & copy icon in code */
+
+  /* Default color shades */
+  --md-default-fg-color:            var(--sz-body-text-color--darkmode);
+  --md-default-fg-color--light:     var(--sz-body-heading-color--darkmode);      /* E.g., `h1` color & TOC viewed items & `$` in code */
+  --md-default-fg-color--lighter:   var(--sz-body-text-color--darkmode);         /* E.g., `¶` sign near `h1-h8` */
+  --md-default-fg-color--lightest:  var(--sz-body-text-color--darkmode);         /* E.g., Copy icon in code */
+  --md-default-bg-color:            var(--sz-body-background-color--darkmode);
+
+  /* Code color shades */
+  --md-code-bg-color:               var(--sz-code-background-color--darkmode);
+
+  /* Typeset color shades */
+  --md-typeset-color:               var(--sz-body-text-color--darkmode);
+
+  /* Typeset `a` color shades */
+  --md-typeset-a-color:             var(--sz-link-color--darkmode);
+
+  /* Footer color shades */
+  --md-footer-fg-color:             var(--sz-body-text-color--darkmode);         /* E.g., Next -> */
+  --md-footer-fg-color--light:      var(--sz-body-text-color--darkmode);         /* E.g., © 2022 EasyDiffraction, Material for MkDocs */
+  --md-footer-fg-color--lighter:    var(--sz-body-text-color--darkmode);         /* E.g. Made with */
+  --md-footer-bg-color:             hsla(0, 0%, 0%, 0.0);                        /* Space with, e.g., Next -> */
+  --md-footer-bg-color--dark:       hsla(0, 0%, 0%, 0.0);                        /* Space with, e.g., © 2022 EasyDiffraction */
+
+  /* Custom colors */
+  --sz-red-color:                   #EF9A9A;
+  --sz-blue-color:                  #81D4FA;
+  --sz-green-color:                 #A5D6A7;
+  --sz-orange-color:                #FFCC80;
+
+  /* Logo display */
+  --md-footer-logo-dark-mode:       block;
+  --md-footer-logo-light-mode:      none;
+}
+
+/*****************/
+/* Custom styles */
+/*****************/
+
+/* Logo */
+
+#logo_light_mode {
+  display: var(--md-footer-logo-light-mode);
+}
+
+#logo_dark_mode {
+  display: var(--md-footer-logo-dark-mode);
+}
+
+/* Customize default styles of MkDocs Material */
+
+/* Hide navigation title */
+label.md-nav__title[for="__drawer"] {
+  height: 0;
+}
+
+/* Hide site title (first topic) while keeping page title and version selector */
+.md-header__topic:first-child .md-ellipsis {
+  display: none;
+}
+
+/* Increase logo size */
+.md-logo :is(img, svg) {
+  height: 1.8rem !important;
+}
+
+/* Hide GH repo with counts (top right page corner) */
+.md-header__source {
+  display: none;
+}
+
+/* Hide GH repo with counts (navigation bar in mobile view) */
+.md-nav__source {
+  display: none;
+}
+
+/* Ensure all horizontal lines in the navigation list are removed or hidden */
+.md-nav__item {
+  /* Removes any border starting from the second level */
+  border: none !important;
+  /* Modifies the background color to hide the first horizontal line */
+  background-color: var(--md-default-bg-color);
+}
+
+/* Increase TOC (on the right) width */
+.md-nav--secondary {
+  margin-left: -10px;
+  margin-right: -4px;
+}
+
+/* */
+.md-nav__item > .md-nav__link {
+    padding-left: 0.5em; /* Default */
+}
+
+/* Change line height of the tabel cells */
+.md-typeset td,
+.md-typeset th {
+  line-height: 1.25 !important;
+}
+
+/* Change vertical alignment of the icon inside the tabel cells */
+.md-typeset td .twemoji {
+  vertical-align: sub !important;
+}
+
+/* Change the width of the primary sidebar */
+/*
+.md-sidebar--primary {
+  width: 240px;
+}
+*/
+
+/* Change the overall width of the page */
+.md-grid {
+  max-width: 116em;
+}
+
+/* Keep prose line length stable when sidebars are hidden at narrower widths */
+.md-main .md-content > .md-content__inner {
+  width: min(100%, 40.5em);
+  margin-left: auto !important;
+  margin-right: auto !important;
+}
+
+/* Needed for mkdocs-jupyter to show download and other buttons on top of the notebook */
+.md-content__button {
+  position: relative !important;
+}
+
+/* Background color of the search input field */
+.md-search__input {
+  background-color: var(--md-code-bg-color) !important;
+}
+
+/* Customize default style of mkdocs-jupyter plugin */
+
+/* Set the width of the notebook to fill 100% and not reduce by the width of .md-content__button's
+Adjust the margins and paddings to fit the defaults in MkDocs Material and do not crop the label in the header
+*/
+.jupyter-wrapper {
+  width: 100% !important;
+  display: flex !important;
+}
+
+.jp-Notebook {
+  padding: 0 !important;
+  margin-top: -3em !important;
+
+  /* Ensure notebook content stretches across the page */
+  width: 100% !important;
+  max-width: 100% !important;
+
+  /* mkdocs-material + some notebook HTML end up as flex */
+  align-items: stretch !important;
+}
+
+.jp-Notebook .jp-Cell {
+  /* Key: flex children often need min-width: 0 to prevent weird shrink */
+  width: 100% !important;
+  max-width: 100% !important;
+  min-width: 0 !important;
+
+  /* Removes jupyter cell paddings */
+  padding-left: 0 !important;
+}
+
+/* Removes jupyter cell prefixes, like In[123]: */
+.prompt,
+.jp-InputPrompt,
+.jp-OutputPrompt {
+  display: none !important;
+}
+
+/* Removes jupyter output cell padding to align with input cell text */
+.jp-RenderedText {
+  padding-left: 0.85em !important;
+}
+
+/* Extra styling the panda dataframes, on top of the style included in the code */
+table.dataframe {
+  float: left;
+  margin-left: 0.75em !important;
+  margin-bottom: 0.5em !important;
+  font-size: var(--jp-code-font-size) !important;
+  color: var(--md-primary-bg-color) !important;
+  /* Allow table cell wrapping in MkDocs-Jupyter outputs */
+  /*
+  table-layout: auto !important;
+  width: auto !important;
+  */
+}
+
+/* Allow wrap for the last column */
+/*
+table.dataframe td:last-child,
+table.dataframe th:last-child {
+  white-space: normal !important;
+  word-break: break-word !important;
+}
+*/
+
+/* Custom styles for the CIF files */
+
+.cif {
+  padding-left: 1em;
+  padding-right: 1em;
+  padding-top: 1px;
+  padding-bottom: 1px;
+  background-color: var(--md-code-bg-color);
+  font-size: small;
+}
+.red {
+  color: var(--sz-red-color);
+}
+.green {
+  color: var(--sz-green-color);
+}
+.blue {
+  color: var(--sz-blue-color);
+}
+.orange {
+  color: var(--sz-orange-color);
+}
+.grey {
+  color: grey;
+}
+
+/**********/
+/* Labels */
+/**********/
+
+.label-cif {
+  padding-top: 0.5ex;
+  padding-bottom: 0.5ex;
+  padding-left: 0.9ex;
+  padding-right: 0.9ex;
+  border-radius: 1ex;
+  color: var(--md-default-fg-color) !important;
+  background-color: var(--md-code-bg-color);
+}
+
+p .label-cif, li .label-cif {
+  vertical-align: 5%;
+  font-size: 12px;
+}
+
+.label-cif:hover {
+  color: white !important;
+}
+
+.label-experiment {
+  padding-top: 0.25ex;
+  padding-bottom: 0.6ex;
+  padding-left: 0.9ex;
+  padding-right: 0.9ex;
+  border-radius: 1ex;
+  color: var(--md-default-fg-color) !important;
+  background-color: rgba(55, 189, 249, 0.1);
+}
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+p .label-experiment, li .label-experiment {
+  vertical-align: 5%;
+  font-size: 12px;
+}
+
+h1 .label-experiment {
+  padding-top: 0.05ex;
+  padding-bottom: 0.4ex;
+  padding-left: 0.9ex;
+  padding-right: 0.9ex;
+  border-radius: 0.75ex;
+  color: var(--md-default-fg-color) !important;
+  background-color: rgba(55, 189, 249, 0.1);
+}
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+  color: white !important;
+}
diff --git a/docs/docs/assets/stylesheets/scipp_style.css b/docs/docs/assets/stylesheets/scipp_style.css
new file mode 100644
index 0000000..2727d42
--- /dev/null
+++ b/docs/docs/assets/stylesheets/scipp_style.css
@@ -0,0 +1,495 @@
+/* CSS stylesheet for displaying scipp objects in jupyterlab.
+* Original source from
+* https://github.com/jsignell/xarray/blob/1d960933ab252e0f79f7e050e6c9261d55568057/xarray/static/css/style.css
+*/
+
+.sc-root {
+  --sc-background-color0: var(--jp-layout-color0, #fff) !important;
+  --sc-background-color1: var(--jp-layout-color1, #fcfcfc) !important;
+  --sc-background-color2: var(--jp-layout-color2, #efefef) !important;
+  --sc-inverse-background-color0: var(--jp-inverse-layout-color4, #111) !important;
+  --sc-font-color0: var(--jp-content-font-color0, #000) !important;
+  --sc-font-color1: var(--jp-content-font-color1, #555) !important;
+  --sc-font-color2: var(--jp-content-font-color2, #888) !important;
+  --sc-font-color3: var(--jp-content-font-color3, #ccc) !important;
+}
+
+body.vscode-dark .sc-root {
+  --sc-font-color0: rgba(255, 255, 255, 1) !important;
+  --sc-font-color1: rgba(255, 255, 255, 0.70) !important;
+  --sc-font-color2: rgba(255, 255, 255, 0.54) !important;
+  --sc-font-color3: rgba(255, 255, 255, 0.38) !important;
+  --sc-border-color: #1F1F1F !important;
+  --sc-disabled-color: #515151 !important;
+  --sc-background-color0: #111111 !important;
+  --sc-background-color1: #111111 !important;
+  --sc-background-color2: #313131 !important;
+}
+
+.sc-wrap {
+  font-size: 14px !important;
+  min-width: 300px !important;
+  max-width: 800px !important;
+}
+
+/* The CSS styling for the inline attributes table */
+.sc-var-attrs .sc-wrap{
+  padding-left: 3em !important;
+}
+
+.sc-header {
+  padding-top: 6px !important;
+  padding-bottom: 6px !important;
+  margin-bottom: 4px !important;
+  border-bottom: solid 1px #ddd !important;
+}
+
+.sc-header > div,
+.sc-header > ul {
+  display: inline !important;
+  margin-top: 0 !important;
+  margin-bottom: 0 !important;
+}
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+.sc-obj-type,
+.sc-array-name {
+  margin-left: 2px !important;
+  margin-right: 10px !important;
+}
+
+.sc-obj-type {
+  color: var(--sc-font-color1) !important;
+}
+
+.sc-underlying-size {
+  color: var(--sc-font-color2) !important;
+}
+
+/* Also override settings of reveal.js as introduced when
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+   There are selectors for `.reveal ul` and `.reveal ul ul`
+   which take precedence over ours and mess up the formatting.*/
+.sc-sections, .reveal .sc-sections {
+  padding-left: 0 !important;
+  display: grid !important;
+  grid-template-columns: 150px auto auto auto 1fr 20px 20px !important;
+}
+
+.sc-section-item {
+  display: contents !important;
+}
+
+.sc-section-item input {
+  display: none !important;
+}
+
+.sc-section-item input:enabled + label {
+  cursor: pointer !important;
+  color: var(--sc-font-color1) !important;
+}
+
+.sc-section-item input:enabled + label:hover {
+  color: var(--sc-font-color0) !important;
+}
+
+.sc-section-summary {
+  grid-column: 1 !important;
+  font-weight: 500 !important;
+}
+
+.sc-section-summary > span {
+  display: inline-block !important;
+  padding-left: 0.5em !important;
+}
+
+.sc-section-summary-in:disabled + label {
+  color: var(--sc-font-color1) !important;
+}
+
+.sc-section-summary-in + label:before {
+  display: inline-block !important;
+  content: '►' !important;
+  font-size: 11px !important;
+  width: 15px !important;
+  text-align: center !important;
+}
+
+.sc-section-summary-in:disabled + label:before {
+  display: none !important;
+}
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+  content: '▼' !important;
+}
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+  display: none !important;
+}
+
+.sc-section-summary,
+.sc-section-inline-details {
+  padding-top: 4px !important;
+  padding-bottom: 4px !important;
+}
+
+.sc-section-inline-details {
+  grid-column: 2 / 6 !important;
+}
+
+.sc-section-details {
+  display: none !important;
+  grid-column: 1 / -1 !important;
+  margin-bottom: 5px !important;
+}
+
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+  display: contents !important;
+}
+
+.sc-array-wrap {
+  grid-column: 1 / -1 !important;
+  display: grid !important;
+  grid-template-columns: 20px auto !important;
+}
+
+.sc-array-wrap > label {
+  grid-column: 1 !important;
+  vertical-align: top !important;
+}
+
+.sc-preview {
+  color: var(--sc-font-color2) !important;
+}
+
+.sc-array-preview,
+.sc-array-data {
+  padding: 0 5px !important;
+  grid-column: 2 !important;
+}
+
+.sc-array-data,
+.sc-array-in:checked ~ .sc-array-preview {
+  display: none !important;
+}
+
+.sc-array-in:checked ~ .sc-array-data,
+.sc-array-preview {
+  display: inline-block !important;
+}
+
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+  display: inline-block !important;
+  list-style: none !important;
+  padding: 0 !important;
+  margin: 0 !important;
+}
+
+.sc-dim-list li {
+  display: inline-block !important;
+  padding: 0 !important;
+  margin: 0 !important;
+}
+
+.sc-dim-list:before {
+  content: '(' !important;
+}
+
+.sc-dim-list:after {
+  content: ')' !important;
+}
+
+.sc-dim-list li:not(:last-child):after {
+  content: ',' !important;
+  padding-right: 5px !important;
+}
+
+/*
+This selector is for avoiding unexpected extra padding
+caused by <span> tag wrapping around the dollar-sign in the Jpyter notebook.
+*/
+.sc-dim-list li span,
+.sc-standalone-var-name > span span,
+.sc-var-name > span span {
+  padding: 0 !important;
+}
+
+.sc-aligned {
+  font-weight: bold !important;
+}
+
+.sc-var-list,
+.sc-var-item,
+.reveal .sc-var-list,
+.reveal .sc-var-item {
+  display: contents !important;
+}
+
+.sc-var-item > div,
+.sc-var-item label,
+.sc-var-item > .sc-var-name span {
+  background-color: var(--sc-background-color1) !important;
+  margin-bottom: 0 !important;
+}
+
+.sc-var-item > .sc-var-name:hover span {
+  padding-right: 5px !important;
+}
+
+.sc-var-list > li:nth-child(odd) > div,
+.sc-var-list > li:nth-child(odd) > label,
+.sc-var-list > li:nth-child(odd) > .sc-var-name span {
+  background-color: var(--sc-background-color2) !important;
+}
+
+.sc-var-name {
+  grid-column: 1 !important;
+}
+
+.sc-var-dims {
+  grid-column: 2 !important;
+}
+
+.sc-var-dtype {
+  grid-column: 3 !important;
+  text-align: right !important;
+  color: var(--sc-font-color2) !important;
+}
+.sc-var-unit{
+  grid-column: 4 !important;
+  text-align: left !important;
+  color: var(--sc-font-color1) !important;
+  max-width: 50pt !important;
+  text-overflow: ellipsis !important;
+}
+.sc-value-preview {
+  grid-column: 5 !important;
+}
+.sc-var-preview-variances{
+  text-align:right !important;
+}
+
+.sc-sections .sc-section-item .sc-section-summary,
+.sc-sections .sc-section-item .sc-section-inline-details,
+.sc-section-item .sc-var-list .sc-var-item > div,
+.sc-section-item .sc-var-list .sc-var-item > label,
+.sc-section-details .sc-var-list .sc-var-item > div,
+.sc-section-details .sc-var-list .sc-var-item > label {
+  margin-top: 0 !important;
+  margin-bottom: 0 !important;
+}
+
+.sc-var-name,
+.sc-var-dims,
+.sc-var-dtype,
+.sc-var-unit,
+.sc-preview,
+.sc-attrs dt {
+  white-space: nowrap !important;
+  overflow: hidden !important;
+  text-overflow: ellipsis !important;
+  padding-right: 10px !important;
+}
+
+.sc-var-name:hover,
+.sc-var-dims:hover,
+.sc-var-dtype:hover,
+.sc-var-unit:hover,
+.sc-attrs dt:hover {
+  overflow: visible !important;
+  width: auto !important;
+  z-index: 1 !important;
+}
+
+.sc-var-attrs {
+  display: block !important;
+}
+.sc-var-data, .reveal .sc-var-data {
+  display: none !important;
+}
+.sc-var-attrs,
+.sc-var-data {
+  background-color: var(--sc-background-color0) !important;
+  padding-bottom: 5px !important;
+}
+
+.sc-var-attrs-in:checked ~ .sc-var-attrs {
+  display: none !important;
+}
+.sc-var-data-in:checked ~ .sc-var-data {
+  display: block !important;
+}
+
+.sc-var-data > table {
+  float: right !important;
+}
+
+.sc-var-name span,
+.sc-var-data {
+  padding-left: 25px !important;
+}
+
+.sc-var-attrs,
+.sc-var-data {
+  grid-column: 1 / -1 !important;
+}
+
+dl.sc-attrs {
+  padding: 0 !important;
+  margin: 0 !important;
+  display: grid !important;
+  grid-template-columns: 125px auto !important;
+}
+
+.sc-attrs dt, dd {
+  padding: 0 !important;
+  margin: 0 !important;
+  float: left !important;
+  padding-right: 10px !important;
+  width: auto !important;
+}
+
+.sc-attrs dt {
+  font-weight: normal !important;
+  grid-column: 1 !important;
+}
+
+.sc-attrs dt:hover span {
+  display: inline-block !important;
+  padding-right: 10px !important;
+}
+
+.sc-attrs dd {
+  grid-column: 2 !important;
+  white-space: pre-wrap !important;
+  word-break: break-all !important;
+}
+
+.sc-icon-database,
+.sc-icon-file-text2 {
+  display: inline-block !important;
+  vertical-align: middle !important;
+  width: 1em !important;
+  height: 1.5em !important;
+  stroke-width: 0 !important;
+  stroke: currentColor !important;
+  fill: currentColor !important;
+}
+
+label.sc-hide-icon svg{
+  opacity: 0;
+}
+
+.sc-standalone-var-name{
+  grid-column: 1/3 !important;
+}
+
+.sc-standalone-var-name span{
+  padding-left: 25px !important;
+  padding-right:10px !important;
+}
+
+.sc-title {
+  font-weight:bold !important;
+  font-size:1.5em !important;
+}
+
+.sc-subtitle {
+  font-weight:normal !important;
+  font-style:italic !important;
+  text-align:left !important;
+  font-size:1.2em !important;
+  padding: 1px !important;
+}
+
+.sc-label {
+  fill: var(--sc-font-color0, #444444) !important;
+  text-anchor: middle !important;
+}
+
+.sc-name {
+  fill: var(--sc-font-color0, #111111) !important;
+}
+
+.sc-inset-line {
+  stroke: var(--sc-font-color1) !important;
+  stroke-width: 0.05 !important;
+  stroke-dasharray: 0.2, 0.2 !important;
+}
+
+.sc-log-wrap {
+  height: 25ex;
+  resize: vertical;
+  overflow-y: scroll;
+  display: flex;
+  flex-direction: column-reverse;
+  border: 1px solid !important;
+  border-color: var(--jp-border-color2) !important;
+  background-color: var(--sc-background-color1) !important;
+}
+
+div.sc-log {
+  line-height: 2.5ex !important;
+}
+
+table.sc-log {
+  table-layout: auto !important;
+  border-collapse: collapse !important;
+}
+
+tr.sc-log:nth-child(even) {
+  background-color: var(--sc-background-color0) !important;
+}
+
+tr.sc-log > td {
+  vertical-align: top !important;
+  padding-bottom: 0.5ex !important;
+}
+
+.sc-log-time-stamp {
+  min-width: 22ch !important;
+  font-family: var(--jp-code-font-family) !important;
+  color: var(--sc-font-color2) !important;
+}
+
+.sc-log-level {
+  min-width: 10ch !important;
+}
+
+tr.sc-log-debug td.sc-log-level {
+  color: var(--jp-accent-color1) !important;
+}
+
+tr.sc-log-info td.sc-log-level {
+  color: var(--jp-info-color1) !important;
+}
+
+tr.sc-log-warning td.sc-log-level {
+  color: var(--jp-warn-color1) !important;
+}
+
+tr.sc-log-error td.sc-log-level {
+  font-weight: bold !important;
+  color: var(--jp-error-color2) !important;
+}
+
+tr.sc-log-critical td.sc-log-level {
+  font-weight: bold !important;
+  color: var(--sc-background-color0) !important;
+  background-color: var(--jp-error-color1) !important;
+}
+
+.sc-log-message {
+  white-space: pre-wrap !important;
+  width: 100% !important;
+}
+
+.sc-log-html-payload {
+  white-space: normal !important;
+}
+
+.sc-log-name {
+  padding-right: 0.5em !important;
+  text-align: right !important;
+  white-space: pre-wrap !important;
+  color: var(--sc-font-color3) !important;
+}
diff --git a/docs/docs/index.md b/docs/docs/index.md
new file mode 100644
index 0000000..93c9fee
--- /dev/null
+++ b/docs/docs/index.md
@@ -0,0 +1,21 @@
+![](assets/images/logo_dark.svg#gh-dark-mode-only)![](assets/images/logo_light.svg#gh-light-mode-only)
+
+# Neutron imaging data analysis
+
+Here is a brief overview of the main documentation sections:
+
+- [:material-information-slab-circle: Introduction](introduction/index.md)
+  – Provides a description of EasyImaging, including its purpose,
+  licensing, latest release details, and contact information.
+- [:material-cog-box: Installation & Setup](installation-and-setup/index.md)
+  – Guides users through system requirements, environment configuration,
+  and the installation process.
+- [:material-book-open-variant: User Guide](user-guide/index.md) – Covers
+  core concepts, key terminology, workflow steps, and essential
+  parameters for effective use of EasyImaging.
+- [:material-school: Tutorials](tutorials/index.md) – Offers practical,
+  step-by-step examples demonstrating common workflows and data analysis
+  tasks.
+- [:material-code-braces-box: API Reference](api-reference/index.md) – An
+  auto-generated reference detailing the available functions and modules
+  in EasyImaging.
diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md
new file mode 100644
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--- /dev/null
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@@ -0,0 +1,278 @@
+---
+icon: material/cog-box
+---
+
+# :material-cog-box: Installation & Setup
+
+**EasyImaging** is a cross-platform Python library compatible with
+**Python 3.11** through **3.13**.
+
+To install and set up EasyImaging, we recommend using
+[**Pixi**](https://pixi.prefix.dev), a modern package manager for
+Windows, macOS, and Linux.
+
+??? note "Main benefits of using Pixi"
+
+    - **Ease of use**: Pixi simplifies the installation process, making it
+      accessible even for users with limited experience in package management.
+    - **Python version control**: Pixi allows specifying and managing different
+      Python versions for each project, ensuring compatibility.
+    - **Isolated environments**: Pixi creates isolated environments for each
+      project, preventing conflicts between different package versions.
+    - **PyPI and Conda support**: Pixi can install packages from both PyPI and
+      Conda repositories, providing access to a wide range of libraries.
+
+An alternative installation method using the traditional **pip** package
+manager is also provided.
+
+## Installing with Pixi <small>recommended</small> { #installing-with-pixi data-toc-label="Installing with Pixi" }
+
+This section describes the simplest way to set up EasyImaging using
+**Pixi**.
+
+#### Installing Pixi
+
+- Install Pixi by following the instructions on the
+  [official Pixi Installation Guide](https://pixi.prefix.dev/latest/installation).
+
+#### Setting up EasyImaging with Pixi
+
+<!-- prettier-ignore-start -->
+
+- Choose a project location (local drive recommended).
+
+    ??? warning ":fontawesome-brands-windows: Windows + OneDrive"
+
+        We **do not recommend creating a Pixi project inside OneDrive or other
+        synced folders**.
+
+        By default, Pixi creates the virtual environment inside the project
+        directory (in `.pixi/`). On Windows, synced folders such as OneDrive
+        may cause file‑system issues (e.g., path-length limitations or
+        restricted link operations), which can lead to unexpected install
+        errors or environments being recreated.
+
+        Instead, create your project in a **local directory on your drive**
+        where you have full write permissions.
+
+<!-- prettier-ignore-end -->
+
+- Initialize a new Pixi project and navigate into it:
+  ```txt
+  pixi init easyimaging
+  cd easyimaging
+  ```
+- Set the Python version for the Pixi environment (e.g., 3.13):
+  ```txt
+  pixi add python=3.13
+  ```
+- Add EasyImaging to the Pixi environment from PyPI:
+  ```txt
+  pixi add --pypi easyimaging
+  ```
+- Add a Pixi task to run EasyImaging commands easily:
+  ```txt
+  pixi task add easyimaging "python -m easyimaging"
+  ```
+
+#### Updating Pixi and EasyImaging
+
+- To update all packages in the Pixi environment, including EasyImaging:
+  ```txt
+  pixi update
+  ```
+- To update Pixi itself to the latest version:
+  ```txt
+  pixi self-update
+  ```
+
+#### Uninstalling Pixi
+
+- Follow the
+  [official Pixi Guide](https://pixi.prefix.dev/latest/installation/#uninstall).
+
+## Classical Installation
+
+This section describes how to install EasyImaging using the traditional
+method with **pip**. It is assumed that you are familiar with Python
+package management and virtual environments.
+
+### Environment Setup <small>optional</small> { #environment-setup data-toc-label="Environment Setup" }
+
+We recommend using a **virtual environment** to isolate dependencies and
+avoid conflicts with system-wide packages. If any issues arise, you can
+simply delete and recreate the environment.
+
+#### Creating and Activating a Virtual Environment:
+
+<!-- prettier-ignore-start -->
+
+- Create a new virtual environment:
+  ```txt
+  python3 -m venv venv
+  ```
+- Activate the environment:
+
+    === ":material-apple: macOS"
+        ```txt
+        . venv/bin/activate
+        ```
+    === ":material-linux: Linux"
+        ```txt
+        . venv/bin/activate
+        ```
+    === ":fontawesome-brands-windows: Windows"
+        ```txt
+        . venv/Scripts/activate      # Windows with Unix-like shells
+        .\venv\Scripts\activate.bat  # Windows with CMD
+        .\venv\Scripts\activate.ps1  # Windows with PowerShell
+        ```
+
+- The terminal should now show `(venv)`, indicating that the virtual environment
+  is active.
+
+<!-- prettier-ignore-end -->
+
+#### Deactivating and Removing the Virtual Environment:
+
+<!-- prettier-ignore-start -->
+
+- Exit the environment:
+  ```txt
+  deactivate
+  ```
+- If this environment is no longer needed, delete it:
+
+    === ":material-apple: macOS"
+        ```txt
+        rm -rf venv
+        ```
+    === ":material-linux: Linux"
+        ```txt
+        rm -rf venv
+        ```
+    === ":fontawesome-brands-windows: Windows"
+        ```txt
+        rmdir /s /q venv
+        ```
+
+<!-- prettier-ignore-end -->
+
+### Installing from PyPI { #from-pypi }
+
+EasyImaging is available on **PyPI (Python Package Index)** and can be
+installed using `pip`. To do so, use the following command:
+
+```txt
+pip install easyimaging
+```
+
+To install a specific version of EasyImaging, e.g., 1.0.3:
+
+```txt
+pip install 'easyimaging==1.0.3'
+```
+
+To upgrade to the latest version:
+
+```txt
+pip install --upgrade easyimaging
+```
+
+To upgrade to the latest version and force reinstallation of all
+dependencies (useful if files are corrupted):
+
+```txt
+pip install --upgrade --force-reinstall easyimaging
+```
+
+To check the installed version:
+
+```txt
+pip show easyimaging
+```
+
+### Installing from GitHub <small>alternative</small> { #from-github data-toc-label="Installing from GitHub" }
+
+Installing unreleased versions is generally not recommended but may be
+useful for testing.
+
+To install EasyImaging from the `develop` branch of GitHub, for example:
+
+```txt
+pip install git+https://github.com/easyscience/imaging-lib@develop
+```
+
+To include extra dependencies (e.g., dev):
+
+```txt
+pip install 'easyimaging[dev] @ git+https://github.com/easyscience/imaging-lib@develop'
+```
+
+## How to Run Tutorials
+
+EasyImaging includes a collection of **Jupyter Notebook examples** that
+demonstrate key functionality. These tutorials serve as **step-by-step
+guides** to help users understand the data analysis workflow. They are
+available as **static HTML pages** in the
+[:material-school: Tutorials](../tutorials/index.md) section.
+
+In the next sections, we explain how to set up Jupyter and run the
+tutorials interactively in two different ways: locally or online via
+Google Colab.
+
+If you decide to run the tutorials locally, you need to download them
+first. This can be done individually via the :material-download:
+**Download Notebook** button available on each tutorial page, or all at
+once using the command line, as shown below.
+
+### Run Tutorials Locally with Pixi <small>recommended</small> { #running-with-pixi data-toc-label="Run Tutorials Locally with Pixi" }
+
+- Navigate to your existing Pixi project, created as described in the
+  [Installing with Pixi](#installing-with-pixi) section.
+- Add JupyterLab, Interactive Python shell and the Pixi kernel for
+  Jupyter:
+  ```txt
+  pixi add --pypi jupyterlab ipython pixi-kernel
+  ```
+- Download all the EasyImaging tutorials to the `tutorials/` directory.
+- Start the JupyterLab server in the `tutorials/` directory to access the
+  notebooks:
+  ```txt
+  pixi run jupyter lab tutorials/
+  ```
+- Your web browser should open automatically. Click on one of the
+  `*.ipynb` files and select the `Python (Pixi)` kernel to get started.
+
+### Classical Run Tutorials Locally
+
+- Install Jupyter Notebook, Interactive Python shell and the IPython
+  kernel:
+  ```txt
+  pip install notebook ipython ipykernel
+  ```
+- Add the virtual environment as a Jupyter kernel:
+  ```txt
+  python -m ipykernel install --user --name=venv --display-name "EasyImaging Python kernel"
+  ```
+- Download all the EasyImaging tutorials to the `tutorials/` directory.
+- Start the Jupyter Notebook server in the `tutorials/` directory to
+  access the notebooks:
+  ```txt
+  jupyter notebook tutorials/
+  ```
+- Your web browser should open automatically. Click on one of the
+  `*.ipynb` files and select the `EasyImaging Python kernel` to get
+  started.
+
+### Run Tutorials via Google Colab
+
+**Google Colab** lets you run Jupyter Notebooks in the cloud without any
+local installation. This is the fastest way to start experimenting with
+EasyImaging.
+
+- Ensure you have a **Google account**.
+- Go to the **[:material-school: Tutorials](../tutorials/index.md)**
+  section.
+- Click the :google-colab: **Open in Google Colab** button on any
+  tutorial.
diff --git a/docs/docs/introduction/index.md b/docs/docs/introduction/index.md
new file mode 100644
index 0000000..d5e42c1
--- /dev/null
+++ b/docs/docs/introduction/index.md
@@ -0,0 +1,72 @@
+---
+icon: material/information-slab-circle
+---
+
+# :material-information-slab-circle: Introduction
+
+## Description
+
+**EasyImaging** is a software for performing Bragg-edge calculations
+based on a crystalliographic model and refining its parameters against
+experimental data.
+
+**EasyImaging** is developed both as a Python library and as a
+cross-platform desktop application.
+
+Here, we focus on the Python library. For the graphical user interface
+(GUI), please see the corresponding
+[GUI resources](https://easyscience.github.io/imaging-app).
+
+<!--
+**EasyImaging** is developed using the
+[EasyScience framework](https://easyscience.org).
+-->
+
+## License
+
+**EasyImaging** library is released under the
+[BSD 3-Clause License](https://raw.githubusercontent.com/easyscience/imaging-lib/master/LICENSE).
+
+## Releases
+
+The latest version of the **EasyImaging** library is
+[{{ vars.release_version }}](https://github.com/easyscience/imaging-lib/releases/latest).
+
+For a complete list of new features, bug fixes, and improvements, see the
+[GitHub Releases page](https://github.com/easyscience/imaging-lib/releases).
+
+## Citation
+
+If you use **EasyImaging** library in your work, please cite the specific
+version you used.
+
+All official releases of the **EasyImaging** library are archived on
+Zenodo, each with a version-specific Digital Object Identifier (DOI).
+
+Citation details in various styles (e.g., APA, MLA) and formats (e.g.,
+BibTeX, JSON) are available on the
+[Zenodo archive page](https://doi.org/10.5281/zenodo.18163581).
+
+## Contributing
+
+We welcome contributions of any kind!
+
+**EasyImaging** is intended to be a community-driven, open-source project
+supported by a diverse group of contributors.
+
+The project is maintained by the
+[European Spallation Source (ESS)](https://ess.eu).
+
+If you would like to report a bug or request a new feature, please use
+the
+[GitHub Issue Tracker](https://github.com/easyscience/imaging-lib/issues)
+(A free GitHub account is required.)
+
+To contribute code, documentation, or tests, please see our
+[:material-account-plus: Contributing Guidelines](https://github.com/easyscience/imaging-lib/blob/master/CONTRIBUTING.md)
+for detailed development instructions.
+
+## Get in Touch
+
+For general questions or feedback, please contact us at
+[support@easyscience.org](mailto:support@easyscience.org).
diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md
new file mode 100644
index 0000000..6152008
--- /dev/null
+++ b/docs/docs/tutorials/index.md
@@ -0,0 +1,22 @@
+---
+icon: material/school
+---
+
+# :material-school: Tutorials
+
+This section presents a collection of **Jupyter Notebook** tutorials that
+demonstrate how to use EasyImaging for various tasks. These tutorials
+serve as self-contained, step-by-step **guides** to help users grasp the
+workflow of data analysis using EasyImaging.
+
+Instructions on how to run the tutorials are provided in the
+[:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials)
+section of the documentation.
+
+The tutorials are organized into the following categories:
+
+## Getting Started
+
+- [The **Measurement** class](measurement.ipynb) – A tutorial which
+  explores the purpose and functions of the core-component: The
+  **Measurement** class.
diff --git a/docs/docs/tutorials/measurement.ipynb b/docs/docs/tutorials/measurement.ipynb
new file mode 100644
index 0000000..05c8873
--- /dev/null
+++ b/docs/docs/tutorials/measurement.ipynb
@@ -0,0 +1,4237 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0bfd5e51",
+   "metadata": {},
+   "source": [
+    "# The **Measurement** class\n",
+    "### The class reponsible for holding and handing the measurement data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bfb22357",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import scipp as sc\n",
+    "\n",
+    "from easyimaging import Measurement"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "49155b72",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from easyimaging.datasets import iron_alpha_scitiff\n",
+    "\n",
+    "# If you use your own file, simply specify the path like: 'some_path/some_file.tiff'\n",
+    "scitiff_path = iron_alpha_scitiff()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "747b6794",
+   "metadata": {},
+   "source": [
+    "The **Measurement** class can be created in 3 different ways. The preffered way is by loading a scitiff which holds all the neccesary meta-data, using the `from_scitiff` method."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "c4e759bd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement = Measurement.from_scitiff(filename=scitiff_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "12aa16b3",
+   "metadata": {},
+   "source": [
+    "Alternatively, the **Measurement** class can also be created using a regular Tiff stack, using the `from_tiff_stack` method, and supplying the list of time-of-flights for each frame in the Tiff stack and optionally the x- and y-positions of the pixels."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "de262785",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from easyimaging.datasets import iron_alpha_tiff\n",
+    "\n",
+    "tiff_path = iron_alpha_tiff()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "45d76213",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement = Measurement.from_tiff_stack(\n",
+    "    filename=tiff_path,\n",
+    "    time_of_flights=sc.arange('t', 0, 1501, 1, unit='s'),  # mandatory\n",
+    "    # x_positions=sc.arange('x', 0, 50, 1, unit='mm'), # optional\n",
+    "    # y_positions=sc.arange('y', 0, 50, 1, unit='mm'), # optional\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bbfb8209",
+   "metadata": {},
+   "source": [
+    "The *x_positions* and *y_positions* of the pixels can also be set or overwritten later with the method `set_physical_coord_positions`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "8081110a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement.set_physical_coord_positions(\n",
+    "    x_positions=sc.arange('x', -8, 8, 1, unit='cm'),\n",
+    "    y_positions=sc.arange('y', -8, 8, 1, unit='cm'),\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "700d641a",
+   "metadata": {},
+   "source": [
+    "Finally the **Measurement** class can also be created by directly passing an appropriate scipp `DataArray`. This is useful if working in the same notebook as the reduction is performed. Please be aware that there are strict requirements on the format, coordinates and meta-data of this `DataArray`. Here is an example:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "decf64b7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tof = sc.arange('t', 0, 10, 1, unit='s')\n",
+    "x = sc.arange('x', 0, 7, 1, unit='m')  # optional\n",
+    "y = sc.arange('y', 0, 7, 1, unit='m')  # optional\n",
+    "data = sc.ones(dims=['x', 'y', 't'], shape=[6, 6, 10])\n",
+    "scipp_array = sc.DataArray(data=data, coords={'tof': tof, 'x': x, 'y': y})"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7e6f0618",
+   "metadata": {},
+   "source": [
+    "Note that the *x* and *y* coordinates, corresponding to the previous *x_positions* and *y_positions*, is 1 element longer than the data. That is because we work with bin-edges rathar than bin-centers in the **Measurement** class. You can also provide a bin-center list, but it will internally be converted to bin-edges assuming even bin-sizes.\n",
+    "\n",
+    "Another point to note is that the time-of-flight coordinate is called *'tof'* but it has to have the dimension 't'.\n",
+    "\n",
+    "With this correct DataArray, we can then construct the **Measurement** class"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "531b3ea0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement = Measurement(data_array=scipp_array)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e2273160",
+   "metadata": {},
+   "source": [
+    "To continue to show off the **Measurement** class, we will use the preffered creation method, using the scitiff file."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "577cc5ad",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement = Measurement.from_scitiff(filename=scitiff_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "15eb7fef",
+   "metadata": {},
+   "source": [
+    "The **Measurements** *x_positions*, *y_positions* and *time_of_flights* can all be viewed"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 42,
+   "id": "5aa49556",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
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+       "</svg><style id=\"scipp-style-sheet\">.sc-root{--sc-background-color0:var(--jp-layout-color0,#fff);--sc-background-color1:var(--jp-layout-color1,#fcfcfc);--sc-background-color2:var(--jp-layout-color2,#efefef);--sc-inverse-background-color0:var(--jp-inverse-layout-color4,#111);--sc-font-color0:var(--jp-content-font-color0,#000);--sc-font-color1:var(--jp-content-font-color1,#555);--sc-font-color2:var(--jp-content-font-color2,#888);--sc-font-color3:var(--jp-content-font-color3,#ccc);}body.vscode-dark .sc-root{--sc-font-color0:rgba(255,255,255,1);--sc-font-color1:rgba(255,255,255,0.70);--sc-font-color2:rgba(255,255,255,0.54);--sc-font-color3:rgba(255,255,255,0.38);--sc-border-color:#1F1F1F;--sc-disabled-color:#515151;--sc-background-color0:#111111;--sc-background-color1:#111111;--sc-background-color2:#313131;}.sc-wrap{font-size:14px;min-width:300px;max-width:800px;}.sc-var-attrs 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td{vertical-align:top;padding-bottom:0.5ex;}.sc-log-time-stamp{min-width:22ch;font-family:var(--jp-code-font-family);color:var(--sc-font-color2);}.sc-log-level{min-width:10ch;}tr.sc-log-debug td.sc-log-level{color:var(--jp-accent-color1);}tr.sc-log-info td.sc-log-level{color:var(--jp-info-color1);}tr.sc-log-warning td.sc-log-level{color:var(--jp-warn-color1);}tr.sc-log-error td.sc-log-level{font-weight:bold;color:var(--jp-error-color2);}tr.sc-log-critical td.sc-log-level{font-weight:bold;color:var(--sc-background-color0);background-color:var(--jp-error-color1);}.sc-log-message{white-space:pre-wrap;width:100%;}.sc-log-html-payload{white-space:normal;}.sc-log-name{padding-right:0.5em;text-align:right;white-space:pre-wrap;color:var(--sc-font-color3);}</style><div class='sc-wrap sc-root'><div class='sc-header'><div class='sc-obj-type'>scipp.Variable (324 Bytes)</div></div><ul class='sc-sections'><li class='sc-section-item'><ul class='sc-var-list'><li class='sc-var-item'><div class='sc-standalone-var-name'><span>(x: 17)</span></div><div class='sc-var-dtype'>float32</div><div class='sc-var-unit'>mm</div><div class='sc-value-preview sc-preview'><span><div>-7.0382814, -6.158496, ..., 6.158496, 7.0382814</div></span></div><input id='attrs-caaad467-66d3-421d-864e-b5bc10ec0cef' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-caaad467-66d3-421d-864e-b5bc10ec0cef' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-475307b6-62c3-46e9-8a4e-386e3ecd9396' class='sc-var-data-in' type='checkbox'><label for='data-475307b6-62c3-46e9-8a4e-386e3ecd9396' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
+       "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
+       "        6.158496  ,  7.0382814 ], dtype=float32)</pre></li></ul></li></ul></div></div>"
+      ],
+      "text/plain": [
+       "<scipp.Variable> (x: 17)    float32             [mm]  [-7.03828, -6.1585, ..., 6.1585, 7.03828]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<div><!-- Original source from -->\n",
+       "<!-- https://github.com/jsignell/xarray/blob/1d960933ab252e0f79f7e050e6c9261d55568057/xarray/static/html/icons-svg-inline.html -->\n",
+       "<svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n",
+       "<defs>\n",
+       "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n",
+       "<title>Show/Hide data repr</title>\n",
+       "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n",
+       "<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
+       "<path d=\"M16 26c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
+       "</symbol>\n",
+       "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n",
+       "<title>Show/Hide attributes</title>\n",
+       "<path d=\"M28.681 7.159c-0.694-0.947-1.662-2.053-2.724-3.116s-2.169-2.030-3.116-2.724c-1.612-1.182-2.393-1.319-2.841-1.319h-15.5c-1.378 0-2.5 1.121-2.5 2.5v27c0 1.378 1.122 2.5 2.5 2.5h23c1.378 0 2.5-1.122 2.5-2.5v-19.5c0-0.448-0.137-1.23-1.319-2.841zM24.543 5.457c0.959 0.959 1.712 1.825 2.268 2.543h-4.811v-4.811c0.718 0.556 1.584 1.309 2.543 2.268zM28 29.5c0 0.271-0.229 0.5-0.5 0.5h-23c-0.271 0-0.5-0.229-0.5-0.5v-27c0-0.271 0.229-0.5 0.5-0.5 0 0 15.499-0 15.5 0v7c0 0.552 0.448 1 1 1h7v19.5z\"></path>\n",
+       "<path d=\"M23 26h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
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+       "</symbol>\n",
+       "</defs>\n",
+       "</svg><style id=\"scipp-style-sheet\">.sc-root{--sc-background-color0:var(--jp-layout-color0,#fff);--sc-background-color1:var(--jp-layout-color1,#fcfcfc);--sc-background-color2:var(--jp-layout-color2,#efefef);--sc-inverse-background-color0:var(--jp-inverse-layout-color4,#111);--sc-font-color0:var(--jp-content-font-color0,#000);--sc-font-color1:var(--jp-content-font-color1,#555);--sc-font-color2:var(--jp-content-font-color2,#888);--sc-font-color3:var(--jp-content-font-color3,#ccc);}body.vscode-dark .sc-root{--sc-font-color0:rgba(255,255,255,1);--sc-font-color1:rgba(255,255,255,0.70);--sc-font-color2:rgba(255,255,255,0.54);--sc-font-color3:rgba(255,255,255,0.38);--sc-border-color:#1F1F1F;--sc-disabled-color:#515151;--sc-background-color0:#111111;--sc-background-color1:#111111;--sc-background-color2:#313131;}.sc-wrap{font-size:14px;min-width:300px;max-width:800px;}.sc-var-attrs 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td{vertical-align:top;padding-bottom:0.5ex;}.sc-log-time-stamp{min-width:22ch;font-family:var(--jp-code-font-family);color:var(--sc-font-color2);}.sc-log-level{min-width:10ch;}tr.sc-log-debug td.sc-log-level{color:var(--jp-accent-color1);}tr.sc-log-info td.sc-log-level{color:var(--jp-info-color1);}tr.sc-log-warning td.sc-log-level{color:var(--jp-warn-color1);}tr.sc-log-error td.sc-log-level{font-weight:bold;color:var(--jp-error-color2);}tr.sc-log-critical td.sc-log-level{font-weight:bold;color:var(--sc-background-color0);background-color:var(--jp-error-color1);}.sc-log-message{white-space:pre-wrap;width:100%;}.sc-log-html-payload{white-space:normal;}.sc-log-name{padding-right:0.5em;text-align:right;white-space:pre-wrap;color:var(--sc-font-color3);}</style><div class='sc-wrap sc-root'><div class='sc-header'><div class='sc-obj-type'>scipp.Variable (324 Bytes)</div></div><ul class='sc-sections'><li class='sc-section-item'><ul class='sc-var-list'><li class='sc-var-item'><div class='sc-standalone-var-name'><span>(y: 17)</span></div><div class='sc-var-dtype'>float32</div><div class='sc-var-unit'>mm</div><div class='sc-value-preview sc-preview'><span><div>-7.0382814, -6.158496, ..., 6.158496, 7.0382814</div></span></div><input id='attrs-52b23765-9b53-40cd-a0a8-91285fd9114c' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-52b23765-9b53-40cd-a0a8-91285fd9114c' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-7b99a3de-8772-4366-97ec-f5a6b28afdf8' class='sc-var-data-in' type='checkbox'><label for='data-7b99a3de-8772-4366-97ec-f5a6b28afdf8' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([-7.0382814 , -6.158496  , -5.2787113 , -4.398926  , -3.5191407 ,\n",
+       "       -2.6393557 , -1.7595701 , -0.87978506,  0.        ,  0.87978506,\n",
+       "        1.7595701 ,  2.6393552 ,  3.5191412 ,  4.3989263 ,  5.2787113 ,\n",
+       "        6.158496  ,  7.0382814 ], dtype=float32)</pre></li></ul></li></ul></div></div>"
+      ],
+      "text/plain": [
+       "<scipp.Variable> (y: 17)    float32             [mm]  [-7.03828, -6.1585, ..., 6.1585, 7.03828]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<div><!-- Original source from -->\n",
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+       "<svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n",
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+       "<title>Show/Hide data repr</title>\n",
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+       "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n",
+       "<title>Show/Hide attributes</title>\n",
+       "<path d=\"M28.681 7.159c-0.694-0.947-1.662-2.053-2.724-3.116s-2.169-2.030-3.116-2.724c-1.612-1.182-2.393-1.319-2.841-1.319h-15.5c-1.378 0-2.5 1.121-2.5 2.5v27c0 1.378 1.122 2.5 2.5 2.5h23c1.378 0 2.5-1.122 2.5-2.5v-19.5c0-0.448-0.137-1.23-1.319-2.841zM24.543 5.457c0.959 0.959 1.712 1.825 2.268 2.543h-4.811v-4.811c0.718 0.556 1.584 1.309 2.543 2.268zM28 29.5c0 0.271-0.229 0.5-0.5 0.5h-23c-0.271 0-0.5-0.229-0.5-0.5v-27c0-0.271 0.229-0.5 0.5-0.5 0 0 15.499-0 15.5 0v7c0 0.552 0.448 1 1 1h7v19.5z\"></path>\n",
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!important;stroke-width:0;stroke:currentColor;fill:currentColor;}label.sc-hide-icon svg{opacity:0;}.sc-standalone-var-name{grid-column:1/3;}.sc-standalone-var-name span{padding-left:25px;padding-right:10px;}.sc-title{font-weight:bold;font-size:1.5em;}.sc-subtitle{font-weight:normal;font-style:italic;text-align:left;font-size:1.2em;padding:1px;}.sc-label{fill:var(--sc-font-color0,#444444);text-anchor:middle;}.sc-name{fill:var(--sc-font-color0,#111111);}.sc-inset-line{stroke:var(--sc-font-color1);stroke-width:0.05;stroke-dasharray:0.2,0.2;}.sc-log-wrap{height:25ex;resize:vertical;overflow-y:scroll;display:flex;flex-direction:column-reverse;border:1px solid;border-color:var(--jp-border-color2);background-color:var(--sc-background-color1);}div.sc-log{line-height:2.5ex;}table.sc-log{table-layout:auto;border-collapse:collapse;}tr.sc-log:nth-child(even){background-color:var(--sc-background-color0);}tr.sc-log > td{vertical-align:top;padding-bottom:0.5ex;}.sc-log-time-stamp{min-width:22ch;font-family:var(--jp-code-font-family);color:var(--sc-font-color2);}.sc-log-level{min-width:10ch;}tr.sc-log-debug td.sc-log-level{color:var(--jp-accent-color1);}tr.sc-log-info td.sc-log-level{color:var(--jp-info-color1);}tr.sc-log-warning td.sc-log-level{color:var(--jp-warn-color1);}tr.sc-log-error td.sc-log-level{font-weight:bold;color:var(--jp-error-color2);}tr.sc-log-critical td.sc-log-level{font-weight:bold;color:var(--sc-background-color0);background-color:var(--jp-error-color1);}.sc-log-message{white-space:pre-wrap;width:100%;}.sc-log-html-payload{white-space:normal;}.sc-log-name{padding-right:0.5em;text-align:right;white-space:pre-wrap;color:var(--sc-font-color3);}</style><div class='sc-wrap sc-root'><div class='sc-header'><div class='sc-obj-type'>scipp.Variable (11.98 KB)</div></div><ul class='sc-sections'><li class='sc-section-item'><ul class='sc-var-list'><li class='sc-var-item'><div class='sc-standalone-var-name'><span>(t: 1501)</span></div><div class='sc-var-dtype'>float64</div><div class='sc-var-unit'>s</div><div class='sc-value-preview sc-preview'><span><div>0.022, 0.022, ..., 0.092, 0.093</div></span></div><input id='attrs-9f5838b4-957a-4c00-b7a2-06918b0f5ed2' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-9f5838b4-957a-4c00-b7a2-06918b0f5ed2' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ebbda901-1ab0-4430-ac3f-41abdab3c961' class='sc-var-data-in' type='checkbox'><label for='data-ebbda901-1ab0-4430-ac3f-41abdab3c961' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))</pre></li></ul></li></ul></div></div>"
+      ],
+      "text/plain": [
+       "<scipp.Variable> (t: 1501)    float64              [s]  [0.0215873, 0.0216346, ..., 0.0924696, 0.0925169]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "display(measurement.x_positions)  # If available\n",
+    "display(measurement.y_positions)  # If available\n",
+    "display(measurement.time_of_flights)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c3e3409d",
+   "metadata": {},
+   "source": [
+    "The **Measurement** class has a number of plotting methods relying on the underlying *plopp* library from scipp. The simplest plot is a plot of the Tiff stack"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "7e9950e2",
+   "metadata": {},
+   "outputs": [
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+   "id": "d7db0974",
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+    "measurement.plot(time_of_flight=0)"
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+   "metadata": {},
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+    "Pixels with invalid data values, like infinity or NaN, will appear as red. \n",
+    "For further customization of the plot, see https://scipp.github.io/plopp/plotting/image-plot.html and https://scipp.github.io/plopp/generated/plopp.plot.html. Any of the arguments supported here is also supported in the `plot` method.\n",
+    "\n",
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+   "execution_count": 13,
+   "id": "f3cd2bd3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement.rebin(dimensions={'x': 2, 'y': 2})"
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+   "execution_count": 14,
+   "id": "15023563",
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+       " </defs>\n",
+       "</svg>\n"
+      ],
+      "text/plain": [
+       "Figure(600x400, 1 artists)"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.plot(time_of_flight=0)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3b37262c",
+   "metadata": {},
+   "source": [
+    "Further rebinning will rebin the reduced data-set again, yielding an even rougher binning. Rebinning can be reverted and the original data recovered by using the `revert_rebin` method"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "f1f97240",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement.revert_rebin()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bb869ac9",
+   "metadata": {},
+   "source": [
+    "A more useful plotter to inspect the different time-of-flight frames is the `slicer_plot`, which is only available in Jupyter notebooks or similar environments with an interactive graphical backend. The `slicer_plot` has a time-of-flight slider to choose the desired frame to plot.\n",
+    "\n",
+    "To run it, first add the interactive matplotlib widget to your Jupyter notebook:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 36,
+   "id": "75774206",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b1352c5a",
+   "metadata": {},
+   "source": [
+    "Then the slicer plot can be called"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 38,
+   "id": "9d5de1be",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "c5697e2266e54c818c26947db4dfc29d",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…"
+      ]
+     },
+     "execution_count": 38,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.slicer_plot()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3b548b6a",
+   "metadata": {},
+   "source": [
+    "Just like with the regular plot method, any arguments accepted by the underlying plopp backend is supported to further customize the plot, see https://scipp.github.io/plopp/plotting/slicer-plot.html and https://scipp.github.io/plopp/generated/plopp.slicer.html for supported arguments.\n",
+    "\n",
+    "To get the time-of-flight spectrum, the **Measurement** provides the `spectrum` method."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "43c29518",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div><!-- Original source from -->\n",
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+       "<title>Show/Hide data repr</title>\n",
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!important;stroke-width:0;stroke:currentColor;fill:currentColor;}label.sc-hide-icon svg{opacity:0;}.sc-standalone-var-name{grid-column:1/3;}.sc-standalone-var-name span{padding-left:25px;padding-right:10px;}.sc-title{font-weight:bold;font-size:1.5em;}.sc-subtitle{font-weight:normal;font-style:italic;text-align:left;font-size:1.2em;padding:1px;}.sc-label{fill:var(--sc-font-color0,#444444);text-anchor:middle;}.sc-name{fill:var(--sc-font-color0,#111111);}.sc-inset-line{stroke:var(--sc-font-color1);stroke-width:0.05;stroke-dasharray:0.2,0.2;}.sc-log-wrap{height:25ex;resize:vertical;overflow-y:scroll;display:flex;flex-direction:column-reverse;border:1px solid;border-color:var(--jp-border-color2);background-color:var(--sc-background-color1);}div.sc-log{line-height:2.5ex;}table.sc-log{table-layout:auto;border-collapse:collapse;}tr.sc-log:nth-child(even){background-color:var(--sc-background-color0);}tr.sc-log > td{vertical-align:top;padding-bottom:0.5ex;}.sc-log-time-stamp{min-width:22ch;font-family:var(--jp-code-font-family);color:var(--sc-font-color2);}.sc-log-level{min-width:10ch;}tr.sc-log-debug td.sc-log-level{color:var(--jp-accent-color1);}tr.sc-log-info td.sc-log-level{color:var(--jp-info-color1);}tr.sc-log-warning td.sc-log-level{color:var(--jp-warn-color1);}tr.sc-log-error td.sc-log-level{font-weight:bold;color:var(--jp-error-color2);}tr.sc-log-critical td.sc-log-level{font-weight:bold;color:var(--sc-background-color0);background-color:var(--jp-error-color1);}.sc-log-message{white-space:pre-wrap;width:100%;}.sc-log-html-payload{white-space:normal;}.sc-log-name{padding-right:0.5em;text-align:right;white-space:pre-wrap;color:var(--sc-font-color3);}</style><div class='sc-wrap sc-root'><div class='sc-header'><div class='sc-obj-type'>scipp.DataArray (36.84 KB)</div></div><ul class='sc-sections'><li class='sc-section-item'><input id='section-3be01cbb-d091-4f86-b530-129b0e13f773' class='sc-section-summary-in' type='checkbox' disabled ><label for='section-3be01cbb-d091-4f86-b530-129b0e13f773' class='sc-section-summary' >Dimensions:</label><div class='sc-section-inline-details'><ul class='sc-dim-list'><li><span>t</span>: 1500</li></ul></div><div class='sc-section-details'></div></li><li class='sc-section-item'><input id='section-2d7dda63-760c-44fa-bfd7-c9104a9f7579' class='sc-section-summary-in' type='checkbox'  checked><label for='section-2d7dda63-760c-44fa-bfd7-c9104a9f7579' class='sc-section-summary'  title='Expand/collapse section'>Coordinates: <span>(4)</span></label><div class='sc-section-inline-details'></div><div class='sc-section-details'><ul class='sc-var-list'><li class='sc-var-item'><div class='sc-var-name'><span class='sc-aligned'>Ltotal</span></div><div class='sc-var-dims'>()</div><div class='sc-var-dtype'>int64</div><div class='sc-var-unit'>m</div><div class='sc-value-preview sc-preview'><span><div>61</div></span></div><input id='attrs-78d7591d-2dab-4888-9ee7-ad4d93572d02' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-78d7591d-2dab-4888-9ee7-ad4d93572d02' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-acc0d1aa-6716-4edc-8d44-c12472313ceb' class='sc-var-data-in' type='checkbox'><label for='data-acc0d1aa-6716-4edc-8d44-c12472313ceb' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array(61)</pre></span></li><li class='sc-var-item'><div class='sc-var-name'><span>c</span></div><div class='sc-var-dims'>()</div><div class='sc-var-dtype'>string</div><div class='sc-var-unit'></div><div class='sc-value-preview sc-preview'><span><div>intensities</div></span></div><input id='attrs-85371854-ea8c-4545-bdb3-8897f4899c02' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-85371854-ea8c-4545-bdb3-8897f4899c02' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-543932a5-f38f-4d9b-a492-021117272bff' class='sc-var-data-in' type='checkbox'><label for='data-543932a5-f38f-4d9b-a492-021117272bff' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>&#x27;intensities&#x27;</pre></span></li><li class='sc-var-item'><div class='sc-var-name'><span class='sc-aligned'>tof</span></div><div class='sc-var-dims'>(t [bin-edge])</div><div class='sc-var-dtype'>float64</div><div class='sc-var-unit'>s</div><div class='sc-value-preview sc-preview'><span><div>0.022, 0.022, ..., 0.092, 0.093</div></span></div><input id='attrs-3f3dae51-f998-41f9-8ac0-3f4baa5f9fb7' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-3f3dae51-f998-41f9-8ac0-3f4baa5f9fb7' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ae3d2d9a-8647-40b7-911a-79f92be5259b' class='sc-var-data-in' type='checkbox'><label for='data-ae3d2d9a-8647-40b7-911a-79f92be5259b' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))</pre></span></li><li class='sc-var-item'><div class='sc-var-name'><span class='sc-aligned'>wavelength</span></div><div class='sc-var-dims'>(t [bin-edge])</div><div class='sc-var-dtype'>float64</div><div class='sc-var-unit'>Å</div><div class='sc-value-preview sc-preview'><span><div>1.4, 1.403, ..., 5.997, 6.0</div></span></div><input id='attrs-c88d5864-c87e-45b7-aa5c-4a29db729d87' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-c88d5864-c87e-45b7-aa5c-4a29db729d87' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-c74b897b-d0f3-4849-98f7-200cb8221506' class='sc-var-data-in' type='checkbox'><label for='data-c74b897b-d0f3-4849-98f7-200cb8221506' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))</pre></span></li></ul></div></li><li class='sc-section-item'><input id='section-6d4e0fd3-667f-4cab-a2f1-1d00021e2426' class='sc-section-summary-in' type='checkbox'  checked><label for='section-6d4e0fd3-667f-4cab-a2f1-1d00021e2426' class='sc-section-summary'  title='Expand/collapse section'>Data: <span>(1)</span></label><div class='sc-section-inline-details'></div><div class='sc-section-details'><ul class='sc-var-list'><li class='sc-var-item'><div class='sc-var-name'><span></span></div><div class='sc-var-dims'>(t)</div><div class='sc-var-dtype'>float32</div><div class='sc-var-unit'>𝟙</div><div class='sc-value-preview sc-preview'><span><div>0.5531428, 0.56375575, ..., 0.63517606, 0.63194895</div></span><span><div>σ = 0.002992472, 0.003154994, ..., 0.006249289, 0.006158047</div></span></div><input id='attrs-09dd4981-3816-48a8-bcb6-5a8ebf7570cc' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-09dd4981-3816-48a8-bcb6-5a8ebf7570cc' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-f62b4715-24e6-44f8-8ffe-d4bcf5a0e0d2' class='sc-var-data-in' type='checkbox'><label for='data-f62b4715-24e6-44f8-8ffe-d4bcf5a0e0d2' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([0.5531428 , 0.56375575, 0.5592331 , ..., 0.6236488 , 0.63517606,\n",
+       "       0.63194895], shape=(1500,), dtype=float32)<br><br>Variances (σ²):<br>array([8.9548885e-06, 9.9539866e-06, 9.6888207e-06, ..., 3.6184254e-05,\n",
+       "       3.9053615e-05, 3.7921542e-05], shape=(1500,), dtype=float32)</pre></li></ul></div></li></ul></div></div>"
+      ],
+      "text/plain": [
+       "<scipp.DataArray>\n",
+       "Dimensions: Sizes[t:1500, ]\n",
+       "Coordinates:\n",
+       "* Ltotal                      int64              [m]  ()  61\n",
+       "  c                          string        <no unit>  ()  \"intensities\"\n",
+       "* tof                       float64              [s]  (t [bin-edge])  [0.0215873, 0.0216346, ..., 0.0924696, 0.0925169]\n",
+       "* wavelength                float64             [Å]  (t [bin-edge])  [1.4, 1.40307, ..., 5.99693, 6]\n",
+       "Data:\n",
+       "                            float32  [dimensionless]  (t)  [0.553143, 0.563756, ..., 0.635176, 0.631949]  [8.95489e-06, 9.95399e-06, ..., 3.90536e-05, 3.79215e-05]\n"
+      ]
+     },
+     "execution_count": 18,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.spectrum()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6cb7c47a",
+   "metadata": {},
+   "source": [
+    "By default the `spectrum` method adds up all the pixels of the **Measurement**. \n",
+    "The method returns a scipp `DataArray` with uncertainties and time-of-flights.\n",
+    "\n",
+    "It is also possible to plot the spectrum using the `spectrum_plot` method."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "3cf946ab",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "90742002e2bb4e9aab50053089e2cd50",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.spectrum_plot()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6583f974",
+   "metadata": {},
+   "source": [
+    "Which also accepts plopp supported arguments for plot customization, see: https://scipp.github.io/plopp/plotting/line-plot.html and https://scipp.github.io/plopp/generated/plopp.plot.html\n",
+    "\n",
+    "It is also possible to inspect the spectra of individual pixels using the `spectrum_inspector` plot method. This is also an interactive plot which is only supported in Jupyter notebooks and similar. In the plotted **Measurement**, individual pixels can be clicked (after selecting the point-clicker in the menu on the left) to show their spectrum in the spectrum plot underneath."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "e6da5628",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "fd1de66dd5324bf8856a8e7043a5c102",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.spectrum_inspector()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d444bc2d",
+   "metadata": {},
+   "source": [
+    "Where again the plot(s) can be customized, see https://scipp.github.io/plopp/plotting/inspector-plot.html and https://scipp.github.io/plopp/generated/plopp.inspector.html\n",
+    "\n",
+    "It is also possible to define a region of interest (ROI) to provide the spectrum of a specific designated area. To do this, first the ROI has to be created"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "id": "4969d839",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from easyimaging.regions_of_interest.rectangle_roi import RectangleROI"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "04f49975",
+   "metadata": {},
+   "source": [
+    "It is possible to define the ROI in code by hand, or draw it by hand (as shown further down)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "id": "6de05015",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "roi = RectangleROI(\n",
+    "    x_pixel_range=(15, 35),  # mandatory\n",
+    "    y_pixel_range=(15, 35),  # mandatory\n",
+    "    x_range=(sc.scalar(-2, unit='mm'), sc.scalar(2, unit='mm')),  # optional\n",
+    "    y_range=(sc.scalar(-2, unit='mm'), sc.scalar(2, unit='mm')),  # optional\n",
+    "    unique_name='center_roi',  # custom name for the ROI, optional, has to be unique in computer memory\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "82bd5ce3",
+   "metadata": {},
+   "source": [
+    "The ROI needs the x and y pixel ranges, as they are used as fallback for when the ROI is used on a **Measurement** without *x_positions* and *y_positions*. The *x_range* and *y_range* are optional physical ranges which are prioritized when used on a **Measurement** with *x_positions* and *y_positions*.\n",
+    "\n",
+    "This ROI can then be passed to the `spectrum` method and the `spectrum_plot` method to only sum up the spectrum of this region."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "id": "ed81cad4",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div><!-- Original source from -->\n",
+       "<!-- https://github.com/jsignell/xarray/blob/1d960933ab252e0f79f7e050e6c9261d55568057/xarray/static/html/icons-svg-inline.html -->\n",
+       "<svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n",
+       "<defs>\n",
+       "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n",
+       "<title>Show/Hide data repr</title>\n",
+       "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n",
+       "<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
+       "<path d=\"M16 26c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
+       "</symbol>\n",
+       "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n",
+       "<title>Show/Hide attributes</title>\n",
+       "<path d=\"M28.681 7.159c-0.694-0.947-1.662-2.053-2.724-3.116s-2.169-2.030-3.116-2.724c-1.612-1.182-2.393-1.319-2.841-1.319h-15.5c-1.378 0-2.5 1.121-2.5 2.5v27c0 1.378 1.122 2.5 2.5 2.5h23c1.378 0 2.5-1.122 2.5-2.5v-19.5c0-0.448-0.137-1.23-1.319-2.841zM24.543 5.457c0.959 0.959 1.712 1.825 2.268 2.543h-4.811v-4.811c0.718 0.556 1.584 1.309 2.543 2.268zM28 29.5c0 0.271-0.229 0.5-0.5 0.5h-23c-0.271 0-0.5-0.229-0.5-0.5v-27c0-0.271 0.229-0.5 0.5-0.5 0 0 15.499-0 15.5 0v7c0 0.552 0.448 1 1 1h7v19.5z\"></path>\n",
+       "<path d=\"M23 26h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
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+       "</symbol>\n",
+       "</defs>\n",
+       "</svg><style id=\"scipp-style-sheet\">.sc-root{--sc-background-color0:var(--jp-layout-color0,#fff);--sc-background-color1:var(--jp-layout-color1,#fcfcfc);--sc-background-color2:var(--jp-layout-color2,#efefef);--sc-inverse-background-color0:var(--jp-inverse-layout-color4,#111);--sc-font-color0:var(--jp-content-font-color0,#000);--sc-font-color1:var(--jp-content-font-color1,#555);--sc-font-color2:var(--jp-content-font-color2,#888);--sc-font-color3:var(--jp-content-font-color3,#ccc);}body.vscode-dark .sc-root{--sc-font-color0:rgba(255,255,255,1);--sc-font-color1:rgba(255,255,255,0.70);--sc-font-color2:rgba(255,255,255,0.54);--sc-font-color3:rgba(255,255,255,0.38);--sc-border-color:#1F1F1F;--sc-disabled-color:#515151;--sc-background-color0:#111111;--sc-background-color1:#111111;--sc-background-color2:#313131;}.sc-wrap{font-size:14px;min-width:300px;max-width:800px;}.sc-var-attrs 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td{vertical-align:top;padding-bottom:0.5ex;}.sc-log-time-stamp{min-width:22ch;font-family:var(--jp-code-font-family);color:var(--sc-font-color2);}.sc-log-level{min-width:10ch;}tr.sc-log-debug td.sc-log-level{color:var(--jp-accent-color1);}tr.sc-log-info td.sc-log-level{color:var(--jp-info-color1);}tr.sc-log-warning td.sc-log-level{color:var(--jp-warn-color1);}tr.sc-log-error td.sc-log-level{font-weight:bold;color:var(--jp-error-color2);}tr.sc-log-critical td.sc-log-level{font-weight:bold;color:var(--sc-background-color0);background-color:var(--jp-error-color1);}.sc-log-message{white-space:pre-wrap;width:100%;}.sc-log-html-payload{white-space:normal;}.sc-log-name{padding-right:0.5em;text-align:right;white-space:pre-wrap;color:var(--sc-font-color3);}</style><div class='sc-wrap sc-root'><div class='sc-header'><div class='sc-obj-type'>scipp.DataArray (36.84 KB)</div></div><ul class='sc-sections'><li class='sc-section-item'><input id='section-4312601f-27f6-4e3b-8598-4553b9e44afd' class='sc-section-summary-in' type='checkbox' disabled ><label for='section-4312601f-27f6-4e3b-8598-4553b9e44afd' class='sc-section-summary' >Dimensions:</label><div class='sc-section-inline-details'><ul class='sc-dim-list'><li><span>t</span>: 1500</li></ul></div><div class='sc-section-details'></div></li><li class='sc-section-item'><input id='section-ae3413df-2d32-4e19-9c06-91b974c5a2c6' class='sc-section-summary-in' type='checkbox'  checked><label for='section-ae3413df-2d32-4e19-9c06-91b974c5a2c6' class='sc-section-summary'  title='Expand/collapse section'>Coordinates: <span>(4)</span></label><div class='sc-section-inline-details'></div><div class='sc-section-details'><ul class='sc-var-list'><li class='sc-var-item'><div class='sc-var-name'><span class='sc-aligned'>Ltotal</span></div><div class='sc-var-dims'>()</div><div class='sc-var-dtype'>int64</div><div class='sc-var-unit'>m</div><div class='sc-value-preview sc-preview'><span><div>61</div></span></div><input id='attrs-41b058ac-1e54-4efd-b1ed-bb303673616b' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-41b058ac-1e54-4efd-b1ed-bb303673616b' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-18bba5bd-8307-42d5-bb5f-0d3c68744d6a' class='sc-var-data-in' type='checkbox'><label for='data-18bba5bd-8307-42d5-bb5f-0d3c68744d6a' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array(61)</pre></span></li><li class='sc-var-item'><div class='sc-var-name'><span>c</span></div><div class='sc-var-dims'>()</div><div class='sc-var-dtype'>string</div><div class='sc-var-unit'></div><div class='sc-value-preview sc-preview'><span><div>intensities</div></span></div><input id='attrs-485bad3a-1a1b-4545-bd67-f15f80c47f3c' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-485bad3a-1a1b-4545-bd67-f15f80c47f3c' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1929e71d-5b50-4e84-900b-b4ee445b0297' class='sc-var-data-in' type='checkbox'><label for='data-1929e71d-5b50-4e84-900b-b4ee445b0297' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>&#x27;intensities&#x27;</pre></span></li><li class='sc-var-item'><div class='sc-var-name'><span class='sc-aligned'>tof</span></div><div class='sc-var-dims'>(t [bin-edge])</div><div class='sc-var-dtype'>float64</div><div class='sc-var-unit'>s</div><div class='sc-value-preview sc-preview'><span><div>0.022, 0.022, ..., 0.092, 0.093</div></span></div><input id='attrs-c4c553af-afc6-4e92-ba9f-1e773cbf9c33' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-c4c553af-afc6-4e92-ba9f-1e773cbf9c33' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-e7d9f86f-a0a2-450c-9609-b95da49efcce' class='sc-var-data-in' type='checkbox'><label for='data-e7d9f86f-a0a2-450c-9609-b95da49efcce' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([0.02158728, 0.02163456, 0.02168185, ..., 0.09242233, 0.09246961,\n",
+       "       0.0925169 ], shape=(1501,))</pre></span></li><li class='sc-var-item'><div class='sc-var-name'><span class='sc-aligned'>wavelength</span></div><div class='sc-var-dims'>(t [bin-edge])</div><div class='sc-var-dtype'>float64</div><div class='sc-var-unit'>Å</div><div class='sc-value-preview sc-preview'><span><div>1.4, 1.403, ..., 5.997, 6.0</div></span></div><input id='attrs-57c025fb-067f-469b-8301-b836f5674caa' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-57c025fb-067f-469b-8301-b836f5674caa' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-521555ca-6c62-42b6-985c-eaab42593b30' class='sc-var-data-in' type='checkbox'><label for='data-521555ca-6c62-42b6-985c-eaab42593b30' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([1.4       , 1.40306667, 1.40613333, ..., 5.99386667, 5.99693333,\n",
+       "       6.        ], shape=(1501,))</pre></span></li></ul></div></li><li class='sc-section-item'><input id='section-1705328b-9e0d-4e4c-ba0c-9252e65e2e0b' class='sc-section-summary-in' type='checkbox'  checked><label for='section-1705328b-9e0d-4e4c-ba0c-9252e65e2e0b' class='sc-section-summary'  title='Expand/collapse section'>Data: <span>(1)</span></label><div class='sc-section-inline-details'></div><div class='sc-section-details'><ul class='sc-var-list'><li class='sc-var-item'><div class='sc-var-name'><span></span></div><div class='sc-var-dims'>(t)</div><div class='sc-var-dtype'>float32</div><div class='sc-var-unit'>𝟙</div><div class='sc-value-preview sc-preview'><span><div>0.36840674, 0.3425866, ..., 0.46642005, 0.45523798</div></span><span><div>σ = 0.0058153444, 0.0056076236, ..., 0.013006445, 0.012870439</div></span></div><input id='attrs-ecb899b6-1dcc-4da9-a1db-aaf8eda34e6e' class='sc-var-attrs-in' type='checkbox' disabled><label for='attrs-ecb899b6-1dcc-4da9-a1db-aaf8eda34e6e' class='sc-hide-icon' title='Show/Hide attributes'><svg class='icon sc-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-656b852f-2073-46c0-8f71-a1744a87190a' class='sc-var-data-in' type='checkbox'><label for='data-656b852f-2073-46c0-8f71-a1744a87190a' title='Show/Hide data repr'><svg class='icon sc-icon-database'><use xlink:href='#icon-database'></use></svg></label><pre class='sc-var-data'>Values:<br>array([0.36840674, 0.3425866 , 0.35694158, ..., 0.43976402, 0.46642005,\n",
+       "       0.45523798], shape=(1500,), dtype=float32)<br><br>Variances (σ²):<br>array([3.3818233e-05, 3.1445445e-05, 3.3600576e-05, ..., 1.4671838e-04,\n",
+       "       1.6916762e-04, 1.6564821e-04], shape=(1500,), dtype=float32)</pre></li></ul></div></li></ul></div></div>"
+      ],
+      "text/plain": [
+       "<scipp.DataArray>\n",
+       "Dimensions: Sizes[t:1500, ]\n",
+       "Coordinates:\n",
+       "* Ltotal                      int64              [m]  ()  61\n",
+       "  c                          string        <no unit>  ()  \"intensities\"\n",
+       "* tof                       float64              [s]  (t [bin-edge])  [0.0215873, 0.0216346, ..., 0.0924696, 0.0925169]\n",
+       "* wavelength                float64             [Å]  (t [bin-edge])  [1.4, 1.40307, ..., 5.99693, 6]\n",
+       "Data:\n",
+       "                            float32  [dimensionless]  (t)  [0.368407, 0.342587, ..., 0.46642, 0.455238]  [3.38182e-05, 3.14454e-05, ..., 0.000169168, 0.000165648]\n"
+      ]
+     },
+     "execution_count": 24,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.spectrum(roi=roi)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "1e142cfe",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "013a16a07ed147cbbfd3f8ed4e2180e4",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.spectrum_plot(roi=roi)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e3a815ca",
+   "metadata": {},
+   "source": [
+    "In general, an ROI should be added to a **Measurement** class to be used later in fitting"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "id": "123de71f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement.regions_of_interest.append(roi)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "82322c4f",
+   "metadata": {},
+   "source": [
+    "When the ROI is added to a **Measurement**, it can also be used in `spectrum` and `spectrum_plot` methods by simply passing its unique name"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "id": "01bb61d2",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "4b8de46e94f24f72adabec77e114abf8",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(icon='home', la…"
+      ]
+     },
+     "execution_count": 27,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.spectrum_plot(roi='center_roi')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d0b28a05",
+   "metadata": {},
+   "source": [
+    "As prevously promised, the ROI can also be drawn easily by hand, using the `roi_creator` tool. After opening the tool, click the bottom option in the control panel on the left to activate the ROI drawing tool.\n",
+    "\n",
+    "Controls when ROI drawing tool is activated:\n",
+    "- Left-click to make new ROI's\n",
+    "- Left-click and hold on ROI vertices to resize ROI's\n",
+    "- Right-click and hold to drag/move the entire ROI\n",
+    "- Middle-click to delete an ROI"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "id": "7ff41a8e-7dd2-4a19-9d09-8a9221963459",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "40221aacaf994af1a7462168f20bdfae",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Box(children=(InteractiveFigure(children=(HBar(), HBar(children=(VBar(children=(Toolbar(children=(ButtonTool(i…"
+      ]
+     },
+     "execution_count": 28,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.roi_creator()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5dec8e7c",
+   "metadata": {},
+   "source": [
+    "The ROI's drawn with the `roi_creator` tool will appear in the **Measurements** list of regions of interest with default _unique_names_."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "id": "5ef8713d-4844-4afa-ac26-309ed2154613",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "EasyList of length 1 of type(s) [<class 'easyimaging.regions_of_interest.rectangle_roi.RectangleROI'>]"
+      ]
+     },
+     "execution_count": 29,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "measurement.regions_of_interest"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "185948f8",
+   "metadata": {},
+   "source": [
+    "To easier identify specific ROI's, rename ROI's with memorable unique_names. Be aware that each unique_name can only exist once in memory, if a desired unique_name is currently occupied by another object, you might have to restart the notebook to clear the memory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 30,
+   "id": "41a4cd39",
+   "metadata": {
+    "tags": [
+     "hide-in-docs"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "figs = measurement.roi_creator()\n",
+    "# Draw a rectangle\n",
+    "figs[0].toolbar['inspect']._tool.start()\n",
+    "figs[0].toolbar['inspect']._tool.click(x=-0.004, y=-0.004, button=1)\n",
+    "figs[0].toolbar['inspect']._tool.click(x=0.004, y=0.004, button=1)\n",
+    "figs[0].toolbar['inspect']._tool.stop()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "id": "f02fe391",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "measurement.regions_of_interest[1].unique_name = 'best_roi'  # Requires that an ROI was drawn using the roi_creator tool."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "default",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/docs/user-guide/index.md b/docs/docs/user-guide/index.md
new file mode 100644
index 0000000..0bf0eae
--- /dev/null
+++ b/docs/docs/user-guide/index.md
@@ -0,0 +1,24 @@
+---
+icon: material/book-open-variant
+---
+
+# :material-book-open-variant: User Guide
+
+This section provides an overview of the **core concepts**, **key
+parameters** and **workflow steps** required for using EasyImaging
+effectively.
+
+Here is a brief overview of the User Guide sections:
+
+- [Glossary](#) – Defines common terms and labels used throughout the
+  documentation.
+- [Concept](#) – Introduces the overall idea behind data analysis in
+  EasyImaging.
+- [Data Format](#) – Explains the data structures and file formats used
+  by EasyImaging.
+- [Parameters](#) – Describes how parameters are structured, named, and
+  accessed within the EasyImaging.
+- [First Steps](#) – Shows how to begin using EasyImaging in Python or
+  Jupyter notebooks.
+- [Analysis Workflow](#) – Breaks down the data analysis pipeline into
+  practical, sequential steps.
diff --git a/docs/includes/abbreviations.md b/docs/includes/abbreviations.md
new file mode 100644
index 0000000..682f16f
--- /dev/null
+++ b/docs/includes/abbreviations.md
@@ -0,0 +1,15 @@
+<!-- prettier-ignore-start -->
+
+*[CIF]: Crystallographic Information File.
+*[curl]: Command-line tool for transferring data with URLs.
+*[GitHub]: A web-based platform for version control and collaboration.
+*[Google Colab]: Cloud service that allows you to run Jupyter Notebooks in the cloud.
+*[IUCr]: International Union of Crystallography.
+*[Jupyter Notebook]: An open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text.
+*[JupyterLab]: Web-based interactive development environment for notebooks, code, and data.
+*[pip]: Package installer for Python.
+*[PyPI]: The Python Package Index is a repository of software for the Python programming language.
+*[Conda]: Conda is a cross-platform, language-agnostic binary package manager.
+*[Pixi]: A modern package manager for Windows, macOS, and Linux.
+
+<!-- prettier-ignore-end -->
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
new file mode 100644
index 0000000..6e5a42c
--- /dev/null
+++ b/docs/mkdocs.yml
@@ -0,0 +1,208 @@
+# Project information
+site_name: EasyImaging Library
+site_url: https://easyscience.github.io/imaging-lib
+
+# Repository
+repo_url: https://github.com/easyscience/imaging-lib
+edit_uri: edit/develop/docs/
+
+# Copyright
+copyright: © 2024-2026 EasyImaging
+
+# Sets the theme and theme-specific configuration
+theme:
+  name: material
+  custom_dir: overrides
+  features:
+    #- content.action.edit # Temporary disable edit button (until decided on which branch to use and where to host the notebooks)
+    #- content.action.view
+    - content.code.annotate
+    - content.code.copy # Auto generated button to copy a code block's content
+    - content.tooltips
+    - navigation.footer
+    - navigation.indexes
+    #- navigation.instant # Instant loading, but it causes issues with rendering equations
+    #- navigation.sections
+    - navigation.top # Back-to-top button
+    - navigation.tracking # Anchor tracking
+    - search.highlight
+    - search.share
+    - search.suggest
+    - toc.follow
+  palette:
+    # Palette toggle for light mode
+    - media: '(prefers-color-scheme: light)'
+      scheme: default
+      primary: custom
+      toggle:
+        icon: fontawesome/solid/sun
+        name: Switch to dark mode
+    # Palette toggle for dark mode
+    - media: '(prefers-color-scheme: dark)'
+      scheme: slate
+      primary: custom
+      toggle:
+        icon: fontawesome/solid/moon
+        name: Switch to light mode
+  font:
+    text: Mulish
+    code: Roboto Mono
+  icon:
+    edit: material/file-edit-outline
+  favicon: assets/images/favicon.png
+  logo_dark_mode: assets/images/logo_dark.svg
+  logo_light_mode: assets/images/logo_light.svg
+
+# A set of key-value pairs, where the values can be any valid YAML
+# construct, that will be passed to the template
+extra:
+  generator: false # Disable `Made with Material for MkDocs` (bottom left)
+  social: # Extra icons in the bottom right corner
+    - icon: easyscience # File: overrides/.icons/easyscience.svg
+      link: https://easyscience.org
+      name: EasyScience Framework Webpage
+    - icon: easyimaging # File: overrides/.icons/easyimaging.svg
+      link: https://easyscience.github.io/imaging
+      name: EasyImaging Main Webpage
+    - icon: app # File: overrides/.icons/app.svg
+      link: https://easyscience.github.io/imaging-app
+      name: EasyImaging Application Docs
+    - icon: fontawesome/brands/github # Name as in Font Awesome
+      link: https://github.com/easyscience/imaging-lib
+      name: EasyImaging Library Source Code on GitHub
+  # Set custom variables to be used in Markdown and HTML files
+  vars:
+    ci_branch: !ENV CI_BRANCH
+    github_repository: !ENV GITHUB_REPOSITORY
+    release_version: !ENV RELEASE_VERSION
+    docs_version: !ENV DOCS_VERSION
+    notebooks_dir: !ENV NOTEBOOKS_DIR
+  # Renders a version selector in the header
+  version:
+    provider: mike
+
+# Customization to be included by the theme
+extra_css:
+  - assets/stylesheets/extra.css
+  - assets/stylesheets/scipp_style.css # Scipp's style.css got overwritten by the Material theme.
+
+extra_javascript:
+  - assets/javascripts/extra.js
+  # MathJax for rendering mathematical expressions
+  - assets/javascripts/mathjax.js # Custom MathJax config to ensure compatibility with mkdocs-jupyter
+  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js # Official MathJax CDN
+
+# A list of extensions beyond the ones that MkDocs uses by default (meta, toc, tables, and fenced_code)
+markdown_extensions:
+  - abbr
+  - admonition
+  - attr_list
+  - def_list
+  - footnotes
+  - pymdownx.arithmatex: # rendering of equations and integrates with MathJax or KaTeX
+      generic: true
+  - pymdownx.blocks.caption
+  - pymdownx.details
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+      options:
+        custom_icons:
+          - docs/overrides/.icons
+  - pymdownx.highlight: # whether highlighting should be carried out during build time by Pygments
+      use_pygments: true
+      pygments_lang_class: true
+  - pymdownx.snippets:
+      auto_append:
+        - docs/includes/abbreviations.md
+  - pymdownx.superfences: # whether highlighting should be carried out during build time by Pygments
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
+  - pymdownx.tabbed: # enables content tabs
+      alternate_style: true
+  - pymdownx.tasklist:
+      custom_checkbox: true
+  - toc:
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+
+# A list of plugins (with optional configuration settings) to use when building the site
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+  - inline-svg
+  - markdownextradata # Plugin that injects the mkdocs.yml extra variables into the Markdown template
+  - mike # Plugin that makes it easy to deploy multiple versions of the docs
+  - mkdocs-jupyter:
+      include: ['*.ipynb'] # Default: ['*.py', '*.ipynb']
+      execute: false # Do not execute notebooks during build. They are expected to be pre-executed.
+      allow_errors: false
+      include_source: true
+      include_requirejs: true # Required for Plotly
+      #custom_mathjax_url: 'https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js' # See 'extra_javascript' above
+      ignore_h1_titles: true # Use titles defined in the nav section below
+      remove_tag_config:
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+            docstring_style: numpy
+            group_by_category: true
+            members_order: source
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+            show_category_heading: true
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+            summary: true
+            relative_crossrefs: true
+            scoped_crossrefs: true
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+          inventories:
+            - url: https://scipp.github.io/objects.inv
+            - url: https://numpy.org/doc/stable/objects.inv
+            - url: https://easyscience.github.io/core/2.3.1/objects.inv
+            - url: https://scipp.github.io/scitiff/objects.inv
+            - url: https://scipp.github.io/plopp/objects.inv
+  - search
+
+# Determines additional directories to watch when running mkdocs serve
+watch:
+  - includes
+  - overrides
+  - ../src
+
+# Exclude files and folders from the global navigation
+not_in_nav: |
+  index.md
+
+# Format and layout of the global navigation for the site
+nav:
+  - Introduction:
+      - Introduction: introduction/index.md
+  - Installation & Setup:
+      - Installation & Setup: installation-and-setup/index.md
+  - User Guide:
+      - User Guide: user-guide/index.md
+  - Tutorials:
+      - Tutorials: tutorials/index.md
+      - Getting Started:
+          - The Measurement class: tutorials/measurement.ipynb
+  - API Reference:
+      - API Reference: api-reference/index.md
+      - Measurement: api-reference/measurement/measurement.md
+      - regions_of_interest:
+          - regions_of_interest: api-reference/regions_of_interest/index.md
+          - RectangleROI: api-reference/regions_of_interest/rectangle_roi.md
diff --git a/docs/overrides/.icons/app.svg b/docs/overrides/.icons/app.svg
new file mode 100644
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diff --git a/docs/overrides/.icons/easyimaging.svg b/docs/overrides/.icons/easyimaging.svg
new file mode 100644
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+        <title>Main circle</title>
+      </path>
+    </g>
+  </g>
+</svg>
\ No newline at end of file
diff --git a/docs/overrides/.icons/easyscience.svg b/docs/overrides/.icons/easyscience.svg
new file mode 100644
index 0000000..fb51491
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+</svg>
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diff --git a/docs/overrides/.icons/google-colab.svg b/docs/overrides/.icons/google-colab.svg
new file mode 100644
index 0000000..9cd9d1b
--- /dev/null
+++ b/docs/overrides/.icons/google-colab.svg
@@ -0,0 +1,7 @@
+<svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg">
+  <path d="M4.54,9.46,2.19,7.1a6.93,6.93,0,0,0,0,9.79l2.36-2.36A3.59,3.59,0,0,1,4.54,9.46Z" style="" fill="#E8710A"></path>
+  <path d="M2.19,7.1,4.54,9.46a3.59,3.59,0,0,1,5.08,0l1.71-2.93h0l-.1-.08h0A6.93,6.93,0,0,0,2.19,7.1Z" style="" fill="#F9AB00"></path>
+  <path d="M11.34,17.46h0L9.62,14.54a3.59,3.59,0,0,1-5.08,0L2.19,16.9a6.93,6.93,0,0,0,9,.65l.11-.09" style="" fill="#F9AB00"></path>
+  <path d="M12,7.1a6.93,6.93,0,0,0,0,9.79l2.36-2.36a3.59,3.59,0,1,1,5.08-5.08L21.81,7.1A6.93,6.93,0,0,0,12,7.1Z" style="" fill="#F9AB00"></path>
+  <path d="M21.81,7.1,19.46,9.46a3.59,3.59,0,0,1-5.08,5.08L12,16.9A6.93,6.93,0,0,0,21.81,7.1Z" style="" fill="#E8710A"></path>
+</svg>
diff --git a/docs/overrides/main.html b/docs/overrides/main.html
new file mode 100644
index 0000000..2e14682
--- /dev/null
+++ b/docs/overrides/main.html
@@ -0,0 +1,39 @@
+{% extends "base.html" %}
+
+{% block content %}
+
+{% if page.nb_url %}
+  {# Parse notebook path/URL #}
+  {% set parts = page.nb_url.split('/') %}
+  {% set tutorial_name = parts[-2] %}
+  {% set filename = parts[-1] %}
+
+  {# Colab url #}
+  {% set base_colab_url = "https://colab.research.google.com/github/" %}
+  {% set colab_url =
+    base_colab_url ~ config.extra.vars.github_repository ~
+    "/blob/gh-pages/" ~ config.extra.vars.docs_version ~
+    "/tutorials/" ~ tutorial_name ~ "/" ~ filename
+  %}
+
+  {# Download link: relative to the current page #}
+  {% set file_url = filename %}
+
+  {# Open in Colab (absolute GitHub URL; works anywhere) #}
+  <a href="{{ colab_url }}"
+     title="Open in Google Colab"
+     class="md-content__button md-icon">
+    {% include ".icons/google-colab.svg" %}
+  </a>
+
+  {# Download: use a RELATIVE link to the file next to this page #}
+  <a href="{{ file_url }}"
+     download="{{ file_url }}"
+     title="Download Notebook"
+     class="md-content__button md-icon">
+    {% include ".icons/material/download.svg" %}
+  </a>
+{% endif %}
+
+{{ super() }}
+{% endblock content %}
diff --git a/docs/overrides/partials/logo.html b/docs/overrides/partials/logo.html
new file mode 100644
index 0000000..78fa69c
--- /dev/null
+++ b/docs/overrides/partials/logo.html
@@ -0,0 +1,15 @@
+{% if ( config.theme.logo_light_mode and config.theme.logo_dark_mode ) %}
+<img
+  id="logo_light_mode"
+  src="{{ config.theme.logo_light_mode | url }}"
+  alt="logo"
+/>
+<img
+  id="logo_dark_mode"
+  src="{{ config.theme.logo_dark_mode | url }}"
+  alt="logo"
+/>
+{% elif config.theme.logo %}
+<img src="{{ config.theme.logo | url }}" alt="logo" />
+{% else %} {% set icon = config.theme.icon.logo or "material/library" %} {%
+include ".icons/" ~ icon ~ ".svg" %} {% endif %}
diff --git a/pixi.lock b/pixi.lock
index 2b05de2..5bfeb2f 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,1504 +1,3407 @@
-version: 6
+version: 7
+platforms:
+- name: linux-64
+- name: osx-arm64
+- name: win-64
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   default:
     channels:
+    - url: https://conda.anaconda.org/nodefaults/
     - url: https://conda.anaconda.org/conda-forge/
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     packages:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py313h07c4f96_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.6.0-py313h18e8e13_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py313hf159716_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py313hf46b229_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.21-py313h5d5ffb9_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-hbde042b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20260107.1-cxx17_h7b12aa8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.2.0-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.2.0-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.2.0-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.68.1-h877daf1_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.22-h280c20c_1.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.2-h5347b49_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py313h3dea7bd_1.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-2026.5.1-py313hafbe609_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/tornado-6.5.7-py313h07c4f96_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h09e67af_11.conda
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+  - colorcet ; extra == 'dev-optional'
+  - fiona<=1.9.6 ; python_full_version < '3.9' and extra == 'dev-optional'
+  - geopandas ; extra == 'dev-optional'
+  - inflect ; extra == 'dev-optional'
+  - jupyterlab ; extra == 'dev-optional'
+  - kaleido>=1.3.0 ; extra == 'dev-optional'
+  - numpy>=1.22 ; extra == 'dev-optional'
+  - orjson ; extra == 'dev-optional'
+  - pandas ; extra == 'dev-optional'
+  - pdfrw ; extra == 'dev-optional'
+  - pillow ; extra == 'dev-optional'
+  - plotly-geo ; extra == 'dev-optional'
+  - polars[timezone] ; extra == 'dev-optional'
+  - pyarrow ; extra == 'dev-optional'
+  - pyshp ; extra == 'dev-optional'
+  - pytest ; extra == 'dev-optional'
+  - pytz ; extra == 'dev-optional'
+  - requests ; extra == 'dev-optional'
+  - ruff==0.11.12 ; extra == 'dev-optional'
+  - scikit-image ; extra == 'dev-optional'
+  - scipy ; extra == 'dev-optional'
+  - shapely ; extra == 'dev-optional'
+  - statsmodels ; extra == 'dev-optional'
+  - vaex ; python_full_version < '3.10' and extra == 'dev-optional'
+  - xarray ; extra == 'dev-optional'
+  - numpy>=1,<2 ; extra == 'dev-pandas1'
+  - pandas>=1,<2 ; extra == 'dev-pandas1'
+  - setuptools<82 ; extra == 'dev-pandas1'
+  - pandas>=2,<3 ; extra == 'dev-pandas2'
+  - pandas>=3 ; python_full_version >= '3.11' and extra == 'dev-pandas3'
+  - numpy>=1.22 ; extra == 'express'
+  - kaleido>=1.3.0 ; extra == 'kaleido'
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/e2/cc/e097523dd85c9cf5d354f78310927f1656c422bd7b2613b2db3e3f9a0f2c/webcolors-25.10.0-py3-none-any.whl
-  name: webcolors
-  version: 25.10.0
-  sha256: 032c727334856fc0b968f63daa252a1ac93d33db2f5267756623c210e57a4f1d
-  requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
-  name: webencodings
-  version: 0.5.1
-  sha256: a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78
-- pypi: https://files.pythonhosted.org/packages/34/db/b10e48aa8fff7407e67470363eac595018441cf32d5e1001567a7aeba5d2/websocket_client-1.9.0-py3-none-any.whl
-  name: websocket-client
-  version: 1.9.0
-  sha256: af248a825037ef591efbf6ed20cc5faa03d3b47b9e5a2230a529eeee1c1fc3ef
+- pypi: https://files.pythonhosted.org/packages/fa/bc/8b8ec5a4bfc5b9cf3ce27a118339e994f88410be5677c96493e0ea28e76d/dunamai-1.26.1-py3-none-any.whl
+  name: dunamai
+  version: 1.26.1
+  sha256: 2727d939c5b4257cb01ea404372803b477f5176e5a347c43beaf89cd5072e853
   requires_dist:
-  - pytest ; extra == 'test'
-  - websockets ; extra == 'test'
-  - python-socks ; extra == 'optional'
-  - wsaccel ; extra == 'optional'
-  - sphinx>=6.0 ; extra == 'docs'
-  - sphinx-rtd-theme>=1.1.0 ; extra == 'docs'
-  - myst-parser>=2.0.0 ; extra == 'docs'
+  - importlib-metadata>=1.6.0 ; python_full_version < '3.8'
+  - packaging>=20.9
+  requires_python: '>=3.5'
+- pypi: https://files.pythonhosted.org/packages/fb/12/5911ae3eeec47800503a238d971e51722ccea5feb8569b735184d5fcdbc0/toolz-1.1.0-py3-none-any.whl
+  name: toolz
+  version: 1.1.0
+  sha256: 15ccc861ac51c53696de0a5d6d4607f99c210739caf987b5d2054f3efed429d8
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/3f/0e/fa3b193432cfc60c93b42f3be03365f5f909d2b3ea410295cf36df739e31/widgetsnbextension-4.0.15-py3-none-any.whl
-  name: widgetsnbextension
-  version: 4.0.15
-  sha256: 8156704e4346a571d9ce73b84bee86a29906c9abfd7223b7228a28899ccf3366
-  requires_python: '>=3.7'
-- pypi: https://files.pythonhosted.org/packages/a4/f5/10b68b7b1544245097b2a1b8238f66f2fc6dcaeb24ba5d917f52bd2eed4f/wsproto-1.3.2-py3-none-any.whl
-  name: wsproto
-  version: 1.3.2
-  sha256: 61eea322cdf56e8cc904bd3ad7573359a242ba65688716b0710a5eb12beab584
-  requires_dist:
-  - h11>=0.16.0,<1
-  requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/66/fe/b1e10b08d287f518994f1e2ff9b6d26f0adeecd8dd7d533b01bab29a3eda/yarl-1.23.0-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
-  name: yarl
-  version: 1.23.0
-  sha256: 34b6cf500e61c90f305094911f9acc9c86da1a05a7a3f5be9f68817043f486e4
+- pypi: https://files.pythonhosted.org/packages/fb/76/641ae371508676492379f16e2fa48f4e2c11741bd63c48be4b12a6b09cba/aiosignal-1.4.0-py3-none-any.whl
+  name: aiosignal
+  version: 1.4.0
+  sha256: 053243f8b92b990551949e63930a839ff0cf0b0ebbe0597b0f3fb19e1a0fe82e
   requires_dist:
-  - idna>=2.0
-  - multidict>=4.0
-  - propcache>=0.2.1
-  requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/67/b6/8925d68af039b835ae876db5838e82e76ec87b9782ecc97e192b809c4831/yarl-1.23.0-cp313-cp313-macosx_10_13_x86_64.whl
-  name: yarl
-  version: 1.23.0
-  sha256: 4a42e651629dafb64fd5b0286a3580613702b5809ad3f24934ea87595804f2c5
+  - frozenlist>=1.1.0
+  - typing-extensions>=4.2 ; python_full_version < '3.13'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/fd/7b/122376b1fd3c62c1ed9dc80c931ace4844b3c55407b6fb2d199377c9736f/pydantic-2.13.4-py3-none-any.whl
+  name: pydantic
+  version: 2.13.4
+  sha256: 45a282cde31d808236fd7ea9d919b128653c8b38b393d1c4ab335c62924d9aba
   requires_dist:
-  - idna>=2.0
-  - multidict>=4.0
-  - propcache>=0.2.1
-  requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/7a/84/266e8da36879c6edcd37b02b547e2d9ecdfea776be49598e75696e3316e1/yarl-1.23.0-cp313-cp313-win_amd64.whl
-  name: yarl
-  version: 1.23.0
-  sha256: baaf55442359053c7d62f6f8413a62adba3205119bcb6f49594894d8be47e5e3
+  - annotated-types>=0.6.0
+  - pydantic-core==2.46.4
+  - typing-extensions>=4.14.1
+  - typing-inspection>=0.4.2
+  - email-validator>=2.0.0 ; extra == 'email'
+  - tzdata ; python_full_version >= '3.9' and sys_platform == 'win32' and extra == 'timezone'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/fe/c4/225c87bae08c8b9ec99030cd48ae9c4eca050a59bf5c2255853e18c87b50/watchdog-6.0.0-cp313-cp313-macosx_11_0_arm64.whl
+  name: watchdog
+  version: 6.0.0
+  sha256: a175f755fc2279e0b7312c0035d52e27211a5bc39719dd529625b1930917345b
   requires_dist:
-  - idna>=2.0
-  - multidict>=4.0
-  - propcache>=0.2.1
-  requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/ae/50/06d511cc4b8e0360d3c94af051a768e84b755c5eb031b12adaaab6dec6e5/yarl-1.23.0-cp313-cp313-macosx_11_0_arm64.whl
-  name: yarl
-  version: 1.23.0
-  sha256: 7c6b9461a2a8b47c65eef63bb1c76a4f1c119618ffa99ea79bc5bb1e46c5821b
+  - pyyaml>=3.10 ; extra == 'watchmedo'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/fe/d7/a71b12b625c44cfcb95d41397752edccc0a731903081609cffd6720f671d/asteval-1.0.9-py3-none-any.whl
+  name: asteval
+  version: 1.0.9
+  sha256: 60513ea5d608d27bdb0cf3785dc993a6c3adeaee45f1bded0953a09e904e461f
   requires_dist:
-  - idna>=2.0
-  - multidict>=4.0
-  - propcache>=0.2.1
+  - build ; extra == 'dev'
+  - twine ; extra == 'dev'
+  - sphinx ; extra == 'doc'
+  - pytest ; extra == 'test'
+  - pytest-cov ; extra == 'test'
+  - coverage ; extra == 'test'
+  - asteval[dev,doc,test] ; extra == 'all'
   requires_python: '>=3.10'
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
-  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
-  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libzlib >=1.3.1,<2.0a0
-  license: BSD-3-Clause
-  license_family: BSD
-  purls: []
-  size: 601375
-  timestamp: 1764777111296
diff --git a/pixi.toml b/pixi.toml
index 08d4ee0..6a4cbf3 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -1,54 +1,274 @@
+###########
+# WORKSPACE
+###########
+
 [workspace]
-name = "easyimaging"
-channels = ["conda-forge"]
-platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
 
-[dependencies]
-python = ">=3.11,<3.14"
+# Supported platforms for the lock file (pixi.lock)
+platforms = ['win-64', 'linux-64', 'osx-arm64']
+
+# Channels for fetching packages
+channels = ['nodefaults', 'conda-forge']
+
+##########
+# FEATURES
+##########
+
+# Default features:
+
+[activation.env]
+PYTHONIOENCODING = 'utf-8'
+
+[system-requirements]
+# Set minimum supported version for macOS to be 14.0 to ensure packages
+# like `scipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64)
+# are used instead of building from source. This is a workaround for
+# Pixi, see https://github.com/prefix-dev/pixi/issues/5667
+macos = '14.0'
+
+# Non-default features:
+
+# Set specific Python versions to be used in CI testing.
+
+[feature.py-min.dependencies]
+python = '3.11.*'
+
+[feature.py-max.dependencies]
+python = '3.13.*'
+
+# Development dependencies for local development and testing with
+# editable installations.
+
+[feature.dev.dependencies]
+nodejs = '*'      # Required for Prettier (non-Python formatting)
+jupyterlab = '*'  # Jupyter notebooks
+ipython = '*'     # Interactive Python shell
+pixi-kernel = '*' # Pixi Jupyter kernel
 
 [feature.dev.pypi-dependencies]
-# Development dependencies
-easyimaging = { path = ".", extras = ["dev"], editable = true }
+pip = '*'
+easyimaging = { path = '.', editable = true, extras = ['dev'] }
+
+# User-like behavior for testing with pip-installed dependencies instead
+# of editable installations.
 
-[feature.docs.pypi-dependencies]
-# Documentation dependencies
-easyimaging = { path = ".", extras = ["docs"], editable = true }
+[feature.user.dependencies]
+jupyterlab = '*'  # Jupyter notebooks
+ipython = '*'     # Interactive Python shell
+pixi-kernel = '*' # Pixi Jupyter kernel
 
-[feature.build.pypi-dependencies]
-# build dependencies
-easyimaging = { path = ".", extras = ["build"], editable = true }
+[feature.user.pypi-dependencies]
+pip = '*'
+easyimaging = '*'
+
+##############
+# ENVIRONMENTS
+##############
 
 [environments]
-# Default environment with basic build setup
-default = ["build"]
-# Development environment with build, dev, and docs features
-dev = ["build", "dev", "docs"]
+
+# The `default` feature is always included in all environments.
+# Additional features can be specified per environment.
+
+# Specific environments for CI testing with different Python versions.
+py-311-env = { features = ['py-min', 'dev'] }
+py-313-env = { features = ['py-max', 'dev'] }
+
+# The `default` environment is developer-oriented for local development
+# and testing with editable installation of the current package.
+default = { features = ['py-max', 'dev'] }
+
+# The `user` environment allows testing with pip-installed dependencies
+# instead of editable installation of the current package.
+user = { features = ['py-max', 'user'] }
+
+#######
+# TASKS
+#######
 
 [tasks]
-# Development tasks
-test = "pytest --cov=src/easyimaging tests --cov-branch --cov-report=xml:coverage-unit.xml"
-test-unit = "pytest tests/unit_tests"
-test-integration = "pytest tests/integration_tests"
 
-# Code quality tasks
-lint-check = "ruff check ."
-lint = "ruff check . --fix"
-format-check = "ruff format . --check"
-format = "ruff format ."
+##################
+# 🧪 Testing Tasks
+##################
+
+unit-tests = 'python -m pytest tests/unit/ --color=yes -v'
+functional-tests = 'python -m pytest tests/functional/ --color=yes -v'
+integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v'
+notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --color=yes -n auto -v'
+
+test = { depends-on = ['unit-tests'] }
+
+###########
+# ✔️ Checks
+###########
+
+pyproject-check = 'python -m validate_pyproject pyproject.toml'
+docstring-lint-check = 'pydoclint --quiet src/'
+notebook-lint-check = 'nbqa ruff docs/docs/tutorials/'
+py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/'
+py-format-check = 'ruff format --check src/ tests/ docs/docs/tutorials/'
+nonpy-format-check = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .'
+nonpy-format-check-modified = 'python tools/nonpy_prettier_modified.py'
+
+check = 'pre-commit run --hook-stage manual --all-files'
+
+##########
+# 🛠️ Fixes
+##########
+
+docstring-transform = 'pixi run docstripy src/ -s=numpy -w'
+docstring-format-fix = 'format-docstring src/'
+notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/'
+py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/'
+py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/'
+py-format-fix = 'ruff format src/ tests/ docs/docs/tutorials/'
+nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .'
+nonpy-format-fix-modified = 'python tools/nonpy_prettier_modified.py --write'
+success-message = 'echo "✅ All auto-formatting steps completed successfully!"'
+
+fix = { depends-on = [
+  'docstring-format-fix',
+  'py-format-fix',
+  'py-lint-fix',
+  'nonpy-format-fix',
+  'notebook-lint-fix',
+  'success-message',
+] }
+
+####################
+# 🧮 Code Complexity
+####################
+
+complexity-check = 'radon cc -s src/'
+complexity-check-json = 'radon cc -s -j src/'
+maintainability-check = 'radon mi src/'
+maintainability-check-json = 'radon mi -j src/'
+raw-metrics = 'radon raw -s src/'
+raw-metrics-json = 'radon raw -s -j src/'
+
+#############
+# 📊 Coverage
+#############
+
+unit-tests-coverage = 'pixi run unit-tests --cov=src/easyimaging --cov-report=term-missing'
+functional-tests-coverage = 'pixi run functional-tests --cov=src/easyimaging --cov-report=term-missing'
+integration-tests-coverage = 'pixi run integration-tests --cov=src/easyimaging --cov-report=term-missing'
+docstring-coverage = 'interrogate -c pyproject.toml src/easyimaging'
+
+cov = { depends-on = [
+  'docstring-coverage',
+  'unit-tests-coverage',
+  'integration-tests-coverage',
+] }
+
+########################
+# 📓 Notebook Management
+########################
+
+notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb'
+notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb'
+notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/'
+notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v'
+
+notebook-prepare = { depends-on = [
+  #'notebook-convert',
+  'notebook-strip',
+  #'notebook-tweak',
+] }
+
+########################
+# 📚 Documentation Tasks
+########################
+
+docs-vars = "JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS='ignore::RuntimeWarning'"
+docs-pre = 'pixi run docs-vars python -m mkdocs'
+docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml'
+docs-serve-dirty = 'pixi run docs-serve --dirty'
+docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml'
+docs-build-local = 'pixi run docs-build --no-directory-urls'
+
+docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect'
+docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages'
+
+docs-update-assets = 'python tools/update_docs_assets.py'
+
+##############################
+# 📦 Template Management Tasks
+##############################
+
+copier-copy = 'copier copy gh:easyscience/templates . --data-file ../imaging/.copier-answers.yml --data template_type=lib'
+copier-recopy = 'copier recopy --data-file ../imaging/.copier-answers.yml --data template_type=lib'
+copier-update = 'copier update --data-file ../imaging/.copier-answers.yml --data template_type=lib'
+
+#####################
+# 🪝 Pre-commit Hooks
+#####################
+
+pre-commit-clean = 'pre-commit clean'
+pre-commit-install = 'pre-commit install --hook-type pre-commit --hook-type pre-push --overwrite'
+pre-commit-uninstall = 'pre-commit uninstall --hook-type pre-commit --hook-type pre-push'
+pre-commit-setup = { depends-on = [
+  'pre-commit-clean',
+  'pre-commit-uninstall',
+  'pre-commit-install',
+] }
+
+#################
+# 🐙️ GitHub Tasks
+#################
+
+repo-wiki = 'gh api -X PATCH repos/easyscience/imaging-lib -f has_wiki=false'
+repo-discussions = 'gh api -X PATCH repos/easyscience/imaging-lib -f has_discussions=true'
+repo-description = "gh api -X PATCH repos/easyscience/imaging-lib -f description='Neutron imaging data analysis'"
+repo-homepage = "gh api -X PATCH repos/easyscience/imaging-lib -f homepage='https://easyscience.github.io/imaging-lib'"
+repo-config = { depends-on = [
+  'repo-wiki',
+  'repo-discussions',
+  'repo-description',
+  'repo-homepage',
+] }
+
+master-protection = 'gh api -X POST repos/easyscience/imaging-lib/rulesets --input .github/configs/rulesets-master.json'
+develop-protection = 'gh api -X POST repos/easyscience/imaging-lib/rulesets --input .github/configs/rulesets-develop.json'
+gh-pages-protection = 'gh api -X POST repos/easyscience/imaging-lib/rulesets --input .github/configs/rulesets-gh-pages.json'
+branch-protection = { depends-on = [
+  'master-protection',
+  'develop-protection',
+  'gh-pages-protection',
+] }
+
+pages-deployment = 'gh api -X POST repos/easyscience/imaging-lib/pages --input .github/configs/pages-deployment.json'
+
+github-labels = 'python tools/update_github_labels.py'
+
+#########################
+# ⚖️ SPDX License Headers
+#########################
+
+license-remove = 'python tools/license_headers.py remove src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'
+license-add = 'python tools/license_headers.py add src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'
+license-check = 'python tools/license_headers.py check src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'
+
+####################################
+# 🚀 Other Development & Build Tasks
+####################################
 
-# Build tasks
-build = "python -m build"
-clean = "rm -rf dist/ build/ *.egg-info/"
-update-lock = "pixi update"
+default-build = 'python -m build'
+dist-build = 'python -m build --wheel --outdir dist'
 
-# Tox tasks
-tox = "tox"
+npm-config = 'npm config set registry https://registry.npmjs.org/'
+prettier-install = 'npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml'
 
-# Documentation tasks
-docs-build = "sphinx-build -b html docs/src docs/_build/html"
-docs-clean = "rm -rf docs/_build/"
+clean-pycache = "find . -type d -name '__pycache__' -prune -exec rm -rf '{}' +"
 
-[pypi-dependencies] # == [feature.default.pypi-dependencies]
-# Editable install of the package itself
-easyimaging = { path = ".", editable = true }
+post-install = { depends-on = [
+  'npm-config',
+  'prettier-install',
+  #'pre-commit-setup',
+] }
 
+##########################
+# 🔗 Main Package Shortcut
+##########################
+easyimaging = 'python -m easyimaging'
diff --git a/prettierrc.toml b/prettierrc.toml
new file mode 100644
index 0000000..2e02224
--- /dev/null
+++ b/prettierrc.toml
@@ -0,0 +1,22 @@
+plugins = [
+  "prettier-plugin-toml", # use the TOML plugin
+]
+
+endOfLine = 'lf'     # change line endings to LF
+proseWrap = 'always' # change wrapping in Markdown files
+semi = false         # remove semicolons
+singleQuote = true   # use single quotes instead of double quotes
+tabWidth = 2         # change tab width to 2 spaces
+useTabs = false      # use spaces instead of tabs
+
+printWidth = 88 # wrap lines at 88 characters
+
+[[overrides]]
+files = ["*.md"]
+[overrides.options]
+printWidth = 73 # wrap Markdown files at 73 characters
+
+[[overrides]]
+files = ["*.yml", "*.yaml"]
+[overrides.options]
+printWidth = 88 # wrap YAML files at 88 characters
diff --git a/pyproject.toml b/pyproject.toml
index 8135388..74a093a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,163 +1,345 @@
-[build-system]
-requires = [
-    "hatchling<=1.21.0",
-    "setuptools-git-versioning",
-]
-build-backend = "hatchling.build"
-
-[tool.setuptools-git-versioning]
-enabled = true
+###############################
+# Configuration for the project
+###############################
 
 [project]
-name = "EasyImaging"
-dynamic = ["version"]
-description = "Python package for bragg-edge analysis"
-readme = "README.md"
-authors = [{name = "EasyScience contributors"}]
-license = { file = "LICENSE" }
+name = 'easyimaging'
+dynamic = ['version'] # Use versioningit to manage the version
+description = 'Neutron imaging data analysis'
+authors = [{ name = 'EasyScience contributors' }]
+readme = 'README.md'
+license = 'BSD-3-Clause'
+license-files = ['LICENSE']
 classifiers = [
-    "License :: OSI Approved :: BSD License",
-    "Operating System :: OS Independent",
-    "Topic :: Scientific/Engineering",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
-    "Development Status :: 3 - Alpha"
+  'Intended Audience :: Science/Research',
+  'Topic :: Scientific/Engineering',
+  'License :: OSI Approved :: BSD License',
+  'Operating System :: OS Independent',
+  'Programming Language :: Python :: 3 :: Only',
+  'Programming Language :: Python :: 3',
+  'Programming Language :: Python :: 3.11',
+  'Programming Language :: Python :: 3.12',
+  'Programming Language :: Python :: 3.13',
+  'Development Status :: 3 - Alpha',
 ]
-requires-python = ">=3.11,<3.14"
+requires-python = '>=3.11, <3.14'
 dependencies = [
-    "easyscience>=2.2.0",
-    "scitiff",
-    "essimaging",
-    "plopp",
-    "ncrystal[composer]"
+  'easyscience>=2.2.0', # The base library of the EasyScience framework
+  'scitiff',            # The data-format loader/saver for neutron tiffs
+  'essimaging',         # The ESS imaging reduction module
+  'plopp',              # The plotting library of scipp
+  'ncrystal[composer]', # The backend calculator
+  'pooch',              # Data downloader
 ]
 
 [project.optional-dependencies]
-build = [
-    "hatchling <= 1.21.0",
-    "setuptools-git-versioning",
-    "build"
-]
 dev = [
-    "build",
-    "codecov>=2.1.11",
-    "flake8>=6.0.0",
-    "ipykernel",
-    "jupyter>=1.0.0",
-    "jupyterlab",
-    "plopp",
-    "pytest>=5.2",
-    "pytest-cov>=3.0.0",
-    "ruff",
-    "tox-gh-actions",
-    "ipython==9.7.0",
-    "matplotlib==3.10.7",
-    "ipympl==0.9.8",
-]
-docs = [
-    "doc8",
-    "readme-renderer",
-    "sphinx_autodoc_typehints", 
-    "sphinx_book_theme",
-    "sphinx_gallery",
-    "toml"
+  'GitPython',                       # Interact with Git repositories
+  'build',                           # Building the package
+  'pre-commit',                      # Pre-commit hooks
+  'jinja2',                          # Templating
+  'nbmake',                          # Building notebooks
+  'nbstripout',                      # Strip output from notebooks
+  'nbqa',                            # Linting and formatting notebooks
+  'pytest',                          # Testing
+  'pytest-cov',                      # Test coverage
+  'pytest-xdist',                    # Enable parallel testing
+  'ruff',                            # Linting and formatting code
+  'radon',                           # Code complexity and maintainability
+  'validate-pyproject[all]',         # Validate pyproject.toml
+  'versioningit',                    # Automatic versioning from git tags
+  'jupytext',                        # Jupyter notebook text format support
+  'jupyterquiz',                     # Quizzes in Jupyter notebooks
+  'pydoclint',                       # Docstring linter
+  'format-docstring',                # Docstring formatter
+  'docstripy',                       # Convert docstrings to other formats
+  'interrogate',                     # Docstring coverage checker
+  'copier',                          # Template management
+  'mike',                            # MkDocs: Versioned documentation support
+  'mkdocs',                          # Static site generator
+  'mkdocs-material',                 # Documentation framework on top of MkDocs
+  'mkdocs-autorefs',                 # MkDocs: Auto-references support
+  'mkdocs-jupyter',                  # MkDocs: Jupyter notebook support
+  'mkdocs-plugin-inline-svg',        # MkDocs: Inline SVG support
+  'mkdocs-markdownextradata-plugin', # MkDocs: Markdown extra data support, such as global variables
+  'mkdocstrings-python',             # MkDocs: Python docstring support
+  'pyyaml',                          # YAML parser
+  'spdx-headers',                    # SPDX license header validation
 ]
 
 [project.urls]
-homepage = "https://docs.easyimaging.org"
-documentation = "https://docs.easyimaging.org"
+Homepage = 'https://easyscience.github.io/imaging'
+Documentation = 'https://easyscience.github.io/imaging-lib'
+'Release Notes' = 'https://github.com/easyscience/imaging-lib/releases'
+'Source Code' = 'https://github.com/easyscience/imaging-lib'
+'Issue Tracker' = 'https://github.com/easyscience/imaging-lib/issues'
 
-[tool.hatch.version]
-path = "src/easyimaging/__version__.py"
+############################
+# Build system configuration
+############################
+
+[build-system]
+build-backend = 'hatchling.build'
+requires = ['hatchling', 'versioningit']
+
+#############################
+# Configuration for hatchling
+#############################
+
+# 'hatch' -- Build system for Python
+# https://hatch.pypa.io/
+
+[tool.hatch.build.targets.wheel]
+packages = ['src/easyimaging']
 
 [tool.hatch.metadata]
 allow-direct-references = true
 
-[tool.hatch.build.targets.sdist]
-packages = ["src"]
+[tool.hatch.version]
+source = 'versioningit' # Use versioningit to manage the version
+
+################################
+# Configuration for versioningit
+################################
 
-[tool.hatch.build.targets.wheel]
-packages = ["src/easyimaging"]
+# 'versioningit' -- Versioning from git tags
+# https://versioningit.readthedocs.io/
+
+# Versioningit generates versions from git tags, so we don't need to
+# either specify them statically in pyproject.toml or save them in the
+# source code. Do not use {distance} in the version format, as it
+# forces a version bump for every commit, which triggers unnecessary
+# pixi.lock update without any changes to the source code.
+
+[tool.versioningit.format]
+distance = '{base_version}+dev{distance}'            # example: 1.2.3.post4+dev3
+dirty = '{base_version}+dirty{distance}'             # example: 0.5.8+dirty3
+distance-dirty = '{base_version}+devdirty{distance}' # example: 0.5.8+devdirty3
+
+# Configure how versioningit detects versions from Git
+# - 'match' ensures it only considers tags starting with 'v'
+# - 'default-tag' is used as a fallback when no matching tag is found
+[tool.versioningit.vcs]
+method = 'git'
+match = ['v*']
+default-tag = 'v999.0.0'
+
+################################
+# Configuration for interrogate
+################################
+
+# 'interrogate' -- Docstring coverage checker
+# https://interrogate.readthedocs.io/en/latest/
+
+[tool.interrogate]
+fail-under = 0 # Minimum docstring coverage percentage to pass
+verbose = 1
+#exclude = ['src/**/__init__.py']
+
+#######################################
+# Configuration for coverage/pytest-cov
+#######################################
+
+# 'coverage' -- Code coverage measurement tool
+# https://coverage.readthedocs.io/en/latest/
 
 [tool.coverage.run]
-source = ["src/easyimaging"]
+branch = true    # Measure branch coverage as well
+source = ['src'] # Limit coverage to the source code directory
+
+[tool.coverage.report]
+show_missing = true  # Show missing lines
+skip_covered = false # Skip files with 100% coverage in the report
+fail_under = 0       # Minimum coverage percentage to pass
+
+##########################
+# Configuration for pytest
+##########################
+
+# 'pytest' -- Testing framework
+# https://docs.pytest.org/en/stable/
 
-[tool.github.info]
-organization = 'easyScience'
-repo = "easyimaging"
+[tool.pytest.ini_options]
+addopts = '--import-mode=importlib'
+markers = ['fast: mark test as fast (should be run on every push)']
+testpaths = ['tests']
+
+########################
+# Configuration for ruff
+########################
+
+# 'ruff' -- Python linter and code formatter
+# https://docs.astral.sh/ruff/rules/
 
 [tool.ruff]
-line-length = 127
-exclude = [
-    "docs",
-    "ProofOfConcept*",
-]
+exclude = ['ProofOfConcept*', 'tmp']
+indent-width = 4
+line-length = 127                    # See also `max-line-length` in [tool.ruff.lint.pycodestyle]
+preview = true                       # Enable new rules that are not yet stable, like DOC
+builtins = ['display']               # Clutch-fix/patch to https://github.com/nbQA-dev/nbQA/issues/882
+
+# Formatting options for Ruff
 
 [tool.ruff.format]
-quote-style = "single"
+docstring-code-format = true     # Whether to format code snippets in docstrings
+docstring-code-line-length = 127 # Line length for code snippets in docstrings
+indent-style = 'space'           # PEP 8 recommends using spaces over tabs
+quote-style = 'single'           # But double quotes in docstrings (PEP 8, PEP 257)
 
-[tool.ruff.lint.per-file-ignores]
-# allow asserts in test files
-"*test_*.py" = ["S101"]
+# Linting rules to use with Ruff
 
 [tool.ruff.lint]
-ignore-init-module-imports = true
 select = [
-    # flake8 settings from existing CI setup
-    "E9", "F63", "F7", "F82",
-    # Code should be polished to fulfill all cases below
-    # https://docs.astral.sh/ruff/rules/
-    # pycodestyle
-    "E",
-    # Pyflakes
-    "F",
-    # pyupgrade
-#    "UP",
-    # flake8-bugbear
-#    "B",
-    # flake8-simplify
-#    "SIM",
-    # isort
-    "I",
-    # flake8-bandit
-    "S",
+  # Various rules
+  #'C90',  # https://docs.astral.sh/ruff/rules/#mccabe-c90
+  #'D',   # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+  'F', # https://docs.astral.sh/ruff/rules/#pyflakes-f
+  #'FLY',  # https://docs.astral.sh/ruff/rules/#flynt-fly
+  #'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb
+  'I', # https://docs.astral.sh/ruff/rules/#isort-i
+  #'N',    # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+  #'NPY',  # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
+  #'PGH',  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+  #'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf
+  #'RUF',  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+  #'TRY',  # https://docs.astral.sh/ruff/rules/#tryceratops-try
+  #'UP',   # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+  # pycodestyle (E, W) rules
+  'E', # https://docs.astral.sh/ruff/rules/#error-e
+  'W', # https://docs.astral.sh/ruff/rules/#warning-w
+  # Pylint (PL) rules
+  #'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc
+  #'PLE', # https://docs.astral.sh/ruff/rules/#error-ple
+  #'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr
+  #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw
+  # flake8 rules
+  #'A',     # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+  #'ANN',   # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+  #'ARG',   # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
+  #'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async
+  #'B',     # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+  #'BLE',   # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble
+  #'C4',    # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+  #'COM',   # https://docs.astral.sh/ruff/rules/#flake8-commas-com
+  #'DTZ',   # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  #'EM',    # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  #'FA',    # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
+  #'FBT',   # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt
+  #'FIX',   # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix
+  #'G',     # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+  #'ICN',   # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
+  #'INP',   # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
+  #'ISC',   # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
+  #'LOG',   # https://docs.astral.sh/ruff/rules/#flake8-logging-log
+  #'PIE',   # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+  #'PT',    # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+  #'PTH',   # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+  #'PYI',   # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi
+  #'RET',   # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+  #'RSE',   # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+  'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+  #'SIM',   # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+  #'SLF',   # https://docs.astral.sh/ruff/rules/#flake8-self-slf
+  #'SLOT',  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
+  #'T20',   # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+  #'TC',    # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
+  #'TD',    # https://docs.astral.sh/ruff/rules/#flake8-todos-td
+  #'TID',   # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
+]
+
+# Exceptions to the linting rules
+
+# Ignore specific rules globally
+ignore = [
+  'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/
+  # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint]
+  'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc
+  # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout
+  'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/
+]
+
+# Ignore specific rules in certain files or directories
+[tool.ruff.lint.per-file-ignores]
+'*/__init__.py' = [
+  'F401', # re-exports are intentional in __init__.py
+]
+'tests/**' = [
+  'ANN',    # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+  'D',      # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+  'DOC',    # https://docs.astral.sh/ruff/rules/#pydoclint-doc
+  'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/
+  'S101',   # https://docs.astral.sh/ruff/rules/assert/
+]
+'docs/**' = [
+  'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/
+  'T201',   # https://docs.astral.sh/ruff/rules/print/
 ]
+'docs/docs/tutorials/**' = [
+  'E402', # https://docs.astral.sh/ruff/rules/module-import-not-at-top-of-file/
+]
+
+# Specific options for certain rules
+
+[tool.ruff.lint.flake8-tidy-imports]
+# Disallow all relative imports
+#ban-relative-imports = 'all'
 
 [tool.ruff.lint.isort]
+# Forces all from imports to appear on their own line
 force-single-line = true
 
-[tool.tox]
-legacy_tox_ini = """
-[tox]
-isolated_build = True
-envlist = py{3.11,3.12,3.13}
-[gh-actions]
-python =
-        3.11: py311
-        3.12: py312
-        3.13: py313
-[gh-actions:env]
-PLATFORM =
-    ubuntu-latest: linux
-    macos-latest: macos
-    macos-15-intel: macos-intel
-    windows-latest: windows
-[testenv]
-passenv =
-    CI
-    GITHUB_ACTIONS
-    GITHUB_ACTION
-    GITHUB_REF
-    GITHUB_REPOSITORY
-    GITHUB_HEAD_REF
-    GITHUB_RUN_ID
-    GITHUB_SHA
-    COVERAGE_FILE
-deps = coverage
-commands =
-    pip install -e '.[dev]'
-    pytest --cov --cov-report=xml
-"""
+[tool.ruff.lint.mccabe]
+# Cyclomatic complexity threshold (default is 10)
+max-complexity = 10
+
+[tool.ruff.lint.pycodestyle]
+# PEP 8 line length guidance:
+# https://peps.python.org/pep-0008/#maximum-line-length
+# Use 127 characters as the project-wide maximum for regular code lines.
+# Use 127 characters for docstrings.
+max-line-length = 127 # See also `line-length` in [tool.ruff]
+max-doc-length = 127
+
+[tool.ruff.lint.pydocstyle]
+convention = 'numpy'
+
+[tool.ruff.lint.pylint]
+# Ruff counts `self`/`cls` in max-args; traditional pylint does not.
+# Setting 6 here matches pylint's default of 5 (excluding self).
+max-args = 6
+max-positional-args = 6
+
+#############################
+# Configuration for pydoclint
+#############################
+
+# 'pydoclint' -- Docstring linter, a faster alternative to
+# 'darglint' or 'darglint2'.
+# https://pypi.org/project/pydoclint/
+
+# This is a more advanced docstring linter compared to Ruff's built-in
+# docstring check rules D or DOC. For example, among many other things,
+# it can check that arguments in the docstring, which are used by MkDocs
+# and IDEs to render parameter documentation, remain synchronized with
+# the parameter declarations in the code (in function's signature).
+
+[tool.pydoclint]
+exclude = '\.'              # Temporarily disable pydoclint until we are ready
+style = 'numpy'
+check-style-mismatch = true
+check-arg-defaults = true
+allow-init-docstring = true
+
+####################################
+# Configuration for format-docstring
+####################################
+
+# 'format-docstring' -- Code formatter for docstrings
+# https://github.com/jsh9/format-docstring
+
+[tool.format_docstring]
+exclude = '\.'            # Temporarily disable format-docstring until we are ready
+docstring_style = 'numpy'
+line_length = 127
+fix_rst_backticks = true
+verbose = 'default'
diff --git a/src/easyimaging/__init__.py b/src/easyimaging/__init__.py
index fdd01c7..5ebe66d 100644
--- a/src/easyimaging/__init__.py
+++ b/src/easyimaging/__init__.py
@@ -1,16 +1,10 @@
+# SPDX-FileCopyrightText: 2024 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2024 Easyscience contributors (https://github.com/EasyScience)
 
-# flake8: noqa
-import importlib.metadata
+"""EasyImaging library."""
 
-try:
-    __version__ = importlib.metadata.version(__package__ or __name__)
-except importlib.metadata.PackageNotFoundError:
-    __version__ = '0.0.0'
-
-del importlib
+from importlib.metadata import version
 
 from .measurement import Measurement
 
-__all__ = [Measurement]
+__version__ = version(__package__)
diff --git a/src/easyimaging/__version__.py b/src/easyimaging/__version__.py
deleted file mode 100644
index b8023d8..0000000
--- a/src/easyimaging/__version__.py
+++ /dev/null
@@ -1 +0,0 @@
-__version__ = '0.0.1'
diff --git a/src/easyimaging/datasets.py b/src/easyimaging/datasets.py
new file mode 100644
index 0000000..a563f8d
--- /dev/null
+++ b/src/easyimaging/datasets.py
@@ -0,0 +1,55 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
+
+import pooch
+
+BRAIN = pooch.create(
+    # Use the default cache folder for the operating system
+    path=pooch.os_cache('easyimaging'),
+    # The remote data is on Github
+    base_url='https://raw.githubusercontent.com/easyscience/imaging/refs/heads/master/data/',
+    version=None,
+    # If this is a development version, get the data from the "main" branch
+    version_dev='master',
+    registry={
+        'iron_alpha_scitiff/iron_alpha_v1.tiff': 'sha256:ada3d50a5324362add0b8787e11b87b5f33e1dd7e3862f92face03671a20a282',
+        'iron_alpha_tiff/iron_alpha_v1.tiff': 'sha256:a1e4a14bfff3d7c0e92cc42f65f7931536d01f763ba7df2a0e4c0aac851f3594',
+        'small_test_scitiff/small_test_scitiff_v1.tiff': (
+            'sha256:2ce4088fad10437a1180855fba4ebfefad0c98b252be36d6fc046a1aa6ca922d'
+        ),
+        'small_test_tiff/small_test_tiff_v1.tiff': 'sha256:99e5558db28d0d5d5ca46d159791b3649d5a61b6cb4ff67bedaf5485b7d6ea35',
+    },
+)
+
+
+def iron_alpha_scitiff():
+    """
+    Load the Iron Alpha sample data as a scitiff.
+    """
+    fname = BRAIN.fetch('iron_alpha_scitiff/iron_alpha_v1.tiff')
+    return fname
+
+
+def iron_alpha_tiff():
+    """
+    Load the Iron Alpha sample data as a tiff.
+    """
+    fname = BRAIN.fetch('iron_alpha_tiff/iron_alpha_v1.tiff')
+    return fname
+
+
+def small_test_scitiff():
+    """
+    Load a small test scitiff file.
+    """
+    fname = BRAIN.fetch('small_test_scitiff/small_test_scitiff_v1.tiff')
+    return fname
+
+
+def small_test_tiff():
+    """
+    Load a small test tiff file.
+    """
+    fname = BRAIN.fetch('small_test_tiff/small_test_tiff_v1.tiff')
+    return fname
diff --git a/src/easyimaging/measurement/__init__.py b/src/easyimaging/measurement/__init__.py
index b773640..5dc8def 100644
--- a/src/easyimaging/measurement/__init__.py
+++ b/src/easyimaging/measurement/__init__.py
@@ -1,3 +1,4 @@
-from .measurement import Measurement
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
 
-__all__ = [Measurement]
+from .measurement import Measurement
diff --git a/src/easyimaging/measurement/measurement.py b/src/easyimaging/measurement/measurement.py
index 56e3a2f..8ee91a3 100644
--- a/src/easyimaging/measurement/measurement.py
+++ b/src/easyimaging/measurement/measurement.py
@@ -1,6 +1,6 @@
-#  SPDX-FileCopyrightText: 2026 EasyImaging contributors  <imaging@easyscience.software>
-#  SPDX-License-Identifier: BSD-3-Clause
-#  © 2021-2026 Contributors to the EasyImaging project <https://github.com/easyScience/EasyImaging>
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
 from __future__ import annotations
 
 import warnings
@@ -17,17 +17,84 @@
 from scipp import UnitError
 from scitiff import load_scitiff
 from scitiff import save_scitiff
+from scitiff.io import ImageJMetadataNotFoundWarning
 
+from ..regions_of_interest import RectangleROI
 from ..utils import _is_notebook
 from ..utils import _to_edges
-from .regions import RectROI
 
 Numeric = int | float
 
 
 class Measurement(NewBase):
-    """
-    Class responsible for managing the measurement data of a time-of-flight neutron imaging experiment.
+    """Object responsible for managing and inspecting the **normalized** measurement data of a time-of-flight neutron imaging
+     experiment. This object can be created in 3 ways:
+
+    - by loading the data from a [SciTiff](https://scipp.github.io/scitiff/) file with the
+     [from_scitiff][.from_scitiff] method.<br>
+     This is the recommended approach, as the [SciTiff](https://scipp.github.io/scitiff/) format natively contains all the
+     necessary metadata for the analysis of the measurement data.
+    - by directly providing a properly formatted [`sc.DataArray`][scipp.DataArray] to the constructor.<br>
+     This is mostly useful for when working directly in a reduction notebook.
+    - by loading from a regular .tiff stack file with the [from_tiff_stack][.from_tiff_stack] method.<br>
+     This method is provided to support older datasets that are not in the SciTiff format.
+
+    Examples of all 3 methods are supplied below.
+
+    When the [Measurement][.] object is created, a mask is automatically applied to filter out non-finite values in the data.
+
+    Example
+    -------
+    **Creating a [Measurement][.] instance by loading from a [SciTiff](https://scipp.github.io/scitiff/) file**
+
+    Using the example data provided by the library:
+    ```python
+    from easyimaging.datasets import iron_alpha_scitiff
+    from easyimaging import Measurement
+
+    scitiff_path = iron_alpha_scitiff()
+
+    measurement = Measurement.from_scitiff(filename=scitiff_path)
+    ```
+
+    **Creating a [Measurement][.] instance by directly providing a [`sc.DataArray`][scipp.DataArray]**
+
+    Note that the dimension names must be exactly `'x'`, `'y'`, and `'t'`, and that the coordinate names must be exactly
+     `'x'`, `'y'`, and `'tof'` to be recognised by the constructor, and that the `'tof'` coordinate must be provided, whereas
+     `'x'` and `'y'` are optional:
+    ```python
+    import scipp as sc
+    from easyimaging import Measurement
+
+    tof = sc.arange('t', 0, 10, 1, unit='s')
+    x = sc.arange('x', 0, 7, 1, unit='m')  # Optional
+    y = sc.arange('y', 0, 7, 1, unit='m')  # Optional
+    coords = {'tof': tof, 'x': x, 'y': y}
+    data = sc.ones(dims=['t', 'y', 'x'], shape=[10, 6, 6])
+
+    data_array = sc.DataArray(data=data, coords=coords)
+
+    measurement = Measurement(data_array=data_array)
+    ```
+
+    **Creating a [Measurement][.] instance by loading from a regular .tiff stack file**
+
+    Using the example data provided by the library, note that the time_of_flights must be provided, whereas the x_positions
+     and y_positions are optional:
+    ```python
+    from easyimaging.datasets import iron_alpha_tiff
+    from easyimaging import Measurement
+    import scipp as sc
+
+    tiff_path = iron_alpha_tiff()
+
+    measurement = Measurement.from_tiff_stack(
+        filename=tiff_path,
+        time_of_flights=sc.arange('t', 0, 1501, 1, unit='s'),  # mandatory
+        # x_positions=sc.arange('x', 0, 50, 1, unit='mm'), # optional
+        # y_positions=sc.arange('y', 0, 50, 1, unit='mm'), # optional
+    )
+    ```
     """
 
     def __init__(
@@ -36,6 +103,37 @@ def __init__(
         unique_name: str | None = None,
         display_name: str | None = None,
     ):
+        """Initialize a Measurement instance.
+
+        Parameters
+        ----------
+        data_array : sc.DataArray
+            The measurement data in a [`sc.DataArray`][scipp.DataArray] with dimensions ``('x', 'y', 't')``.<br>
+            Must have a ``'tof'`` coordinate for time-of-flight values in the dimension ``'t'``.<br>
+            Optionally may include ``'x'`` and ``'y'`` coordinates for physical pixel positions.<br>
+            Other coordinates in the [`sc.DataArray`][scipp.DataArray] are ignored.
+        unique_name : str | None
+            A unique identifier for the [`Measurement`][..]. Defaults to ``'Measurement'`` appended by a unique integer.
+        display_name : str | None
+            A prettily formatted name for the [`Measurement`][..]. Defaults to [`unique_name`][..unique_name] if not provided.
+
+        Raises
+        ------
+        TypeError
+            If ``data_array`` is not a [`sc.DataArray`][scipp.DataArray].
+        ValueError
+            If the ``data_array`` is missing the ``'tof'`` coordinate.<br>
+            If the ``'tof'`` coordinate contains negative time-of-flight values.<br>
+            If the ``data_array`` has only one of the ``'x'`` or ``'y'`` coordinates, but not both.<br>
+        DimensionError
+            If the ``'tof'`` coordinate does not have the dimension ``'t'``.<br>
+            If the ``'x'`` and ``'y'`` coordinates do not have the dimensions ``'x'`` and ``'y'``, respectively, when
+             provided.<br>
+            If the ``data_array`` does not have both ``'x'`` and ``'y'`` dimensions.
+        UnitError
+            If the ``'tof'`` coordinate does not have a unit of time.<br>
+            If the ``'x'`` and ``'y'`` coordinates do not have a unit of length, when provided.
+        """
         if not isinstance(data_array, sc.DataArray):
             raise TypeError('data_array must be an instance of scipp.DataArray.')
 
@@ -47,6 +145,12 @@ def __init__(
         if any(data_array.coords['tof'].to(unit='s') < sc.scalar(0, unit='s')):
             raise ValueError('time_of_flight values must be non-negative.')
 
+        # Coordinate names were changed in scitiff.
+        if 'x_pixel_offset' in data_array.coords:
+            data_array.coords['x'] = data_array.coords.pop('x_pixel_offset')
+        if 'y_pixel_offset' in data_array.coords:
+            data_array.coords['y'] = data_array.coords.pop('y_pixel_offset')
+
         if 'x' in data_array.coords and 'y' in data_array.coords:
             self._validate_data_array_coordinate(data_array, 'x', 'x', 'length', 'm')
             self._validate_data_array_coordinate(data_array, 'y', 'y', 'length', 'm')
@@ -73,7 +177,7 @@ def __init__(
         self._full_data_array.coords['x_pixels'] = sc.arange('x', 0, self._full_data_array.sizes['x'] + 1, 1)
         self._full_data_array.coords['y_pixels'] = sc.arange('y', 0, self._full_data_array.sizes['y'] + 1, 1)
 
-        self._regions_of_interest = EasyList(protected_types=(RectROI,))
+        self._regions_of_interest = EasyList(protected_types=(RectangleROI,))
 
         non_finite_mask = ~sc.isfinite(self._full_data_array.data)
         self._full_data_array.masks['non_finite'] = non_finite_mask
@@ -82,22 +186,38 @@ def __init__(
     def from_scitiff(
         cls, filename: str | Path, unique_name: str | None = None, display_name: str | None = None
     ) -> Measurement:  # noqa: E501
-        """
-        Create a Measurement instance by loading data from a SciTIFF file.
+        """Create a `Measurement` object by loading normalized image data from a **SciTiff** file.
+
+        Time-of-flight values and other relevant metadata, such as the flight-path, are automatically extracted from the file,
+        if present.
+
+        Uses the [SciTiff](https://scipp.github.io/scitiff/) library's
+         [`load_scitiff`][scitiff.load_scitiff] method internally to load the data.
+
+        Example
+        ----------
+        An example of how to use this method is given in the [Measurement][..] class description.
 
         Parameters
         ----------
         filename : str | Path
-            Path to the SciTIFF file.
+            The path to the [SciTiff](https://scipp.github.io/scitiff/) file.
         unique_name : str | None
-            Unique identifier for the measurement.
+            A unique identifier for the [`Measurement`][..]. Defaults to ``'Measurement'`` appended by a unique integer.
         display_name : str | None
-            Display name for the measurement.
+            A prettily formatted name for the [`Measurement`][..]. Defaults to [`unique_name`][..unique_name] if not provided.
 
         Returns
         -------
         Measurement
-            An instance of the Measurement class containing the loaded data.
+            An instance of the [`Measurement`][..] class containing the loaded data.
+
+        Raises
+        ------
+        TypeError
+            If ``filename`` is not a string or a [`Path`](https://docs.python.org/3/library/pathlib.html) object.
+        RuntimeError
+            If the ``filename`` cannot be loaded or is not a valid [SciTiff](https://scipp.github.io/scitiff/) file.
         """
         if not isinstance(filename, (str, Path)):
             raise TypeError('filename must be a string or Path object.')
@@ -121,38 +241,70 @@ def from_tiff_stack(
         unique_name: str | None = None,
         display_name: str | None = None,
     ) -> Measurement:
-        """
-        Create a Measurement instance by loading data from a TIFF stack file.
+        """Create a `Measurement` object by loading normalized image data from a regular **TIFF** stack file.
+
+        Since a regular TIFF file does not contain the necessary metadata for Bragg-edge imaging,
+         such as **time-of-flight** values for each frame in the image stack, they have to be provided manually.
+
+        The optional metadata can also be set after the object has already been created.
+
+        Example
+        ----------
+        An example of how to use this method is given in the [Measurement][..] class description.
 
         Parameters
         ----------
         filename : str | Path
-            Path to the TIFF stack file.
+            The path to the TIFF stack file.
         time_of_flights : sc.Variable | np.ndarray
-            Array of time-of-flight values corresponding to the frames in the TIFF stack.
-            If a numpy array is provided, the unit is assumed to be seconds.
+            A 1-dimensional array of <nobr>time-of-flight</nobr> values corresponding to the frames in the TIFF stack.<br>
+            If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of seconds.
         x_positions : sc.Variable | np.ndarray | None
-            Array of x-coordinate positions for the pixels.
-            If a numpy array is provided, the unit is assumed to be meters.
+            A 1-dimensional array of physical x-axis positions for the TIFF stack pixels.<br>
+            If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters.
         y_positions : sc.Variable | np.ndarray | None
-            Array of y-coordinate positions for the pixels.
-            If a numpy array is provided, the unit is assumed to be meters.
+            A 1-dimensional array of physical y-axis positions for the TIFF stack pixels.<br>
+            If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters.
         unique_name : str | None
-            Unique identifier for the measurement.
+            A unique identifier for the [`Measurement`][..].<br>
+            Defaults to ``'Measurement'`` appended by a unique integer.
         display_name : str | None
-            Display name for the measurement.
+            A prettily formatted name for the [`Measurement`][..]. Defaults to [`unique_name`][..unique_name] if not provided.
 
         Returns
         -------
         Measurement
-            An instance of the Measurement class containing the loaded data.
+            An instance of the [`Measurement`][..] class containing the loaded and provided data.
+
+        Raises
+        ------
+        TypeError
+            If ``filename`` is not a string or a [`Path`](https://docs.python.org/3/library/pathlib.html) object.<br>
+            If ``time_of_flights``, ``x_positions``, or ``y_positions`` are not a [`sc.Variable`][scipp.Variable] or a
+             [numpy.ndarray][numpy.ndarray].<br>
+        ValueError
+            If ``time_of_flights`` is not 1-dimensional with the same length as the number of frames in the TIFF stack.<br>
+            If either ``x_positions`` or ``y_positions`` are not 1-dimensional with the same length as the number of pixels in
+             the corresponding dimension of the TIFF stack.<br>
+            If the ``'time_of_flights'`` contain negative values.<br>
+        UnitError
+            If ``time_of_flights`` is a [`sc.Variable`][scipp.Variable] that does not have a unit of time.<br>
+            If either ``x_positions`` or ``y_positions`` are a [`sc.Variable`][scipp.Variable] without a unit of
+             length.
+        RuntimeError
+            If the ``filename`` cannot be loaded.<br>
+            If the file is a [SciTiff](https://scipp.github.io/scitiff/) file: Use [from_scitiff][..from_scitiff] instead.
         """
         if not isinstance(filename, (str, Path)):
             raise TypeError('filename must be a string or Path object.')
-        try:
-            data_array = load_scitiff(filename)['image']
-        except Exception as e:
-            raise RuntimeError(f"Failed to load TIFF stack file '{filename}': {e}") from e
+
+        # We know this is not a scitiff, so supress that warning
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore', category=ImageJMetadataNotFoundWarning)
+            try:
+                data_array = load_scitiff(filename)['image']
+            except Exception as e:
+                raise RuntimeError(f"Failed to load TIFF stack file '{filename}': {e}") from e
 
         try:
             data_array = data_array.rename_dims({'dim_0': 't', 'dim_1': 'y', 'dim_2': 'x'})
@@ -198,14 +350,28 @@ def from_tiff_stack(
         return instance
 
     def save_scitiff(self, filename: str | Path) -> None:
-        """
-        Save the measurement data to a SciTIFF file with its time-of-flight and physical coordinate information.
-        Note that it is the rebinned data array that is saved if rebinning has been applied.
+        """Save the `Measurement` data to a **SciTiff** file with the time-of-flight values and other provided metadata.
+
+        Note that [SciTiff](https://scipp.github.io/scitiff/) does not support ``float64`` precision numbers, so if the
+         [`Measurement`][..] contains data of type ``float64``, it will be downcast to ``float32`` when saving, causing a small
+          loss of precision.
 
         Parameters
         ----------
         filename : str | Path
-            Path to the output SciTIFF file.
+            Path to the output [SciTiff](https://scipp.github.io/scitiff/) file.
+
+        Raises
+        ------
+        TypeError
+            If ``filename`` is not a string or a [`Path`](https://docs.python.org/3/library/pathlib.html) object.
+        RuntimeError
+            If the file cannot be written to the specified ``filename`` path.
+
+        Warns
+        -----
+        UserWarning
+            If the [Measurement][..] object's data is of type ``float64``; It will be downcast to ``float32``.
         """
         if not isinstance(filename, (str, Path)):
             raise TypeError('filename must be a string or Path object.')
@@ -226,23 +392,42 @@ def save_scitiff(self, filename: str | Path) -> None:
 
     @property
     def data_array_copy(self) -> sc.DataArray:
-        """
-        Get the current data array of the measurement, either rebinned or the original full resolution.
-        Note that this will make a full copy of the data array, so it should be used with caution for large datasets.
+        """Get a full deep copy of the current data array. This attribute is **read-only**.
+
+        Returns the rebinned data array if rebinning has been applied, otherwise the
+        original full-resolution data array. Use with caution for large datasets to avoid memory issues.
+
+        Returns
+        -------
+        sc.DataArray
+            A deep copy of the current data array.
         """
         return self._data_array.copy(deep=True)
 
-    @data_array_copy.setter
-    def data_array_copy(self, value: sc.DataArray) -> None:
-        raise AttributeError(
-            'Cannot set data_array, it is a read-only property. '
-            'Please make a new Measurement instance if you want to use a different data array.'
-        )
+    # Can't have setters due to MkDocstrings then showing the property as writable.
+    # @data_array_copy.setter
+    # def data_array_copy(self, value: sc.DataArray) -> None:
+    #     """Raise AttributeError — ``data_array_copy`` is a read-only property.
+
+    #     Raises
+    #     ------
+    #     AttributeError
+    #         Always. To use a different data array, create a new :class:`Measurement` instance.
+    #     """
+    #     raise AttributeError(
+    #         'Cannot set data_array, it is a read-only property. '
+    #         'Please make a new Measurement instance if you want to use a different data array.'
+    #     )
 
     @property
     def _data_array(self) -> sc.DataArray:
-        """
-        Get the current data array, either rebinned or the original full resolution.
+        """Get the current data array, either rebinned or the original full resolution.
+
+        Returns
+        -------
+        sc.DataArray
+            The rebinned data array if rebinning has been applied, otherwise the
+            original full-resolution data array.
         """
         if hasattr(self, '_rebinned_data_array'):
             return self._rebinned_data_array
@@ -250,28 +435,49 @@ def _data_array(self) -> sc.DataArray:
 
     @_data_array.setter
     def _data_array(self, value: sc.DataArray) -> None:
-        raise AttributeError('Cannot set _data_array, it is a read-only property.')
+        """Raise AttributeError — ``_data_array`` is a read-only property.
 
-    @property
-    def x_positions(self) -> sc.Variable | None:
-        """
-        Get the x-coordinate positions of the pixels, if available.
+        Raises
+        ------
+        AttributeError
+            Always.
         """
-        if self._has_physical_coords:
-            return self._data_array.coords['x'].copy()
-        return None
+        raise AttributeError('Cannot set _data_array, it is a read-only property.')
 
-    @x_positions.setter
-    def x_positions(self, value: sc.Variable | np.ndarray) -> None:
-        """
-        Set the x-coordinate positions of the pixels.
+    @property
+    def x_positions(self) -> sc.Variable:
+        """The x-coordinates of the physical positions of the pixels.
 
         Parameters
         ----------
         value : sc.Variable | np.ndarray
-            The new x-coordinate positions to set.
+            The new x-coordinate positions to set.<br>
             If a numpy array is provided, the unit is assumed to be meters.
+
+        Returns
+        -------
+        sc.Variable
+            A copy of the physical x-coordinate positions as a [`sc.Variable`][scipp.Variable].
+
+        Raises
+        ------
+        ValueError
+            If physical coordinate positions are not set (use
+            [`set_physical_coord_positions`][..set_physical_coord_positions] to set)<br>
+            If ``value`` is not 1-dimensional with the same length as the number of pixels (or pixel-edges) in the x-dimension.
+        TypeError
+            If ``value`` is not a [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray].
+        UnitError
+            If ``value`` is a [`sc.Variable`][scipp.Variable] and does not have a unit of length.
         """
+        if self._has_physical_coords:
+            return self._data_array.coords['x'].copy()
+        else:
+            raise ValueError('Physical coordinate positions are not set for this Measurement.')
+
+    @x_positions.setter
+    def x_positions(self, value: sc.Variable | np.ndarray) -> None:
+        # Setters have no docstrings. They should be written in the getter docstring instead.
         if not self._has_physical_coords:
             raise ValueError(
                 'Cannot set x_positions before setting all physical coordinate positions. '
@@ -289,25 +495,39 @@ def x_positions(self, value: sc.Variable | np.ndarray) -> None:
         self._data_array.coords['x'] = value
 
     @property
-    def y_positions(self) -> sc.Variable | None:
-        """
-        Get the y-coordinate positions of the pixels, if available.
-        """
-        if self._has_physical_coords:
-            return self._data_array.coords['y'].copy()
-        return None
-
-    @y_positions.setter
-    def y_positions(self, value: sc.Variable | np.ndarray) -> None:
-        """
-        Set the y-coordinate positions of the pixels.
+    def y_positions(self) -> sc.Variable:
+        """The y-coordinates of the physical positions of the pixels.
 
         Parameters
         ----------
         value : sc.Variable | np.ndarray
-            The new y-coordinate positions to set.
+            The new y-coordinate positions to set.<br>
             If a numpy array is provided, the unit is assumed to be meters.
+
+        Returns
+        -------
+        sc.Variable
+            A copy of the physical y-coordinate positions as a [`sc.Variable`][scipp.Variable].
+
+        Raises
+        ------
+        ValueError
+            If physical coordinate positions are not set (use
+            [`set_physical_coord_positions`][..set_physical_coord_positions] to set)<br>
+            If ``value`` is not 1-dimensional with the same length as the number of pixels (or pixel-edges) in the y-dimension.
+        TypeError
+            If ``value`` is not a [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray].
+        UnitError
+            If ``value`` is a [`sc.Variable`][scipp.Variable] and does not have a unit of length.
         """
+        if self._has_physical_coords:
+            return self._data_array.coords['y'].copy()
+        else:
+            raise ValueError('Physical coordinate positions are not set for this Measurement.')
+
+    @y_positions.setter
+    def y_positions(self, value: sc.Variable | np.ndarray) -> None:
+        # Setters have no docstrings. They should be written in the getter docstring instead.
         if not self._has_physical_coords:
             raise ValueError(
                 'Cannot set y_positions before setting all physical coordinate positions. '
@@ -327,17 +547,28 @@ def y_positions(self, value: sc.Variable | np.ndarray) -> None:
     def set_physical_coord_positions(
         self, x_positions: sc.Variable | np.ndarray, y_positions: sc.Variable | np.ndarray
     ) -> None:
-        """
-        Set the physical coordinate positions for the measurement corresponding to the pixel indices.
+        """Set the physical xy-coordinate positions for the pixels of the measurement image stack.
 
         Parameters
         ----------
         x_positions : sc.Variable | np.ndarray
-            The x-coordinate positions to set.
-            If a numpy array is provided, the unit is assumed to be meters.
+            A 1-dimensional array of physical x-axis positions for the image stack pixels.<br>
+            If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters.
         y_positions : sc.Variable | np.ndarray
-            The y-coordinate positions to set.
-            If a numpy array is provided, the unit is assumed to be meters.
+            A 1-dimensional array of physical y-axis positions for the image stack pixels.<br>
+            If a [numpy array][numpy.ndarray] is provided, it is assumed to be in units of meters.
+
+        Raises
+        ------
+        TypeError
+            If either of ``x_positions`` or ``y_positions`` are not a [`sc.Variable`][scipp.Variable] or a
+             [numpy.ndarray][numpy.ndarray].
+        ValueError
+            If either ``x_positions`` or ``y_positions`` are not 1-dimensional with the same length as the number of pixels in
+             the corresponding dimension of the image stack.
+        UnitError
+            If either ``x_positions`` or ``y_positions`` are a [`sc.Variable`][scipp.Variable] without a unit of
+             length.
         """
         x_positions = self._validate_provided_coord(
             data_array=self._data_array,
@@ -362,8 +593,12 @@ def set_physical_coord_positions(
         self._has_physical_coords = True
 
     def delete_physical_coord_positions(self) -> None:
-        """
-        Delete the physical coordinate positions for the measurement.
+        """Delete the physical coordinate positions for the pixels of the measurement image stack.
+
+        Raises
+        ------
+        ValueError
+            If the [Measurement][..] does not currently have physical coordinate positions set.
         """
         if self._has_physical_coords:
             del self._data_array.coords['x']
@@ -374,22 +609,34 @@ def delete_physical_coord_positions(self) -> None:
 
     @property
     def time_of_flights(self) -> sc.Variable:
-        """
-        Get the time-of-flight values of the measurement.
-        """
-        return self._data_array.coords['tof'].copy()
-
-    @time_of_flights.setter
-    def time_of_flights(self, value: sc.Variable | np.ndarray) -> None:
-        """
-        Set the time-of-flight values of the measurement.
+        """The time-of-flight values of the measurement.
 
         Parameters
         ----------
         value : sc.Variable | np.ndarray
-            The new time-of-flight values to set.
+            The new time-of-flight values to set.<br>
             If a numpy array is provided, the unit is assumed to be seconds.
+
+        Returns
+        -------
+        sc.Variable
+            A copy of the time-of-flight values as a [`sc.Variable`][scipp.Variable].
+
+        Raises
+        ------
+        ValueError
+            If ``value`` is not 1-dimensional with the same length as the number of frames.<br>
+            If any element in ``value`` is negative.
+        TypeError
+            If ``value`` is not a [`sc.Variable`][scipp.Variable] or [`np.ndarray`][numpy.ndarray].
+        UnitError
+            If ``value`` is a [`sc.Variable`][scipp.Variable] and does not have a unit of time.
         """
+        return self._data_array.coords['tof'].copy()
+
+    @time_of_flights.setter
+    def time_of_flights(self, value: sc.Variable | np.ndarray) -> None:
+        # Setters have no docstrings. They should be written in the getter docstring instead.
         value = self._validate_provided_coord(
             data_array=self._data_array,
             coord=value,
@@ -404,30 +651,100 @@ def time_of_flights(self, value: sc.Variable | np.ndarray) -> None:
         self._data_array.coords['tof'] = value
 
     @property
-    def regions_of_interest(self) -> EasyList[RectROI]:
-        """
-        Get the list of regions of interest (ROIs) defined for this measurement.
+    def regions_of_interest(self) -> EasyList[RectangleROI]:
+        """The list of regions of interest (ROIs) defined for this measurement.<br> This attribute is **read-only**.
+
+        The returned list is an [EasyList][easyscience.base_classes.EasyList] of
+         [regions of interest][...regions_of_interest.RectangleROI] objects.
+        To modify the list or set new ROIs, interact directly with the returned list.
+
+        Example
+        -------
+        ```python
+        measurement.regions_of_interest.append(new_roi)  # Add a new ROI to the measurement
+        measurement.regions_of_interest.remove('existing_roi')  # Remove an existing ROI
+        ```
+
+        Returns
+        -------
+        EasyList[RectangleROI]
+            A list of the regions of interest (ROIs) attached to this measurement.
         """
         return self._regions_of_interest
 
-    @regions_of_interest.setter
-    def regions_of_interest(self, value: EasyList[RectROI]) -> None:
-        raise AttributeError(
-            'Cannot set regions_of_interest, it is a read-only property. '
-            'Please simply add or remove ROIs directly from the list.'
-        )
+    # Can't have setters due to MkDocstrings then showing the property as writable.
+    # @regions_of_interest.setter
+    # def regions_of_interest(self, value: EasyList[RectangleROI]) -> None:
+    #     """Raise AttributeError — ``regions_of_interest`` is a read-only property.
+
+    #     Raises
+    #     ------
+    #     AttributeError
+    #         Always. Add or remove ROIs directly from the list instead.
+    #     """
+    #     raise AttributeError(
+    #         'Cannot set regions_of_interest, it is a read-only property. '
+    #         'Please simply add or remove ROIs directly from the list.'
+    #     )
 
     def rebin(self, dimensions: dict[str, Numeric]) -> None:
-        """
-        Rebin the measurement image stack. This operation reduces the resolution of the data by combining adjacent pixels or time bins.
-        The rebinned dimensions must be evenly divisible by their specific rebin factor.
+        """Rebin the measurement image stack.
+
+        This operation increases the signal-to-noise ratio of the [Measurement][..] data, at the cost of a reduced resolution,
+         by averaging adjacent pixels.<br>
+        The rebinned dimensions must be evenly divisible by their specific rebin factors, as the operation is otherwise
+         ill-defined.
+
+        Repeating this operation will rebin the already rebinned data, not the original data.<br>
+        This operation can be undone by using the [revert_rebin][..revert_rebin] method,
+         which restores the original full-resolution data.
+
+        Example
+        -------
+        Setting up a [Measurement][..]:
+        ```python
+        import scipp as sc
+        from easyimaging import Measurement
+
+        tof = sc.arange('t', 0, 10, 1, unit='s')
+        coords = {'tof': tof}
+        data = sc.ones(dims=['t', 'y', 'x'], shape=[10, 6, 6])
+
+        data_array = sc.DataArray(data=data, coords=coords)
+
+        measurement = Measurement(data_array=data_array)
+        ```
+        Halve the spatial resolution by rebinning by a factor of 2 in both dimensions:
+        ```python
+        measurement.rebin({'x': 2, 'y': 2})
+        ```
+        You can also rebin by different factors in the different dimensions,
+         if the `Measurement` data dimensions are evenly divisible by those factors:
+        ```python
+        measurement.rebin({'x': 3, 'y': 2})
+        ```
+        You can also rebin only one dimension, leaving the other unchanged:
+        ```python
+        measurement.rebin({'x': 2})
+        ```
 
         Parameters
         ----------
-        dimensions : dict[str, int]
-            A dictionary specifying the rebinning factors for each dimension.
-            For example, {'t': 2} will rebin the time dimension by a factor of 2.
-        """  # noqa: E501
+        dimensions : dict[str, int | float]
+            A dictionary of dimension-rebin factor pairs, specifying the rebinning factors for each dimension.
+
+        Raises
+        ------
+        TypeError
+            If ``dimensions`` is not a `dict`.<br>
+            If any keys in ``dimensions`` are not strings.<br>
+            If a rebin factor is not a positive integer (or integer-valued float).
+        ValueError
+            If a dimension size is not evenly divisible by the requested rebin factor.
+        KeyError
+            If rebinning of the ``'t'`` dimension is requested (not yet supported).<br>
+            If rebinning is attempted on a non-existing dimension.
+        """
         if not isinstance(dimensions, dict):
             raise TypeError('dimensions must be a dictionary mapping dimension names to rebin factors.')
         if all(isinstance(value, Numeric) and value == 1 for value in dimensions.values()):  # Reverts to original data
@@ -435,7 +752,7 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None:
             return
         sizes = dimensions.copy()
         if 't' in dimensions:
-            raise ValueError("Rebinning of the time-of-flight ('t') dimension is not yet supported.")
+            raise KeyError("Rebinning of the time-of-flight ('t') dimension is not yet supported.")
         for dim, value in dimensions.items():
             if not isinstance(dim, str):
                 raise TypeError(f'Dimension keys must be strings. Got {type(dim)} for {dim} instead.')
@@ -446,11 +763,12 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None:
             if isinstance(value, float) and value.is_integer():  # I allow eg. 2.0 as well as 2
                 value = int(value)
             if not isinstance(value, int) or value < 1:
-                raise ValueError(f"Rebin size for dimension '{dim}' must be a positive integer of at least 1.")
+                raise TypeError(f"Rebin size for dimension '{dim}' must be a positive integer of at least 1.")
             if self._full_data_array.sizes[dim] % value != 0:
                 raise ValueError(
-                    f"Dimension '{dim}' with size {self._full_data_array.sizes[dim]} is not evenly divisible by rebin size {value}."  # noqa: E501
-                )  # noqa: E501
+                    f"Dimension '{dim}' with size {self._full_data_array.sizes[dim]} is not"
+                    f' evenly divisible by the requested rebin factor {value}.'
+                )
             sizes[dim] = int(self._data_array.sizes[dim] // value)  # Convert to target size
         temp_array = essimaging.tools.analysis.resize(self._data_array, sizes=sizes, method='mean')
         non_finite_mask = ~sc.isfinite(temp_array.data)
@@ -458,29 +776,54 @@ def rebin(self, dimensions: dict[str, Numeric]) -> None:
         self._rebinned_data_array = temp_array
 
     def revert_rebin(self) -> None:
-        """
-        Revert any rebinning applied to the measurement data, restoring it to its original resolution.
+        """Revert any rebinning applied to the measurement data, restoring it to its original resolution.
+
+        This method undos the rebinning performed by the [rebin][..rebin] method, if it has been applied.
+
+        Warns
+        ------
+        UserWarning
+            If no rebinning has been applied and the measurement data is already in its original state.
         """
         if hasattr(self, '_rebinned_data_array'):
             del self._rebinned_data_array
         else:
-            warnings.warn('No rebinning to revert. The data array is already in its original state.', UserWarning)
+            warnings.warn(
+                'No rebinning to revert. The data array is already in its original state.',
+                UserWarning,
+            )
+
+    # -------------------------------------------------------------------------------------------------------------------------
+    # ----------------------------------------- Plotting methods --------------------------------------------------------------
+    # -------------------------------------------------------------------------------------------------------------------------
 
     def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> None:
-        """
-        Plot the measurement image at a specific time-of-flight.
-        If no time-of-flight is provided, the plot will average over all time-of-flight values.
+        """Plot the 2d spatial measurement image data.
+
+        If no `time-of-flight` is provided, the plot will average over all time-of-flight values.<br>
+        If `time-of-flight` is provided as a [Scipp](https://scipp.github.io/) variable scalar, the nearest time-of-flight
+         frame in time will be plotted.
+
+        This method uses the [plopp](https://scipp.github.io/plopp/plotting/image-plot.html) library for plotting.
 
-        This method uses the plopp library for plotting:
-        https://scipp.github.io/plopp/plotting/image-plot.html
+        To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function.
+        See [plopp.plot][] for which keyword arguments are available and how to use them.
 
         Parameters
         ----------
         time_of_flight : int | sc.Variable | None
-            The time-of-flight value to plot. If None, the time-of-flight axis is averaged.
-        kwargs : dict
-            Additional keyword arguments to pass to the plotting function.
-            See https://scipp.github.io/plopp/generated/plopp.plot.html for options.
+            The time-of-flight value to plot, as an index (int) or a value (sc.Variable).<br>
+            If None, the time-of-flight axis is averaged.
+        **kwargs : dict
+            Additional keyword arguments to pass to the plotting function.<br>
+            See [plopp.plot][] for options.
+
+        Raises
+        ------
+        TypeError
+            If ``time_of_flight`` is not an integer, a `sc.Variable` scalar, or ``None``.
+        UnitError
+            If a `sc.Variable` ``time_of_flight`` is provided without a unit of time.
         """
         if time_of_flight is None:
             title_suffix = ' (averaged over TOF)'
@@ -495,44 +838,50 @@ def plot(self, time_of_flight: int | sc.Variable | None = None, **kwargs) -> Non
         else:
             raise TypeError('time_of_flight must be an integer, scipp scalar, or None.')
 
-        plot_kwargs_defaults = self._plot_defaults()
-        plot_kwargs_defaults['title'] = self.display_name + title_suffix
+        if time_of_flight is None:
+            plot_array = self._data_array.mean('t')
+        elif isinstance(time_of_flight, int):
+            plot_array = self._data_array['t', time_of_flight]
+        elif isinstance(time_of_flight, sc.Variable):
+            plot_array = self._data_array['tof', time_of_flight]
 
         # Overwrite defaults with any user-provided kwargs
+        plot_kwargs_defaults = self._plot_defaults()
+        plot_kwargs_defaults['title'] = self.display_name + title_suffix
+        plot_kwargs_defaults['cmax'] = min(3.0, float(plot_array.max().value * 1.1))
         plot_kwargs_defaults.update(kwargs)
 
-        if time_of_flight is None:
-            plot = self._data_array.mean('t').plot(**plot_kwargs_defaults)
-        elif isinstance(time_of_flight, int):
-            plot = self._data_array['t', time_of_flight].plot(**plot_kwargs_defaults)
-        elif isinstance(time_of_flight, sc.Variable):
-            plot = self._data_array['tof', time_of_flight].plot(**plot_kwargs_defaults)
+        plot = plot_array.plot(**plot_kwargs_defaults)
         if _is_notebook():
             return plot
         else:
             plot.show()
 
     def slicer_plot(self, **kwargs) -> None:
-        """
-        Launch an interactive slicer plot for exploring the measurement data.
+        """Launch an interactive slicer plot for exploring the 2d spatial measurement image data.
+
+        This method uses the [plopp](https://scipp.github.io/plopp/plotting/slicer-plot.html) library for interactive slicing.
 
-        This method uses the plopp library for interactive slicing:
-        https://scipp.github.io/plopp/plotting/slicer-plot.html
+        To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function.
+        See [plopp.slicer][] for which keyword arguments are available and how to use them.
 
         Parameters
         ----------
-        kwargs : dict
-            Additional keyword arguments to pass to the slicer function.
-            See https://scipp.github.io/plopp/generated/plopp.slicer.html for options.
+        **kwargs : dict
+            Additional keyword arguments to pass to the slicer function.<br>
+            See [plopp.slicer][] for options.
+
+        Raises
+        ------
+        RuntimeError
+            If called outside a Jupyter notebook environment.
         """
         slicer_kwargs_defaults = self._plot_defaults()
-        slicer_kwargs_defaults.update(
-            {
-                'title': self.display_name + ' - Time of Flight Slicer',
-                'keep': ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'],
-                'mode': 'single',
-            }
-        )
+        slicer_kwargs_defaults.update({
+            'title': self.display_name + ' - Time of Flight Slicer',
+            'keep': ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'],
+            'mode': 'single',
+        })
         slicer_kwargs_defaults['coords'].append('tof')
 
         # Overwrite defaults with any user-provided kwargs
@@ -544,56 +893,100 @@ def slicer_plot(self, **kwargs) -> None:
             raise RuntimeError('Interactive slicer is only supported in Jupyter notebooks.')
 
     def spectrum_inspector(self, **kwargs) -> None:
-        """
-        Launch an interactive spectrum inspector plot for exploring the measurement data.
+        """Launch an interactive spectrum inspector plot for exploring the measurements time-of-flight spectrums.
+
+        This method uses the [plopp](https://scipp.github.io/plopp/plotting/inspector-plot.html) library for interactive
+         inspection.
 
-        This method uses the plopp library for interactive inspection:
-        https://scipp.github.io/plopp/plotting/inspector-plot.html
+        To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function.
+        See [plopp.inspector][] for which keyword arguments are available and how to use them.
+
+        Interactive controls
+        --------
+        Click the ![](../../assets/images/crosshairs_dark.png#gh-dark-mode-only){width=15px}
+        ![](../../assets/images/crosshairs_light.png#gh-light-mode-only){width=15px} button in the toolbar on the left to
+         activate/deactivate the spectrum investigator tool. When active, the following controls are available:
+
+        - Left-click on a pixel to make a new point and view the spectrum for that pixel
+        - Left-click and drag existing points to adjust which pixel's spectrum is being viewed
+        - Middle-click on a point to delete it and remove its spectrum
 
         Parameters
         ----------
-        kwargs : dict
-            Additional keyword arguments to pass to the inspector function.
-            See https://scipp.github.io/plopp/generated/plopp.inspector.html for options.
+        **kwargs : dict
+            Additional keyword arguments to pass to the inspector function.<br>
+            See [plopp.inspector][] for options.
+
+        Raises
+        ------
+        RuntimeError
+            If called outside a Jupyter notebook environment.
         """
         inspector_kwargs_defaults = self._plot_defaults()
         inspector_kwargs_defaults['ymax'] = inspector_kwargs_defaults['cmax']
-        inspector_kwargs_defaults.update(
-            {
-                'title': self.display_name + ' - Spectrum Inspector',
-                'ymin': 0.0,
-                'dim': 't',
-                'orientation': 'vertical',
-                'operation': 'mean',
-                'mode': 'point',
-            }
-        )
+        inspector_kwargs_defaults.update({
+            'title': self.display_name + ' - Spectrum Inspector',
+            'ymin': 0.0,
+            'dim': 'Time of flight',  # Due to https://github.com/scipp/plopp/issues/566
+            'orientation': 'vertical',
+            'operation': 'mean',
+            'mode': 'point',
+        })
         # Overwrite defaults with any user-provided kwargs
         inspector_kwargs_defaults.update(kwargs)
 
+        # Hack to cirmunvent the bug in https://github.com/scipp/plopp/issues/566
+        temp_array = self._data_array.drop_coords(self._data_array.coords)
+        if self._has_physical_coords:
+            temp_array.coords['x'] = self._data_array.coords['x']
+            temp_array.coords['y'] = self._data_array.coords['y']
+        temp_array.coords['x_pixels'] = self._data_array.coords['x_pixels']
+        temp_array.coords['y_pixels'] = self._data_array.coords['y_pixels']
+        temp_array.coords['Time of flight'] = self._data_array.coords['tof']
+        temp_array = temp_array.rename_dims({'t': 'Time of flight'})
+
         if _is_notebook():
-            return pp.inspector(self._data_array, **inspector_kwargs_defaults)
+            return pp.inspector(temp_array, **inspector_kwargs_defaults)
         else:
             raise RuntimeError('Interactive spectrum inspector is only supported in Jupyter notebooks.')
 
     def roi_creator(self, **kwargs) -> None:
-        """
-        Launch an interactive ROI creator for defining regions of interest on the measurement data.
+        """Launch an interactive Region Of Interest (ROI) creator for defining regions of interest on the measurement data.
+
+        This method uses the [plopp](https://scipp.github.io/plopp/plotting/roi-selector.html) library for interactive ROI
+         creation. ROI's created with this method are automatically added to the [Measurement][..] object's
+         [list of ROIs][..regions_of_interest].
 
-        This method uses the plopp library for interactive ROI creation:
-        https://scipp.github.io/plopp/plotting/roi-selector.html
+        To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function.
+        See [plopp.inspector][] for which keyword arguments are available and how to use them.
 
-        Controls:
-        - Left-click to make new rectangles
-        - Left-click and hold on rectangle vertices to resize rectangle
-        - Right-click and hold to drag/move the entire rectangle
-        - Middle-click to delete rectangle
+        Interactive controls
+        --------
+        Click the ![](../../assets/images/vector-square_dark.png#gh-dark-mode-only){width=15px}
+         ![](../../assets/images/vector-square_light.png#gh-light-mode-only){width=15px} button in the toolbar on the left to
+         activate/deactivate the ROI creator tool. When active, the following controls are available:
+
+        - Left-click to start drawing a new rectangular ROI, and left-click again to finish drawing the rectangle and create
+         the ROI
+        - Left-click and hold on ROI corners to resize the ROI
+        - Right-click and hold to drag/move the entire ROI
+        - Middle-click in the ROI to delete it
+
+        Example
+        ---------
+        An example on how to use this method is shown in the tutorial:
+         [The **Measurement** class](../../tutorials/measurement.ipynb).
 
         Parameters
         ----------
-        kwargs : dict
-            Additional keyword arguments to pass to the ROI creator function.
-            See https://scipp.github.io/plopp/generated/plopp.inspector.html for options.
+        **kwargs : dict
+            Additional keyword arguments to pass to the inspector function.<br>
+            See [plopp.inspector][] for options.
+
+        Raises
+        ------
+        RuntimeError
+            If called outside a Jupyter notebook environment.
         """
 
         if not _is_notebook():
@@ -601,20 +994,30 @@ def roi_creator(self, **kwargs) -> None:
 
         roi_selector_kwargs_defaults = self._plot_defaults()
         roi_selector_kwargs_defaults['ymax'] = roi_selector_kwargs_defaults['cmax']
-        roi_selector_kwargs_defaults.update(
-            {
-                'title': self.display_name + ' - ROI Creator',
-                'ymin': 0.0,
-                'dim': 't',
-                'orientation': 'vertical',
-                'operation': 'mean',
-                'mode': 'rectangle',
-            }
-        )
+        roi_selector_kwargs_defaults.update({
+            'title': self.display_name + ' - ROI Creator',
+            'ymin': 0.0,
+            'dim': 'Time of flight',  # Due to https://github.com/scipp/plopp/issues/566
+            'orientation': 'vertical',
+            'operation': 'mean',
+            'mode': 'rectangle',
+            # 'autoscale' : False,
+        })
         # Overwrite defaults with any user-provided kwargs
         roi_selector_kwargs_defaults.update(kwargs)
 
-        plots = pp.inspector(self._data_array, **roi_selector_kwargs_defaults)
+        # Hack to cirmunvent the bug in https://github.com/scipp/plopp/issues/566
+        temp_array = self._data_array.drop_coords(self._data_array.coords)
+        if self._has_physical_coords:
+            temp_array.coords['x'] = self._data_array.coords['x']
+            temp_array.coords['y'] = self._data_array.coords['y']
+        temp_array.coords['x_pixels'] = self._data_array.coords['x_pixels']
+        temp_array.coords['y_pixels'] = self._data_array.coords['y_pixels']
+        temp_array.coords['Time of flight'] = self._data_array.coords['tof']
+        temp_array = temp_array.rename_dims({'t': 'Time of flight'})
+
+        plots = pp.inspector(temp_array, **roi_selector_kwargs_defaults)
+        # plots = pp.inspector(self._data_array, **roi_selector_kwargs_defaults)
 
         # -------------------------------------------------------------------------------------------------
         # -------------------------- Plot the existing ROIs on the plot -----------------------------------
@@ -655,9 +1058,20 @@ def roi_creator(self, **kwargs) -> None:
 
         # The callback to be used by the Scipp RectangleTool when drawing a new rectangle.
         def create_rectangle_roi(rect, roi_list, data_array):
+            """Create a new :class:`RectangleROI` from a drawn rectangle and append it to ``roi_list``.
+
+            Parameters
+            ----------
+            rect :
+                The rectangle object provided by the plopp RectangleTool.
+            roi_list : EasyList[RectangleROI]
+                The list of ROIs to append the new ROI to.
+            data_array : sc.DataArray
+                The data array used to derive pixel and physical coordinate ranges.
+            """
             # Get the pixel and physical coordinate ranges from the rectangle vertices using the helper method.
             x_pixel_range, y_pixel_range, x_range, y_range = Measurement._ranges_from_rectangle(rect, data_array)
-            new_roi = RectROI(
+            new_roi = RectangleROI(
                 x_pixel_range=x_pixel_range,
                 y_pixel_range=y_pixel_range,
                 x_range=x_range,
@@ -668,6 +1082,17 @@ def create_rectangle_roi(rect, roi_list, data_array):
 
         # The callback to be used by the Scipp RectangleTool when dragging the corners of an existing rectangle.
         def edit_rectangle_roi(rect, roi_list, data_array):
+            """Update the matching :class:`RectangleROI` in ``roi_list`` when a rectangle is resized.
+
+            Parameters
+            ----------
+            rect :
+                The rectangle object provided by the plopp RectangleTool.
+            roi_list : EasyList[RectangleROI]
+                The list of ROIs containing the ROI to update.
+            data_array : sc.DataArray
+                The data array used to derive updated coordinate ranges.
+            """
             x_pixel_range, y_pixel_range, x_range, y_range = Measurement._ranges_from_rectangle(rect, data_array)
             # Find the ROI corresponding to the rectangle being edited based on the stored rectangle ID.
             for roi in roi_list:
@@ -680,6 +1105,15 @@ def edit_rectangle_roi(rect, roi_list, data_array):
                 matching_roi.set_physical_coord_range(x_range, y_range)
 
         def delete_rectangle_roi(rect, roi_list):
+            """Remove the :class:`RectangleROI` corresponding to ``rect`` from ``roi_list``.
+
+            Parameters
+            ----------
+            rect :
+                The rectangle object provided by the plopp RectangleTool.
+            roi_list : EasyList[RectangleROI]
+                The list of ROIs from which the matching ROI will be removed.
+            """
             for roi in roi_list:
                 if hasattr(roi, '_rect_ids') and rect.id in roi._rect_ids:
                     roi_list.remove(roi)
@@ -690,7 +1124,11 @@ def delete_rectangle_roi(rect, roi_list):
         # -------------------------------------------------------------------------------------------------
 
         plots[0].toolbar['inspect']._tool.on_create(
-            partial(create_rectangle_roi, roi_list=self.regions_of_interest, data_array=self._data_array)
+            partial(
+                create_rectangle_roi,
+                roi_list=self.regions_of_interest,
+                data_array=self._data_array,
+            )
         )
 
         plots[0].toolbar['inspect']._tool.on_change(
@@ -703,24 +1141,34 @@ def delete_rectangle_roi(rect, roi_list):
 
         return plots
 
-    def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray:
-        """
-        Extract the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI).
-        If no ROI is provided, the spectrum is calculated over the entire image.
+    def spectrum(self, roi: RectangleROI | str | None = None) -> sc.DataArray:
+        """Extract the measured time-of-flight spectrum in a specified Region Of Interest (ROI).
+
+        The ROI can either be passed directly as an object, or by its ``unique_name`` as a string, if it has been added to
+         the measurement's [regions of interest list][..regions_of_interest].
+
+        If no ROI is provided, the spectrum is calculated over the entire measurement image stack.
 
         Parameters
         ----------
-        roi : RectROI | str | None
-            The region of interest for which to extract the spectrum.
-            If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs.
+        roi : RectangleROI | str | None
+            The ROI for which to extract the spectrum.<br>
+            If a string, it should be the ``unique_name`` of a ROI in the [regions_of_interest][] list.<br>
 
         Returns
         -------
         sc.DataArray
-            A DataArray containing the spectrum data.
+            A 1-D [sc.DataArray][scipp.DataArray] containing the spatially averaged time-of-flight spectrum.
+
+        Raises
+        ------
+        TypeError
+            If ``roi`` is not a [`RectangleROI`][RectangleROI], string, or ``None``.
+        KeyError
+            If a string ``roi`` does not match the `unique_name` of any ROI in [`regions_of_interest`][regions_of_interest].
         """
-        if roi is not None and not isinstance(roi, (RectROI, str)):
-            raise TypeError('roi must be a string, None, or an instance of RectROI.')
+        if roi is not None and not isinstance(roi, (RectangleROI, str)):
+            raise TypeError('roi must be a string, None, or an instance of RectangleROI.')
 
         if isinstance(roi, str):
             if roi in self.regions_of_interest:
@@ -740,31 +1188,51 @@ def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray:
             spectrum_data = self._data_array['x_pixels', x_slice]['y_pixels', y_slice].mean(dim=['x', 'y'])
         return spectrum_data
 
-    def spectrum_plot(self, roi: RectROI | str | None = None, **kwargs) -> None:
-        """
-        Plot the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI).
-        If no ROI is provided, the spectrum is calculated over the entire image.
+    def spectrum_plot(self, roi: RectangleROI | str | None = None, **kwargs) -> None:
+        """Plot the measured time-of-flight spectrum in a specified Region Of Interest (ROI).
+
+        The ROI can either be passed directly as an object, or by its ``unique_name`` as a string, if it has been added to
+         the measurement's [regions of interest list][..regions_of_interest].
 
-        This method uses the plopp library for plotting:
-        https://scipp.github.io/plopp/plotting/line-plot.html
+        If no ROI is provided, the spectrum is calculated over the entire measurement image stack.
+
+        This method uses the [plopp](https://scipp.github.io/plopp/plotting/line-plot.html) library for plotting.
+
+        To customize the plot appearance, additional keyword arguments can be passed to the underlying plopp plotting function.
+         See [plopp.plot][] for which keyword arguments are available and how to use them.
 
         Parameters
         ----------
-        roi : RectROI | str | None
-            The region of interest for which to plot the spectrum.
-            If a string is provided, it should be the unique name of a predefined ROI in the measurement's list of ROIs.
-        kwargs : dict
-            Additional keyword arguments to pass to the plotting function.
-            See https://scipp.github.io/plopp/generated/plopp.plot.html for options.
+        roi : RectangleROI | str | None
+            The ROI for which to extract the spectrum.<br>
+            If a string, it should be the ``unique_name`` of a ROI in the [regions_of_interest][] list.<br>
+        **kwargs : dict
+            Additional keyword arguments to pass to the plotting function.<br>
+            See [plopp.plot][] for options.
+
+        Raises
+        ------
+        TypeError
+            If ``roi`` is not a [`RectangleROI`][RectangleROI], string, or ``None``.
+        KeyError
+            If a string ``roi`` does not match the `unique_name` of any ROI in [`regions_of_interest`][regions_of_interest].
         """
         spectrum_data = self.spectrum(roi=roi)
 
+        if roi is None:
+            roi_name = 'entire image'
+        elif isinstance(roi, str):
+            roi_name = f"ROI '{roi}'"
+        else:
+            roi_name = f"ROI '{roi.unique_name}'"
+
         plot_kwargs_defaults = {
-            'title': self.display_name + ' - Spectrum',
-            'xlabel': 'Time of Flight',
+            'title': self.display_name + ' - Spectrum of ' + roi_name,
+            'xlabel': f'Time of flight [{spectrum_data.coords["tof"].unit}]',
             'ylabel': 'Transmission',
             'ymin': 0.0,
-            'ymax': 3.0,
+            'ymax': min(3.0, float(spectrum_data.max().value * 1.1)),
+            'coords': ['tof'],
         }
         # Overwrite defaults with any user-provided kwargs
         plot_kwargs_defaults.update(kwargs)
@@ -783,6 +1251,28 @@ def _validate_data_array_coordinate(
         expected_dim_string: str,
         expected_unit: str,
     ) -> None:
+        """Validate that a named coordinate of a data array has the expected dimension and unit.
+
+        Parameters
+        ----------
+        data_array : sc.DataArray
+            The data array whose coordinate is to be validated.
+        coord_name : str
+            Name of the coordinate to validate.
+        expected_dim : str
+            The single dimension name the coordinate must have (e.g. ``'t'``).
+        expected_dim_string : str
+            Human-readable name of the physical dimension (e.g. ``'time'``).
+        expected_unit : str
+            The SI unit string the coordinate must be convertible to (e.g. ``'s'``).
+
+        Raises
+        ------
+        DimensionError
+            If the coordinate does not have exactly the expected dimension.
+        UnitError
+            If the coordinate cannot be converted to ``expected_unit``.
+        """
         if data_array.coords[coord_name].dims != (expected_dim,):
             raise DimensionError(f"'{coord_name}' coordinate must be of dimension '{expected_dim}'.")
         try:
@@ -802,6 +1292,43 @@ def _validate_provided_coord(
         expected_dim_string: str,
         expected_unit: str,
     ) -> sc.Variable:
+        """Validate and normalise a coordinate array provided by the caller.
+
+        Accepts either a :class:`scipp.Variable` or a :class:`numpy.ndarray` and
+        returns a validated :class:`scipp.Variable`. A numpy array is wrapped with
+        ``dim`` and ``expected_unit``.
+
+        Parameters
+        ----------
+        data_array : sc.DataArray
+            The data array the coordinate will be assigned to (used for length checks).
+        coord : sc.Variable | np.ndarray
+            The coordinate values to validate.
+        coord_name : str
+            Human-readable name of the coordinate (used in error messages).
+        dim : str
+            Dimension name along which the coordinate runs (e.g. ``'t'``).
+        length_context : str
+            Description of what the length should match (used in error messages).
+        expected_dim_string : str
+            Human-readable name of the physical dimension (e.g. ``'time'``).
+        expected_unit : str
+            The SI unit string the coordinate must be convertible to (e.g. ``'s'``).
+
+        Returns
+        -------
+        sc.Variable
+            The validated (and possibly converted) coordinate variable.
+
+        Raises
+        ------
+        TypeError
+            If ``coord`` is not a :class:`scipp.Variable` array or :class:`numpy.ndarray`.
+        ValueError
+            If the length of ``coord`` does not match the dimension size of ``data_array``.
+        UnitError
+            If ``coord`` cannot be converted to ``expected_unit``.
+        """
         if not (isinstance(coord, sc.Variable) and coord.sizes) and not isinstance(coord, np.ndarray):
             raise TypeError(f'{coord_name} must be a scipp Variable or a numpy ndarray.')
         if len(coord) not in (data_array.sizes[dim], data_array.sizes[dim] + 1):
@@ -818,6 +1345,31 @@ def _validate_provided_coord(
     def _ranges_from_rectangle(
         rect, data_array: sc.DataArray
     ) -> tuple[tuple[int, int], None] | tuple[tuple[int, int], tuple[sc.Variable, sc.Variable]]:  # noqa: E501
+        """Convert rectangle vertices from the plopp RectangleTool to pixel and physical coordinate ranges.
+
+        Used internally by :meth:`roi_creator` when the user draws or edits a rectangle.
+
+        Parameters
+        ----------
+        rect :
+            Rectangle object from the plopp RectangleTool exposing a ``vertices`` attribute.
+        data_array : sc.DataArray
+            The current data array, used to determine whether physical coordinates are
+            available and to look up pixel indices.
+
+        Returns
+        -------
+        x_pixel_range : tuple[int, int]
+            ``(x_start, x_end)`` pixel indices.
+        y_pixel_range : tuple[int, int]
+            ``(y_start, y_end)`` pixel indices.
+        x_range : tuple[sc.Variable, sc.Variable] or None
+            ``(x_start, x_end)`` physical coordinates, or ``None`` if no physical
+            coordinates are present.
+        y_range : tuple[sc.Variable, sc.Variable] or None
+            ``(y_start, y_end)`` physical coordinates, or ``None`` if no physical
+            coordinates are present.
+        """
         # To be used in the roi_selector method to convert the rectangle vertices to pixel and
         # physical coordinate ranges for the new ROI.
         x_vertex_list, y_vertex_list = rect.vertices
@@ -830,8 +1382,14 @@ def _ranges_from_rectangle(
         else:
             x_unit = data_array.coords['x'].unit
             y_unit = data_array.coords['y'].unit
-            x_range = (sc.scalar(min(x_vertex_list), unit=x_unit), sc.scalar(max(x_vertex_list), unit=x_unit))
-            y_range = (sc.scalar(min(y_vertex_list), unit=y_unit), sc.scalar(max(y_vertex_list), unit=y_unit))
+            x_range = (
+                sc.scalar(min(x_vertex_list), unit=x_unit),
+                sc.scalar(max(x_vertex_list), unit=x_unit),
+            )
+            y_range = (
+                sc.scalar(min(y_vertex_list), unit=y_unit),
+                sc.scalar(max(y_vertex_list), unit=y_unit),
+            )
 
             sliced_data_array = data_array['x', x_range[0] : x_range[1]]['y', y_range[0] : y_range[1]]
 
@@ -843,6 +1401,14 @@ def _ranges_from_rectangle(
         return x_pixel_range, y_pixel_range, x_range, y_range
 
     def _plot_defaults(self):
+        """Return the default keyword arguments shared across all plot methods.
+
+        Returns
+        -------
+        dict
+            A dictionary of default plopp keyword arguments including title, colour-bar
+            label and limits, mask colour, and the coordinate names to use for the axes.
+        """
         return {
             'title': self.display_name,
             'clabel': 'Transmission',
@@ -853,4 +1419,12 @@ def _plot_defaults(self):
         }
 
     def __repr__(self):
+        """Return a string representation of the Measurement.
+
+        Returns
+        -------
+        str
+            A human-readable summary including the display name, data shape, and the
+            display names of all associated regions of interest.
+        """
         return f'{self.display_name} with shape {self._data_array.shape} and regions of interest: {[roi.display_name for roi in self.regions_of_interest]}'  # noqa: E501
diff --git a/src/easyimaging/measurement/regions.py b/src/easyimaging/measurement/regions.py
deleted file mode 100644
index 78323e8..0000000
--- a/src/easyimaging/measurement/regions.py
+++ /dev/null
@@ -1,285 +0,0 @@
-#  SPDX-FileCopyrightText: 2026 EasyImaging contributors  <imaging@easyscience.software>
-#  SPDX-License-Identifier: BSD-3-Clause
-#  © 2021-2026 Contributors to the EasyImaging project <https://github.com/easyScience/EasyImaging>
-from __future__ import annotations
-
-from typing import Any
-from typing import Dict
-from typing import List
-from typing import Sequence
-from typing import Tuple
-
-import scipp as sc
-from easyscience.base_classes import NewBase
-from scipp import UnitError
-
-
-class RectROI(NewBase):
-    """Class representing a rectangular region of interest (ROI) in an image.
-
-    Physical coordinate ranges are used by default if they are provided and are usable in the Measurement.
-    Otherwise, the obligatory pixel coordinate ranges are used as fallback.
-    """
-
-    def __init__(
-        self,
-        x_pixel_range: Sequence[int],
-        y_pixel_range: Sequence[int],
-        x_range: Sequence[sc.Variable] | None = None,
-        y_range: Sequence[sc.Variable] | None = None,
-        unique_name: str | None = None,
-        display_name: str | None = None,
-    ) -> None:
-        """
-        Initialize a RectROI instance.
-
-        Parameters:
-        x_pixel_range (Sequence[int]): The pixel range for the x-coordinate.
-        y_pixel_range (Sequence[int]): The pixel range for the y-coordinate.
-        x_range (Sequence[sc.Variable], optional): The physical coordinate range for the x-axis.
-        y_range (Sequence[sc.Variable], optional): The physical coordinate range for the y-axis.
-        unique_name (str | None, optional): A unique identifier for the ROI. Defaults to RectROI appended by a unique integer.
-        display_name (str | None, optional): A pretty name for the ROI. Defaults to the unique_name if not provided.
-        """
-        super().__init__(unique_name=unique_name, display_name=display_name)
-        self.set_pixel_coord_range(x_pixel_range, y_pixel_range)
-
-        if x_range is not None and y_range is not None:
-            self.set_physical_coord_range(x_range, y_range)
-        elif x_range is None and y_range is None:
-            self._has_physical_coords = False
-        else:
-            raise ValueError('Both x_range and y_range must be provided together or not at all.')
-
-    def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Sequence[int]) -> None:
-        """Set the pixel coordinate ranges for the ROI.
-        Parameters:
-            x_pixel_range (Sequence[int]): The start and end pixel coordinates in the x direction.
-            y_pixel_range (Sequence[int]): The start and end pixel coordinates in the y direction.
-        """
-        self._check_input_sequence(x_pixel_range, 'x_pixel_range', 'integers', int)
-        self._check_input_sequence(y_pixel_range, 'y_pixel_range', 'integers', int)
-        for index in tuple(x_pixel_range) + tuple(y_pixel_range):
-            if index < 0:
-                raise ValueError('Pixel indices must be non-negative integers.')  # Do I need this check?
-        self._x_pixel_start, self._x_pixel_end = sc.array(values=x_pixel_range, dims='x')
-        self._y_pixel_start, self._y_pixel_end = sc.array(values=y_pixel_range, dims='y')
-
-    def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequence[sc.Variable]) -> None:
-        """Set the physical coordinate ranges for the ROI.
-        Parameters:
-            x_range (Sequence[sc.Variable]): The start and end physical coordinates in the x direction.
-            y_range (Sequence[sc.Variable]): The start and end physical coordinates in the y direction.
-        """
-
-        self._check_input_sequence(x_range, 'x_range', 'scipp scalars', sc.Variable)
-        self._check_input_sequence(y_range, 'y_range', 'scipp scalars', sc.Variable)
-        for scalar in tuple(x_range) + tuple(y_range):
-            self._check_scalar(scalar, 'Physical coordinates')
-        self._x_start, self._x_end = x_range
-        self._y_start, self._y_end = y_range
-        self._has_physical_coords = True
-
-    def delete_physical_coord_range(self) -> None:
-        """Delete the physical coordinate ranges for the ROI."""
-        if self._has_physical_coords:
-            del self._x_start
-            del self._x_end
-            del self._y_start
-            del self._y_end
-            self._has_physical_coords = False
-        else:
-            raise ValueError('Cannot delete physical coordinate ranges because they are not set.')
-
-    def pixel_slice(self) -> Tuple[slice, slice]:
-        """Get the pixel slice corresponding to the ROI.
-
-        Returns:
-            tuple: Two (x,y) slice objects representing the pixel range of the ROI.
-        """
-        return slice(self._x_pixel_start, self._x_pixel_end), slice(self._y_pixel_start, self._y_pixel_end)
-
-    def slice(self) -> Tuple[slice, slice]:
-        """Get the slice corresponding to the ROI, using physical coordinates if available.
-
-        Returns:
-            tuple: Two (x,y) slice objects representing the range of the ROI.
-        """
-        if self._has_physical_coords:
-            return slice(self._x_start, self._x_end), slice(self._y_start, self._y_end)
-        else:
-            raise ValueError('Physical coordinate ranges are not set for this ROI.')
-
-    @property
-    def x_pixel_start(self) -> int:
-        return self._x_pixel_start.value
-
-    @x_pixel_start.setter
-    def x_pixel_start(self, value: int):
-        self._check_index(value, 'x_pixel_start')
-        self._x_pixel_start = sc.scalar(value)
-
-    @property
-    def x_pixel_end(self) -> int:
-        return self._x_pixel_end.value
-
-    @x_pixel_end.setter
-    def x_pixel_end(self, value: int):
-        self._check_index(value, 'x_pixel_end')
-        self._x_pixel_end = sc.scalar(value)
-
-    @property
-    def y_pixel_start(self) -> int:
-        return self._y_pixel_start.value
-
-    @y_pixel_start.setter
-    def y_pixel_start(self, value: int):
-        self._check_index(value, 'y_pixel_start')
-        self._y_pixel_start = sc.scalar(value)
-
-    @property
-    def y_pixel_end(self) -> int:
-        return self._y_pixel_end.value
-
-    @y_pixel_end.setter
-    def y_pixel_end(self, value: int):
-        self._check_index(value, 'y_pixel_end')
-        self._y_pixel_end = sc.scalar(value)
-
-    @property
-    def x_start(self) -> sc.Variable:
-        if self._has_physical_coords:
-            return self._x_start.copy()
-        else:
-            raise ValueError('Physical coordinate ranges are not set for this ROI.')
-
-    @x_start.setter
-    def x_start(self, value: sc.Variable):
-        self._single_coord_setter_check(value, 'x_start')
-        self._check_scalar(value, 'x_start')
-        self._x_start = value
-
-    @property
-    def x_end(self) -> sc.Variable:
-        if self._has_physical_coords:
-            return self._x_end.copy()
-        else:
-            raise ValueError('Physical coordinate ranges are not set for this ROI.')
-
-    @x_end.setter
-    def x_end(self, value: sc.Variable):
-        self._single_coord_setter_check(value, 'x_end')
-        self._check_scalar(value, 'x_end')
-        self._x_end = value
-
-    @property
-    def y_start(self) -> sc.Variable:
-        if self._has_physical_coords:
-            return self._y_start.copy()
-        else:
-            raise ValueError('Physical coordinate ranges are not set for this ROI.')
-
-    @y_start.setter
-    def y_start(self, value: sc.Variable):
-        self._single_coord_setter_check(value, 'y_start')
-        self._check_scalar(value, 'y_start')
-        self._y_start = value
-
-    @property
-    def y_end(self) -> sc.Variable:
-        if self._has_physical_coords:
-            return self._y_end.copy()
-        else:
-            raise ValueError('Physical coordinate ranges are not set for this ROI.')
-
-    @y_end.setter
-    def y_end(self, value: sc.Variable):
-        self._single_coord_setter_check(value, 'y_end')
-        self._check_scalar(value, 'y_end')
-        self._y_end = value
-
-    def _check_input_sequence(self, value: Sequence, name: str, typename: str, expected_type: any) -> None:
-        """
-        Check if the input value is a sequence of the expected type and length.
-        """
-        if not isinstance(value, Sequence) or len(value) != 2:
-            raise TypeError(f'{name} must be a tuple or a list of two {typename}, got a {type(value).__name__}.')
-        if not (isinstance(value[0], expected_type) and isinstance(value[1], expected_type)):
-            raise TypeError(
-                f'{name} must be a tuple or a list of two {typename}, '
-                f'got {type(value[0]).__name__} and {type(value[1]).__name__}.'
-            )
-
-    def _check_index(self, value: int, name: str) -> None:
-        """
-        Check if the input value is a valid index (non-negative integer).
-        """
-        if not isinstance(value, int):
-            raise TypeError(f'{name} index must be an integer.')
-        if value < 0:
-            raise ValueError(f'{name} index must be non-negative.')
-
-    def _check_scalar(self, value: sc.Variable, name: str) -> None:
-        """
-        Check if the input value is a scipp scalar with a unit of length.
-        """
-        if value.dims:
-            raise ValueError(f'{name} must be a scipp scalar (0-dimensional Variable).')
-        try:
-            test_value = value.copy()
-            test_value.to(unit='m')
-        except Exception as e:
-            raise UnitError(f"{name} must be a scipp scalar with a unit of length (e.g., 'm').") from e
-
-    def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None:
-        """
-        Check if the input value is a scipp scalar and if physical coordinates are set.
-        """
-        if not isinstance(value, sc.Variable):
-            raise TypeError(f'{name} must be a scipp scalar.')
-        if not self._has_physical_coords:
-            raise ValueError(
-                f'Cannot set {name} before setting all physical coordinate ranges. '
-                'Please use the set_physical_coord_range method.'
-            )
-
-    def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]:
-        """Convert the RectROI instance to a dictionary representation."""
-        if skip is None:
-            skip = []
-        elif isinstance(skip, str):
-            skip = [skip]
-        skip = list(skip)  # Create a copy of the skip list to avoid modifying the original
-        skip.extend(['x_pixel_range', 'y_pixel_range', 'x_range', 'y_range'])
-        out_dict = super().to_dict(skip=skip)
-        out_dict['x_pixel_range'] = [int(self.x_pixel_start), int(self.x_pixel_end)]
-        out_dict['y_pixel_range'] = [int(self.y_pixel_start), int(self.y_pixel_end)]
-        if self._has_physical_coords:
-            out_dict['x_range'] = [
-                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.x_start)},
-                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.x_end)},
-            ]
-            out_dict['y_range'] = [
-                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.y_start)},
-                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.y_end)},
-            ]
-        return out_dict
-
-    @classmethod
-    def from_dict(cls, input_dict: Dict[str, Any]) -> RectROI:
-        """Create a RectROI instance from a dictionary representation."""
-        temp_dict = input_dict.copy()
-        if 'x_range' in input_dict and 'y_range' in input_dict:
-            temp_dict['x_range'] = [sc.from_dict(item['dict']) for item in input_dict['x_range']]
-            temp_dict['y_range'] = [sc.from_dict(item['dict']) for item in input_dict['y_range']]
-        return super().from_dict(temp_dict)
-
-    def __repr__(self) -> str:
-        repr_str = (
-            f'RectROI(x_pixel_range=({self._x_pixel_start}, {self._x_pixel_end}), '
-            f'y_pixel_range=({self._y_pixel_start}, {self._y_pixel_end})'
-        )
-        if self._has_physical_coords:
-            repr_str += f', x_range=({self._x_start}, {self._x_end}), y_range=({self._y_start}, {self._y_end})'
-        repr_str += ')'
-        return repr_str
diff --git a/src/easyimaging/regions_of_interest/__init__.py b/src/easyimaging/regions_of_interest/__init__.py
new file mode 100644
index 0000000..3ca52e4
--- /dev/null
+++ b/src/easyimaging/regions_of_interest/__init__.py
@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
+from .rectangle_roi import RectangleROI
diff --git a/src/easyimaging/regions_of_interest/rectangle_roi.py b/src/easyimaging/regions_of_interest/rectangle_roi.py
new file mode 100644
index 0000000..06f81c3
--- /dev/null
+++ b/src/easyimaging/regions_of_interest/rectangle_roi.py
@@ -0,0 +1,668 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
+from __future__ import annotations
+
+from typing import Any
+from typing import Dict
+from typing import List
+from typing import Sequence
+from typing import Tuple
+
+import scipp as sc
+from easyscience.base_classes import NewBase
+from scipp import UnitError
+
+
+class RectangleROI(NewBase):
+    """Object representing a rectangular region of interest (ROI) in an image.
+
+    This object is most simply created by the [`roi_creator`][...Measurement.roi_creator] method in the
+      [Measurement][...Measurement] class. Alternatively it can be created manually as shown in the example below.
+
+    Physical coordinate ranges are used by default, if they are provided **and** can be used in the
+      associated [Measurement][...Measurement] class.
+    Otherwise, the obligatory pixel coordinate ranges are used as a fallback.
+
+    Example
+    -------
+    Creating a [RectangleROI][.] instance manually:
+    ```python
+    import scipp as sc
+    from easyimaging.regions_of_interest import RectangleROI
+
+    roi = RectangleROI(
+        x_pixel_range=(10, 50),
+        y_pixel_range=(20, 80),
+        x_range=(sc.scalar(0.0, unit='m'), sc.scalar(10.0, unit='m')),
+        y_range=(sc.scalar(0.0, unit='m'), sc.scalar(5.0, unit='m')),
+        unique_name='my_rectangle_roi',
+    )
+    ```
+    """
+
+    def __init__(
+        self,
+        x_pixel_range: Sequence[int],
+        y_pixel_range: Sequence[int],
+        x_range: Sequence[sc.Variable] | None = None,
+        y_range: Sequence[sc.Variable] | None = None,
+        unique_name: str | None = None,
+        display_name: str | None = None,
+    ) -> None:
+        """Initialize a RectangleROI instance.
+
+        Parameters
+        ----------
+        x_pixel_range : Sequence[int]
+            A two-element integer sequence ``[x_start, x_end]`` indicating the pixel range in the
+            x-direction.
+        y_pixel_range : Sequence[int]
+            A two-element integer sequence ``[y_start, y_end]`` indicating the pixel range in the
+            y-direction.
+        x_range : Sequence[sc.Variable] | None
+            A two-element sequence ``[x_start, x_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length,
+             indicating the spatial coordinate range in the x-direction.<br>
+            Must be provided together with ``y_range``.
+        y_range : Sequence[sc.Variable] | None
+            A two-element sequence ``[y_start, y_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length,
+             indicating the spatial coordinate range in the y-direction.<br>
+            Must be provided together with ``x_range``.
+        unique_name : str | None
+            A unique identifier for the ROI. Defaults to ``'RectangleROI'`` appended by a unique integer.
+        display_name : str | None
+            A prettily formatted name for the ROI. Defaults to [`unique_name`][..unique_name] if not provided.
+
+        Raises
+        ------
+        TypeError
+            If ``x_pixel_range`` or ``y_pixel_range`` is not a two-element sequence of integers.<br>
+            If physical ranges are not two-element sequences of [`sc.Variable`][scipp.Variable].
+        ValueError
+            If any pixel index in ``x_pixel_range`` or ``y_pixel_range`` is negative.<br>
+            If only one of ``x_range`` / ``y_range`` is provided.<br>
+            If any [`sc.Variable`][scipp.Variable] in ``x_range`` or ``y_range`` is not 0-dimensional (i.e., not a scalar).<br>
+        UnitError
+            If any [`sc.Variable`][scipp.Variable] scalar in ``x_range`` or ``y_range`` does not have a unit of length.
+        """
+        super().__init__(unique_name=unique_name, display_name=display_name)
+        self.set_pixel_coord_range(x_pixel_range, y_pixel_range)
+
+        if x_range is not None and y_range is not None:
+            self.set_physical_coord_range(x_range, y_range)
+        elif x_range is None and y_range is None:
+            self._has_physical_coords = False
+        else:
+            raise ValueError('Both x_range and y_range must be provided together or not at all.')
+
+    def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Sequence[int]) -> None:
+        """Set the pixel coordinate ranges defining the ROI.
+
+        Parameters
+        ----------
+        x_pixel_range : Sequence[int]
+            The pixel coordinate range in the x-direction to set.
+            Must be a two-element sequence ``[x_start, x_end]`` of pixel indices defining an x-axis range.
+        y_pixel_range : Sequence[int]
+            The pixel coordinate range in the y-direction to set.
+            Must be a two-element sequence ``[y_start, y_end]`` of pixel indices defining a y-axis range.
+
+        Raises
+        ------
+        TypeError
+            If either argument is not a two-element sequence of integers.
+        ValueError
+            If any pixel index is negative.
+        """
+        self._check_input_sequence(x_pixel_range, 'x_pixel_range', 'integers', int)
+        self._check_input_sequence(y_pixel_range, 'y_pixel_range', 'integers', int)
+        for index in tuple(x_pixel_range) + tuple(y_pixel_range):
+            if index < 0:
+                raise ValueError('Pixel indices must be non-negative integers.')
+        self._x_pixel_start, self._x_pixel_end = sc.array(values=x_pixel_range, dims='x')
+        self._y_pixel_start, self._y_pixel_end = sc.array(values=y_pixel_range, dims='y')
+
+    def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequence[sc.Variable]) -> None:
+        """Set the physical coordinate ranges defining the ROI.
+
+        Parameters
+        ----------
+        x_range : Sequence[sc.Variable]
+            The physical coordinate range in the x-direction to set.
+            Must be a two-element sequence ``[x_start, x_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length
+        y_range : Sequence[sc.Variable]
+            The physical coordinate range in the y-direction to set.
+            Must be a two-element sequence ``[y_start, y_end]`` of [`sc.Variable`][scipp.Variable] scalars with units of length
+
+        Raises
+        ------
+        TypeError
+            If either argument is not a two-element sequence of [`sc.Variable`][scipp.Variable].
+        ValueError
+            If any [`sc.Variable`][scipp.Variable] in ``x_range`` or ``y_range`` is not 0-dimensional (i.e., not a scalar).
+        UnitError
+            If any [`sc.Variable`][scipp.Variable] scalar in ``x_range`` or ``y_range`` does not have a unit of length.
+        """
+
+        self._check_input_sequence(x_range, 'x_range', 'scipp scalars', sc.Variable)
+        self._check_input_sequence(y_range, 'y_range', 'scipp scalars', sc.Variable)
+        for scalar in tuple(x_range) + tuple(y_range):
+            self._check_scalar(scalar, 'Physical coordinates')
+        self._x_start, self._x_end = x_range
+        self._y_start, self._y_end = y_range
+        self._has_physical_coords = True
+
+    def delete_physical_coord_range(self) -> None:
+        """Delete the physical coordinate ranges for the ROI.
+
+        This enforces the ROI to use pixel coordinates only.
+
+        Raises
+        ------
+        ValueError
+            If physical coordinate ranges are not currently set.
+        """
+        if self._has_physical_coords:
+            del self._x_start
+            del self._x_end
+            del self._y_start
+            del self._y_end
+            self._has_physical_coords = False
+        else:
+            raise ValueError('Cannot delete physical coordinate ranges because they are not set.')
+
+    def pixel_slice(self) -> Tuple[slice, slice]:
+        """Get a pixel index slice object corresponding to the ROI.
+
+        Returns
+        -------
+        tuple
+            Two (x,y) slice objects representing the pixel ranges of the ROI.
+        """
+        return slice(self._x_pixel_start, self._x_pixel_end), slice(self._y_pixel_start, self._y_pixel_end)
+
+    def slice(self) -> Tuple[slice, slice]:
+        """Get a physical coordinate slice object corresponding to the ROI.
+
+        Returns
+        -------
+        tuple
+            Two (x,y) slice objects representing the physical coordinate ranges of the ROI.
+
+        Raises
+        ------
+        ValueError
+            If physical coordinate ranges are not set for this ROI.
+        """
+        if self._has_physical_coords:
+            return slice(self._x_start, self._x_end), slice(self._y_start, self._y_end)
+        else:
+            raise ValueError('Physical coordinate ranges are not set for this ROI.')
+
+    @property
+    def x_pixel_start(self) -> int:
+        """Pixel index defining the start of the ROI in the x-direction.
+
+        Parameters
+        ----------
+        value : int
+            A non-negative integer pixel index.
+
+        Returns
+        -------
+        int
+            The x-axis pixel index defining the start of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not an integer.
+        ValueError
+            If ``value`` is negative.
+        """
+        return self._x_pixel_start.value
+
+    @x_pixel_start.setter
+    def x_pixel_start(self, value: int):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._check_index(value, 'x_pixel_start')
+        self._x_pixel_start = sc.scalar(value)
+
+    @property
+    def x_pixel_end(self) -> int:
+        """Pixel index defining the end of the ROI in the x-direction.
+
+        Parameters
+        ----------
+        value : int
+            A non-negative integer pixel index.
+
+        Returns
+        -------
+        int
+            The x-axis pixel index defining the end of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not an integer.
+        ValueError
+            If ``value`` is negative.
+        """
+        return self._x_pixel_end.value
+
+    @x_pixel_end.setter
+    def x_pixel_end(self, value: int):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._check_index(value, 'x_pixel_end')
+        self._x_pixel_end = sc.scalar(value)
+
+    @property
+    def y_pixel_start(self) -> int:
+        """Pixel index defining the start of the ROI in the y-direction.
+
+        Parameters
+        ----------
+        value : int
+            A non-negative integer pixel index.
+
+        Returns
+        -------
+        int
+            The y-axis pixel index defining the start of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not an integer.
+        ValueError
+            If ``value`` is negative.
+        """
+        return self._y_pixel_start.value
+
+    @y_pixel_start.setter
+    def y_pixel_start(self, value: int):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._check_index(value, 'y_pixel_start')
+        self._y_pixel_start = sc.scalar(value)
+
+    @property
+    def y_pixel_end(self) -> int:
+        """Pixel index defining the end of the ROI in the y-direction.
+
+        Parameters
+        ----------
+        value : int
+            A non-negative integer pixel index.
+
+        Returns
+        -------
+        int
+            The y-axis pixel index defining the end of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not an integer.
+        ValueError
+            If ``value`` is negative.
+        """
+        return self._y_pixel_end.value
+
+    @y_pixel_end.setter
+    def y_pixel_end(self, value: int):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._check_index(value, 'y_pixel_end')
+        self._y_pixel_end = sc.scalar(value)
+
+    @property
+    def x_start(self) -> sc.Variable:
+        """Physical coordinate defining the start of the ROI in the x-direction.
+
+        Parameters
+        ----------
+        value : sc.Variable
+            A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit
+             of length.
+
+        Returns
+        -------
+        sc.Variable
+            A copy of the x-axis physical coordinate defining the start of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not a [`sc.Variable`][scipp.Variable].
+        ValueError
+            If physical coordinate ranges are not set (use
+            [`set_physical_coord_range`][..set_physical_coord_range] to set).<br>
+            If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar).
+        UnitError
+            If ``value`` does not have a unit of length.
+        """
+        if self._has_physical_coords:
+            return self._x_start.copy()
+        else:
+            raise ValueError('Physical coordinate ranges are not set for this ROI.')
+
+    @x_start.setter
+    def x_start(self, value: sc.Variable):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._single_coord_setter_check(value, 'x_start')
+        self._check_scalar(value, 'x_start')
+        self._x_start = value
+
+    @property
+    def x_end(self) -> sc.Variable:
+        """Physical coordinate defining the end of the ROI in the x-direction.
+
+        Parameters
+        ----------
+        value : sc.Variable
+            A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit of length.
+
+        Returns
+        -------
+        sc.Variable
+            A copy of the x-axis physical coordinate defining the end of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not a [`sc.Variable`][scipp.Variable].
+        ValueError
+            If physical coordinate ranges are not set (use
+            [`set_physical_coord_range`][..set_physical_coord_range] to set).<br>
+            If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar).
+        UnitError
+            If ``value`` does not have a unit of length.
+        """
+        if self._has_physical_coords:
+            return self._x_end.copy()
+        else:
+            raise ValueError('Physical coordinate ranges are not set for this ROI.')
+
+    @x_end.setter
+    def x_end(self, value: sc.Variable):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._single_coord_setter_check(value, 'x_end')
+        self._check_scalar(value, 'x_end')
+        self._x_end = value
+
+    @property
+    def y_start(self) -> sc.Variable:
+        """Physical coordinate defining the start of the ROI in the y-direction.
+
+        Parameters
+        ----------
+        value : sc.Variable
+            A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit
+             of length.
+
+        Returns
+        -------
+        sc.Variable
+            A copy of the y-axis physical coordinate defining the start of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not a [`sc.Variable`][scipp.Variable].
+        ValueError
+            If physical coordinate ranges are not set (use
+            [`set_physical_coord_range`][..set_physical_coord_range] to set).<br>
+            If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar).
+        UnitError
+            If ``value`` does not have a unit of length.
+        """
+        if self._has_physical_coords:
+            return self._y_start.copy()
+        else:
+            raise ValueError('Physical coordinate ranges are not set for this ROI.')
+
+    @y_start.setter
+    def y_start(self, value: sc.Variable):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._single_coord_setter_check(value, 'y_start')
+        self._check_scalar(value, 'y_start')
+        self._y_start = value
+
+    @property
+    def y_end(self) -> sc.Variable:
+        """Physical coordinate defining the end of the ROI in the y-direction.
+
+        Parameters
+        ----------
+        value : sc.Variable
+            A 0-dimensional [`sc.Variable`][scipp.Variable] scalar with a unit
+             of length.
+
+        Returns
+        -------
+        sc.Variable
+            A copy of the y-axis physical coordinate defining the end of the ROI.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not a [`sc.Variable`][scipp.Variable].
+        ValueError
+            If physical coordinate ranges are not set (use
+            [`set_physical_coord_range`][..set_physical_coord_range] to set).<br>
+            If ``value`` is not a 0-dimensional [`sc.Variable`][scipp.Variable] (i.e., a scalar).
+        UnitError
+            If ``value`` does not have a unit of length.
+        """
+        if self._has_physical_coords:
+            return self._y_end.copy()
+        else:
+            raise ValueError('Physical coordinate ranges are not set for this ROI.')
+
+    @y_end.setter
+    def y_end(self, value: sc.Variable):
+        # Setters have no docstrings. They should be written in the getter docstring instead.
+        self._single_coord_setter_check(value, 'y_end')
+        self._check_scalar(value, 'y_end')
+        self._y_end = value
+
+    def _check_input_sequence(self, value: Sequence, name: str, typename: str, expected_type: any) -> None:
+        """Validate that ``value`` is a two-element sequence of the expected type.
+
+        Parameters
+        ----------
+        value : Sequence
+            The value to validate.
+        name : str
+            Name of the parameter (used in error messages).
+        typename : str
+            Human-readable name of the expected element type (used in error messages).
+        expected_type : type
+            The type each element must be an instance of.
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not a two-element sequence or its elements are not of
+            ``expected_type``.
+        """
+        if not isinstance(value, Sequence) or len(value) != 2:
+            raise TypeError(f'{name} must be a tuple or a list of two {typename}, got a {type(value).__name__}.')
+        if not (isinstance(value[0], expected_type) and isinstance(value[1], expected_type)):
+            raise TypeError(
+                f'{name} must be a tuple or a list of two {typename}, '
+                f'got {type(value[0]).__name__} and {type(value[1]).__name__}.'
+            )
+
+    def _check_index(self, value: int, name: str) -> None:
+        """Validate that ``value`` is a non-negative integer suitable as a pixel index.
+
+        Parameters
+        ----------
+        value : int
+            The value to validate.
+        name : str
+            Name of the parameter (used in error messages).
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not an integer.
+        ValueError
+            If ``value`` is negative.
+        """
+        if not isinstance(value, int):
+            raise TypeError(f'{name} index must be an integer.')
+        if value < 0:
+            raise ValueError(f'{name} index must be non-negative.')
+
+    def _check_scalar(self, value: sc.Variable, name: str) -> None:
+        """Validate that ``value`` is a 0-dimensional :class:`scipp.Variable` with a unit of length.
+
+        Parameters
+        ----------
+        value : sc.Variable
+            The value to validate.
+        name : str
+            Name of the parameter (used in error messages).
+
+        Raises
+        ------
+        ValueError
+            If ``value`` has dimensions (i.e. is not a scalar).
+        UnitError
+            If ``value`` cannot be converted to metres.
+        """
+        if value.dims:
+            raise ValueError(f'{name} must be a scipp scalar (0-dimensional Variable).')
+        try:
+            test_value = value.copy()
+            test_value.to(unit='m')
+        except Exception as e:
+            raise UnitError(f"{name} must be a scipp scalar with a unit of length (e.g., 'm').") from e
+
+    def _single_coord_setter_check(self, value: sc.Variable, name: str) -> None:
+        """Validate preconditions for setting a single physical coordinate scalar.
+
+        Checks that ``value`` is a :class:`scipp.Variable` and that physical coordinate
+        ranges have already been initialised.
+
+        Parameters
+        ----------
+        value : sc.Variable
+            The candidate value to set.
+        name : str
+            Name of the coordinate being set (used in error messages).
+
+        Raises
+        ------
+        TypeError
+            If ``value`` is not a :class:`scipp.Variable`.
+        ValueError
+            If physical coordinate ranges have not been set yet.
+        """
+        if not isinstance(value, sc.Variable):
+            raise TypeError(f'{name} must be a scipp scalar.')
+        if not self._has_physical_coords:
+            raise ValueError(
+                f'Cannot set {name} before setting all physical coordinate ranges. '
+                'Please use the set_physical_coord_range method.'
+            )
+
+    def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]:
+        """Convert the ROI instance to a dictionary representation.
+
+        Used for saving the ROI to file.
+
+        Parameters
+        ----------
+        skip : list[str] | None
+            A list of attribute names to exclude from the output dictionary.<br>
+            The ``'x_pixel_range'``, ``'y_pixel_range'``, ``'x_range'``, and
+            ``'y_range'`` keys are always handled explicitly and appended
+            regardless of this parameter.
+
+        Returns
+        -------
+        dict
+            A dictionary containing the serialised ROI data, including pixel ranges
+            and, if available, physical coordinate ranges encoded as scipp scalar dicts.
+        """
+        if skip is None:
+            skip = []
+        elif isinstance(skip, str):
+            skip = [skip]
+        skip = list(skip)  # Create a copy of the skip list to avoid modifying the original
+        skip.extend(['x_pixel_range', 'y_pixel_range', 'x_range', 'y_range'])
+        out_dict = super().to_dict(skip=skip)
+        out_dict['x_pixel_range'] = [int(self.x_pixel_start), int(self.x_pixel_end)]
+        out_dict['y_pixel_range'] = [int(self.y_pixel_start), int(self.y_pixel_end)]
+        if self._has_physical_coords:
+            out_dict['x_range'] = [
+                {
+                    '@module': 'scipp',
+                    '@version': sc.__version__,
+                    '@class': 'scalar',
+                    'dict': sc.to_dict(self.x_start),
+                },
+                {
+                    '@module': 'scipp',
+                    '@version': sc.__version__,
+                    '@class': 'scalar',
+                    'dict': sc.to_dict(self.x_end),
+                },
+            ]
+            out_dict['y_range'] = [
+                {
+                    '@module': 'scipp',
+                    '@version': sc.__version__,
+                    '@class': 'scalar',
+                    'dict': sc.to_dict(self.y_start),
+                },
+                {
+                    '@module': 'scipp',
+                    '@version': sc.__version__,
+                    '@class': 'scalar',
+                    'dict': sc.to_dict(self.y_end),
+                },
+            ]
+        return out_dict
+
+    @classmethod
+    def from_dict(cls, input_dict: Dict[str, Any]) -> RectangleROI:
+        """Create a [`RectangleROI`][..] instance from a dictionary representation.
+
+        Parameters
+        ----------
+        input_dict : dict
+            A dictionary in a format as produced by [`to_dict`][..to_dict], containing at minimum
+            ``'x_pixel_range'`` and ``'y_pixel_range'`` keys.
+
+        Returns
+        -------
+        RectangleROI
+            A new [`RectangleROI`][..] instance initialised with the data from the dictionary.
+        """
+        temp_dict = input_dict.copy()
+        if 'x_range' in input_dict and 'y_range' in input_dict:
+            temp_dict['x_range'] = [sc.from_dict(item['dict']) for item in input_dict['x_range']]
+            temp_dict['y_range'] = [sc.from_dict(item['dict']) for item in input_dict['y_range']]
+        return super().from_dict(temp_dict)
+
+    def __repr__(self) -> str:
+        """Return a string representation of the RectangleROI.
+
+        Returns
+        -------
+        str
+            A human-readable summary including pixel ranges and, when available,
+            physical coordinate ranges.
+        """
+        repr_str = (
+            f'RectangleROI(x_pixel_range=({self._x_pixel_start}, {self._x_pixel_end}), '
+            f'y_pixel_range=({self._y_pixel_start}, {self._y_pixel_end})'
+        )
+        if self._has_physical_coords:
+            repr_str += f', x_range=({self._x_start}, {self._x_end}), y_range=({self._y_start}, {self._y_end})'
+        repr_str += ')'
+        return repr_str
diff --git a/src/easyimaging/utils/__init__.py b/src/easyimaging/utils/__init__.py
index c680399..7f816d2 100644
--- a/src/easyimaging/utils/__init__.py
+++ b/src/easyimaging/utils/__init__.py
@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
 from .jupyter_notebook_utilities import _is_notebook
 from .scipp_utilities import _to_edges
 
diff --git a/src/easyimaging/utils/jupyter_notebook_utilities.py b/src/easyimaging/utils/jupyter_notebook_utilities.py
index 9c19dc0..883c945 100644
--- a/src/easyimaging/utils/jupyter_notebook_utilities.py
+++ b/src/easyimaging/utils/jupyter_notebook_utilities.py
@@ -1,7 +1,9 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
+
 def _is_notebook() -> bool:
-    """
-    Check if the code is running in a Jupyter notebook environment.
-    """
+    """Check if the code is running in a Jupyter notebook environment."""
     try:
         shell = get_ipython().__class__.__name__  # pyright: ignore[reportUndefinedVariable]
         if shell == 'ZMQInteractiveShell':
diff --git a/src/easyimaging/utils/scipp_utilities.py b/src/easyimaging/utils/scipp_utilities.py
index 3626a1b..a00ccd1 100644
--- a/src/easyimaging/utils/scipp_utilities.py
+++ b/src/easyimaging/utils/scipp_utilities.py
@@ -1,10 +1,11 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
 import scipp as sc
 
 
 def _to_edges(centers: sc.Variable) -> sc.Variable:
-    """
-    Convenience method to convert center coordinates to edge coordinates.
-    """
+    """Convenience method to convert center coordinates to edge coordinates."""
     interior_edges = sc.midpoints(centers)
     return sc.concat(
         [
diff --git a/tests/integration/integration/fitting/test_dummy.py b/tests/integration/integration/fitting/test_dummy.py
new file mode 100644
index 0000000..c61e754
--- /dev/null
+++ b/tests/integration/integration/fitting/test_dummy.py
@@ -0,0 +1,17 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
+import pytest
+
+
+@pytest.mark.fast
+def test_dummy_fast():
+    calculated = 2 + 2
+    expected = 4
+    assert calculated == expected
+
+
+# def test_dummy_slow():
+#     calculated = sum(i * j for i in range(10000) for j in range(10000))
+#     expected = 2499500025000000
+#     assert calculated == expected
diff --git a/tests/integration/integration/scipp-analysis/test_dummy.py b/tests/integration/integration/scipp-analysis/test_dummy.py
new file mode 100644
index 0000000..c61e754
--- /dev/null
+++ b/tests/integration/integration/scipp-analysis/test_dummy.py
@@ -0,0 +1,17 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
+import pytest
+
+
+@pytest.mark.fast
+def test_dummy_fast():
+    calculated = 2 + 2
+    expected = 4
+    assert calculated == expected
+
+
+# def test_dummy_slow():
+#     calculated = sum(i * j for i in range(10000) for j in range(10000))
+#     expected = 2499500025000000
+#     assert calculated == expected
diff --git a/tests/package_test.py b/tests/package_test.py
index 4197cf3..8594634 100644
--- a/tests/package_test.py
+++ b/tests/package_test.py
@@ -1,5 +1,6 @@
+# SPDX-FileCopyrightText: 2024 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
-# Copyright (c) 2024 Easyscience contributors (https://github.com/EasyScience)
+
 import easyimaging as pkg
 
 
diff --git a/tests/small_scitiff.tiff b/tests/small_scitiff.tiff
deleted file mode 100644
index 5ec25b7..0000000
Binary files a/tests/small_scitiff.tiff and /dev/null differ
diff --git a/tests/small_tiff.tiff b/tests/small_tiff.tiff
deleted file mode 100644
index b99b895..0000000
Binary files a/tests/small_tiff.tiff and /dev/null differ
diff --git a/tests/unit_tests/measurement/test_measurement.py b/tests/unit/measurement/test_measurement.py
similarity index 82%
rename from tests/unit_tests/measurement/test_measurement.py
rename to tests/unit/measurement/test_measurement.py
index e031bae..86dd608 100644
--- a/tests/unit_tests/measurement/test_measurement.py
+++ b/tests/unit/measurement/test_measurement.py
@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
 import warnings
 from copy import copy
 from pathlib import Path
@@ -13,7 +16,9 @@
 from scipp import DimensionError
 
 from easyimaging import Measurement
-from easyimaging.measurement.regions import RectROI
+from easyimaging.datasets import small_test_scitiff
+from easyimaging.datasets import small_test_tiff
+from easyimaging.regions_of_interest import RectangleROI
 
 
 class TestMeasurement:
@@ -79,18 +84,22 @@ def valid_roi(self):
         y_pixel_range = (2, 5)
         x_range = (sc.scalar(1.0, unit='m'), sc.scalar(4.0, unit='m'))
         y_range = (sc.scalar(2.0, unit='m'), sc.scalar(5.0, unit='m'))
-        return RectROI(
+        return RectangleROI(
             x_pixel_range=x_pixel_range,
             y_pixel_range=y_pixel_range,
             x_range=x_range,
             y_range=y_range,
-            unique_name='test_roi',
+            # unique_name='test_roi',
             display_name='Test ROI',
         )
 
     def test_init_valid_data_array(self, valid_data_array):
         # When Then
-        measurement = Measurement(data_array=valid_data_array, unique_name='test_measurement', display_name='Test Measurement')
+        measurement = Measurement(
+            data_array=valid_data_array,
+            unique_name='test_measurement',
+            display_name='Test Measurement',
+        )
         # Expect
         assert measurement._data_array is not valid_data_array  # Ensure a copy was made
         assert not sc.any(measurement._data_array.masks['non_finite']).value
@@ -150,15 +159,31 @@ def test_init_invalid_data_array_type(self):
     @pytest.mark.parametrize(
         'new_tof_coordinate, error, expected_message',
         [
-            (None, ValueError, "data array must have a 'tof' coordinate for time-of-flight information."),
-            (sc.scalar(5.0, unit='s'), DimensionError, "'tof' coordinate must be of dimension 't'."),
-            (sc.arange('x', 0, 6, 1, unit='s'), DimensionError, "'tof' coordinate must be of dimension 't'."),
+            (
+                None,
+                ValueError,
+                "data array must have a 'tof' coordinate for time-of-flight information.",
+            ),
+            (
+                sc.scalar(5.0, unit='s'),
+                DimensionError,
+                "'tof' coordinate must be of dimension 't'.",
+            ),
+            (
+                sc.arange('x', 0, 6, 1, unit='s'),
+                DimensionError,
+                "'tof' coordinate must be of dimension 't'.",
+            ),
             (
                 sc.arange('t', 0, 10, 1, unit='m'),
                 sc.UnitError,
                 "'tof' coordinate must have a unit of time, such as \\('s'\\).",
             ),  # noqa: E501 # fmt: skip
-            (sc.arange('t', -5, 5, 1, unit='s'), ValueError, 'time_of_flight values must be non-negative.'),
+            (
+                sc.arange('t', -5, 5, 1, unit='s'),
+                ValueError,
+                'time_of_flight values must be non-negative.',
+            ),
         ],
         ids=[
             'missing_tof',
@@ -182,8 +207,16 @@ def test_init_invalid_tof_coordinates(self, valid_data_array, new_tof_coordinate
         'new_x_coordinate, error, expected_message',
         [
             (sc.scalar(5.0, unit='m'), DimensionError, "'x' coordinate must be of dimension 'x'"),
-            (sc.arange('t', 0, 10, 1, unit='m'), DimensionError, "'x' coordinate must be of dimension 'x'."),
-            (sc.arange('x', 0, 6, 1, unit='s'), sc.UnitError, "'x' coordinate must have a unit of length, such as \\('m'\\)."),  # noqa: E501
+            (
+                sc.arange('t', 0, 10, 1, unit='m'),
+                DimensionError,
+                "'x' coordinate must be of dimension 'x'.",
+            ),
+            (
+                sc.arange('x', 0, 6, 1, unit='s'),
+                sc.UnitError,
+                "'x' coordinate must have a unit of length, such as \\('m'\\).",
+            ),  # noqa: E501
         ],
         ids=[
             'scalar_x',
@@ -203,8 +236,16 @@ def test_init_invalid_x_coordinates(self, valid_data_array, new_x_coordinate, er
         'new_y_coordinate, error, expected_message',
         [
             (sc.scalar(5.0, unit='m'), DimensionError, "'y' coordinate must be of dimension 'y'."),
-            (sc.arange('t', 0, 10, 1, unit='m'), DimensionError, "'y' coordinate must be of dimension 'y'."),
-            (sc.arange('y', 0, 6, 1, unit='s'), sc.UnitError, "'y' coordinate must have a unit of length, such as \\('m'\\)."),  # noqa: E501
+            (
+                sc.arange('t', 0, 10, 1, unit='m'),
+                DimensionError,
+                "'y' coordinate must be of dimension 'y'.",
+            ),
+            (
+                sc.arange('y', 0, 6, 1, unit='s'),
+                sc.UnitError,
+                "'y' coordinate must have a unit of length, such as \\('m'\\).",
+            ),  # noqa: E501
         ],
         ids=[
             'scalar_y',
@@ -232,7 +273,10 @@ def test_init_missing_single_wrong_dimension(self, valid_data_array, dimension):
 
     def test_init_missing_both_wrong_dimensions(self, valid_data_array_no_xy_coords):
         # When
-        invalid_data_array = valid_data_array_no_xy_coords.rename_dims({'x': 'wrong_x', 'y': 'wrong_y'})
+        invalid_data_array = valid_data_array_no_xy_coords.rename_dims({
+            'x': 'wrong_x',
+            'y': 'wrong_y',
+        })
         # Then Expect
         with pytest.raises(DimensionError, match="data array must have both 'x' and 'y' dimensions."):
             Measurement(data_array=invalid_data_array)
@@ -247,7 +291,9 @@ def test_init_missing_single_physical_coordinate(self, valid_data_array, coordin
             Measurement(data_array=invalid_data_array)
 
     @pytest.mark.parametrize(
-        'path', ['tests/small_scitiff.tiff', Path('tests/small_scitiff.tiff')], ids=['str_path', 'Path_object']
+        'path',
+        [small_test_scitiff(), Path(small_test_scitiff())],
+        ids=['str_path', 'Path_object'],
     )
     def test_from_scitiff_valid(self, path):
         # When Then
@@ -277,14 +323,19 @@ def test_from_scitiff_non_existent_file(self):
 
     def test_from_scitiff_not_a_scitiff(self):
         # When
-        path = 'tests/small_tiff.tiff'  # This is a regular TIFF, not a SciTIFF
+        path = small_test_tiff()  # This is a regular TIFF, not a SciTIFF
+        path = path.replace('\\', '/')  # Ensure consistent path format across platforms
         # Then Expect
         with pytest.raises(RuntimeError, match=f"Tiff file '{path}' not a proper SciTIFF file:"):
             Measurement.from_scitiff(
                 filename=path,
             )
 
-    @pytest.mark.parametrize('path', ['tests/small_tiff.tiff', Path('tests/small_tiff.tiff')], ids=['str_path', 'Path_object'])
+    @pytest.mark.parametrize(
+        'path',
+        [small_test_tiff(), Path(small_test_tiff())],
+        ids=['str_path', 'Path_object'],
+    )
     def test_from_tiff_stack_valid_paths(self, path):
         # When Then
         measurement = Measurement.from_tiff_stack(
@@ -300,6 +351,14 @@ def test_from_tiff_stack_valid_paths(self, path):
         assert 'x' not in measurement._data_array.coords
         assert 'y' not in measurement._data_array.coords
 
+    @pytest.mark.filterwarnings('error')
+    def test_from_tiff_stack_no_ImageJ_warning(self):
+        # When Then Expect
+        Measurement.from_tiff_stack(
+            filename=small_test_tiff(),
+            time_of_flights=sc.arange('t', 0, 240, 1, unit='s'),
+        )
+
     @pytest.mark.parametrize(
         'coord, expected',
         [
@@ -311,7 +370,7 @@ def test_from_tiff_stack_valid_paths(self, path):
     def test_from_tiff_stack_valid_time_of_flights(self, coord, expected):
         # When Then
         measurement = Measurement.from_tiff_stack(
-            filename='tests/small_tiff.tiff',
+            filename=small_test_tiff(),
             time_of_flights=coord,
         )
         # Expect
@@ -331,7 +390,7 @@ def test_from_tiff_stack_valid_time_of_flights(self, coord, expected):
     def test_from_tiff_stack_valid_x_positions(self, coord, expected):
         # When Then
         measurement = Measurement.from_tiff_stack(
-            filename='tests/small_tiff.tiff',
+            filename=small_test_tiff(),
             time_of_flights=sc.arange('t', 0, 240, 1, unit='s'),
             x_positions=coord,
             y_positions=sc.arange('y', 0, 1020, 20, unit='cm'),
@@ -354,7 +413,7 @@ def test_from_tiff_stack_valid_x_positions(self, coord, expected):
     def test_from_tiff_stack_valid_y_positions(self, coord, expected):
         # When Then
         measurement = Measurement.from_tiff_stack(
-            filename='tests/small_tiff.tiff',
+            filename=small_test_tiff(),
             time_of_flights=sc.arange('t', 0, 240, 1, unit='s'),
             y_positions=coord,
             x_positions=sc.arange('x', 0, 510, 10, unit='cm'),
@@ -379,14 +438,26 @@ def test_from_tiff_stack_invalid_path(self, path, error):
     @pytest.mark.parametrize(
         'coord, error, expected_message',
         [
-            ('not_a_valid_type', TypeError, 'time_of_flight must be a scipp Variable or a numpy ndarray.'),
+            (
+                'not_a_valid_type',
+                TypeError,
+                'time_of_flight must be a scipp Variable or a numpy ndarray.',
+            ),
             (
                 sc.arange('t', 0, 5, 1, unit='s'),
                 ValueError,
                 'Length of time_of_flight array does not match the number of frames in the TIFF stack.',
             ),  # noqa: E501
-            (sc.scalar(5.0, unit='s'), TypeError, 'time_of_flight must be a scipp Variable or a numpy ndarray.'),
-            (sc.arange('t', 0, 240, 1, unit='m'), sc.UnitError, "time_of_flight must have a unit of time, such as 's'"),
+            (
+                sc.scalar(5.0, unit='s'),
+                TypeError,
+                'time_of_flight must be a scipp Variable or a numpy ndarray.',
+            ),
+            (
+                sc.arange('t', 0, 240, 1, unit='m'),
+                sc.UnitError,
+                "time_of_flight must have a unit of time, such as 's'",
+            ),
         ],
         ids=[
             'invalid_type',
@@ -399,20 +470,28 @@ def test_from_tiff_stack_invalid_time_of_flights(self, coord, error, expected_me
         # When Then Expect
         with pytest.raises(error, match=expected_message):
             Measurement.from_tiff_stack(
-                filename='tests/small_tiff.tiff',
+                filename=small_test_tiff(),
                 time_of_flights=coord,
             )
 
     @pytest.mark.parametrize(
         'coord, error, expected_message',
         [
-            ('not_a_valid_type', TypeError, 'x_positions must be a scipp Variable or a numpy ndarray.'),
+            (
+                'not_a_valid_type',
+                TypeError,
+                'x_positions must be a scipp Variable or a numpy ndarray.',
+            ),
             (
                 sc.arange('x', 0, 10, 1, unit='m'),
                 ValueError,
                 'Length of x_positions array does not match the number of pixels in the x dimension.',
             ),  # noqa: E501
-            (sc.arange('x', 0, 50, 1, unit='s'), sc.UnitError, "x_positions must have a unit of length, such as 'm'"),
+            (
+                sc.arange('x', 0, 50, 1, unit='s'),
+                sc.UnitError,
+                "x_positions must have a unit of length, such as 'm'",
+            ),
         ],
         ids=[
             'invalid_type_x',
@@ -424,7 +503,7 @@ def test_from_tiff_stack_invalid_x_positions(self, coord, error, expected_messag
         # When Then Expect
         with pytest.raises(error, match=expected_message):
             Measurement.from_tiff_stack(
-                filename='tests/small_tiff.tiff',
+                filename=small_test_tiff(),
                 time_of_flights=sc.arange('t', 0, 240, 1, unit='s'),
                 x_positions=coord,
             )
@@ -432,13 +511,21 @@ def test_from_tiff_stack_invalid_x_positions(self, coord, error, expected_messag
     @pytest.mark.parametrize(
         'coord, error, expected_message',
         [
-            ('not_a_valid_type', TypeError, 'y_positions must be a scipp Variable or a numpy ndarray.'),
+            (
+                'not_a_valid_type',
+                TypeError,
+                'y_positions must be a scipp Variable or a numpy ndarray.',
+            ),
             (
                 sc.arange('y', 0, 10, 1, unit='m'),
                 ValueError,
                 'Length of y_positions array does not match the number of pixels in the y dimension.',
             ),  # noqa: E501
-            (sc.arange('y', 0, 50, 1, unit='s'), sc.UnitError, "y_positions must have a unit of length, such as 'm'"),
+            (
+                sc.arange('y', 0, 50, 1, unit='s'),
+                sc.UnitError,
+                "y_positions must have a unit of length, such as 'm'",
+            ),
         ],
         ids=[
             'invalid_type_y',
@@ -450,7 +537,7 @@ def test_from_tiff_stack_invalid_y_positions(self, coord, error, expected_messag
         # When Then Expect
         with pytest.raises(error, match=expected_message):
             Measurement.from_tiff_stack(
-                filename='tests/small_tiff.tiff',
+                filename=small_test_tiff(),
                 time_of_flights=sc.arange('t', 0, 240, 1, unit='s'),
                 y_positions=coord,
             )
@@ -463,7 +550,7 @@ def test_save_scitiff_downcast(self, valid_data_array, tmp_path):
             UserWarning,
             match='The data array is of type float64, which is not directly supported by the SciTIFF format. '
             'It will be downcast to float32 when saving, which may result in loss of precision.',
-        ):  # noqa: E501
+        ):
             measurement.save_scitiff(tmp_path / 'test.tiff')
         assert 'non_finite' in measurement._data_array.masks
 
@@ -534,7 +621,7 @@ def test_data_array_copy_write(self, valid_data_array):
         # Then Expect
         with pytest.raises(
             AttributeError,
-            match='Cannot set data_array, it is a read-only property. Please make a new Measurement instance if you want to use a different data array.',  # noqa: E501
+            match="property 'data_array_copy' of 'Measurement' object has no setter",
         ):
             measurement.data_array_copy = copy(measurement._data_array)
 
@@ -553,7 +640,8 @@ def test_positions_no_coord(self, valid_data_array_no_xy_coords, coordinate):
         # When
         measurement = Measurement(data_array=valid_data_array_no_xy_coords)
         # Then Expect
-        assert getattr(measurement, coordinate) is None
+        with pytest.raises(ValueError, match='Physical coordinate positions are not set for this Measurement.'):
+            getattr(measurement, coordinate)
 
     @pytest.mark.parametrize('coordinate', ['x_positions', 'y_positions'], ids=['x_coordinate', 'y_coordinate'])
     def test_positions_setter_valid(self, valid_data_array, coordinate):
@@ -588,7 +676,10 @@ def test_positions_setter_invalid(self, valid_data_array_no_xy_coords, coordinat
         # When
         measurement = Measurement(data_array=valid_data_array_no_xy_coords)
         # Then Expect
-        with pytest.raises(ValueError, match=f'Cannot set {coordinate} before setting all physical coordinate positions.'):
+        with pytest.raises(
+            ValueError,
+            match=f'Cannot set {coordinate} before setting all physical coordinate positions.',
+        ):
             setattr(measurement, coordinate, sc.arange('x', 0, 10, 1, unit='m'))
 
     # Just a single test, other test-cases are covered by from_tiff_stack tests as both use _validate_provided_coord()
@@ -644,7 +735,10 @@ def test_delete_physical_coord_positions_no_coords(self, valid_data_array_no_xy_
         # When
         measurement = Measurement(data_array=valid_data_array_no_xy_coords)
         # Then Expect
-        with pytest.raises(ValueError, match='Cannot delete physical coordinate positions because they are not set.'):
+        with pytest.raises(
+            ValueError,
+            match='Cannot delete physical coordinate positions because they are not set.',
+        ):
             measurement.delete_physical_coord_positions()
 
     def test_time_of_flights(self, valid_data_array):
@@ -753,7 +847,7 @@ def test_regions_of_interest_setter(self, valid_data_array, valid_roi):
         # Then Expect
         with pytest.raises(
             AttributeError,
-            match='Cannot set regions_of_interest, it is a read-only property. Please simply add or remove ROIs directly from the list.',  # noqa: E501
+            match="property 'regions_of_interest' of 'Measurement' object has no setter",
         ):  # noqa: E501
             measurement.regions_of_interest = EasyList([valid_roi])
 
@@ -872,14 +966,17 @@ def test_rebin_invalid_dimension_type(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(TypeError, match='dimensions must be a dictionary mapping dimension names to rebin factors.'):
+        with pytest.raises(
+            TypeError,
+            match='dimensions must be a dictionary mapping dimension names to rebin factors.',
+        ):
             measurement.rebin(dimensions=['x'])
 
     def test_rebin_time_dimension(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(ValueError, match='Rebinning of the time-of-flight'):
+        with pytest.raises(KeyError, match='Rebinning of the time-of-flight'):
             measurement.rebin(dimensions={'t': 2, 'x': 2})
 
     def test_rebin_invalid_dimensions_key_type(self, valid_data_array):
@@ -900,28 +997,39 @@ def test_rebin_invalid_dimensions_value_type(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(ValueError, match="Rebin size for dimension 'x' must be a positive integer of at least 1."):
+        with pytest.raises(
+            TypeError,
+            match="Rebin size for dimension 'x' must be a positive integer of at least 1.",
+        ):
             measurement.rebin(dimensions={'x': 'not_an_integer'})
 
     def test_rebin_invalid_dimensions_value_zero(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(ValueError, match="Rebin size for dimension 'x' must be a positive integer of at least 1."):
+        with pytest.raises(
+            TypeError,
+            match="Rebin size for dimension 'x' must be a positive integer of at least 1.",
+        ):
             measurement.rebin(dimensions={'x': 0})
 
     def test_rebin_invalid_dimensions_value_negative(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(ValueError, match="Rebin size for dimension 'x' must be a positive integer of at least 1."):
+        with pytest.raises(
+            TypeError,
+            match="Rebin size for dimension 'x' must be a positive integer of at least 1.",
+        ):
             measurement.rebin(dimensions={'x': -2})
 
     def test_rebin_invalid_dimensions_value_non_divisable(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(ValueError, match="Dimension 'x' with size 6 is not evenly divisible by rebin size 4."):
+        with pytest.raises(
+            ValueError, match="Dimension 'x' with size 6 is not evenly divisible by the requested rebin factor 4."
+        ):
             measurement.rebin(dimensions={'x': 4})
 
     def test_revert_rebin(self, valid_data_array):
@@ -941,13 +1049,20 @@ def test_revert_rebin_no_rebin(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.warns(UserWarning, match='No rebinning to revert. The data array is already in its original state.'):
+        with pytest.warns(
+            UserWarning,
+            match='No rebinning to revert. The data array is already in its original state.',
+        ):
             measurement.revert_rebin()
 
     # Without making image comparisons, this is the best we can do to test the plot function
     @pytest.mark.parametrize(
         'time_of_flight, title',
-        [(None, '(averaged over TOF)'), (0, 'at TOF index 0'), (sc.scalar(5.0, unit='s'), 'at TOF=5.0 s')],
+        [
+            (None, '(averaged over TOF)'),
+            (0, 'at TOF index 0'),
+            (sc.scalar(5.0, unit='s'), 'at TOF=5.0 s'),
+        ],
         ids=['sum', 'indice', 'scipp_scalar'],
     )
     def test_plot_coordinates(self, valid_data_array, time_of_flight, title, plot_setup):
@@ -967,6 +1082,16 @@ def test_plot_coordinates(self, valid_data_array, time_of_flight, title, plot_se
         assert fig.view.colormapper.vmax == 1.1
         assert fig.view.colormapper.vmin == 0.0
 
+    def test_plot_automatic_cmax_at_index(self, valid_data_array, plot_setup):
+        # When
+        valid_data_array['t', 0].data *= 0.5  # Scale data at first TOF index to ensure max is below 1.0
+        measurement = Measurement(data_array=valid_data_array)
+        # Then
+        fig = measurement.plot(time_of_flight=0)
+        # Expect
+        assert fig.view.colormapper.vmax == 0.55
+        assert fig.view.colormapper.vmin == 0.0
+
     def test_plot_automatic_cmax(self, valid_data_array, plot_setup):
         # When
         valid_data_array.data *= 10.0  # Scale data to ensure max is above 1.0
@@ -1083,7 +1208,10 @@ def test_spectrum_inspector_fails_outside_notebook(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(RuntimeError, match='Interactive spectrum inspector is only supported in Jupyter notebooks.'):
+        with pytest.raises(
+            RuntimeError,
+            match='Interactive spectrum inspector is only supported in Jupyter notebooks.',
+        ):
             measurement.spectrum_inspector()
 
     def test_spectrum_inspector(self, valid_data_array, plot_setup):
@@ -1107,6 +1235,8 @@ def test_spectrum_inspector(self, valid_data_array, plot_setup):
         assert figs[0].view.colormapper.vmax == 1.1
         assert figs[0].view.colormapper.vmin == 0.0
         assert figs[1].canvas.ymax == 1.1
+        assert figs[1].canvas.dims['x'] == 'Time of flight'
+        assert figs[1].canvas.units['x'] == 's'
 
     def test_spectrum_inspector_user_overwrite(self, valid_data_array, plot_setup):
         # When
@@ -1185,9 +1315,12 @@ def test_roi_creator_create_roi_physical_coordinates(self, valid_data_array, plo
         figs[0].toolbar['inspect']._tool.stop()
         # Expect
         assert figs[1].canvas.ymax == 1.1
+        # The next 2 can only be tested when something is drawn on the plot.
+        assert figs[1].canvas.dims['x'] == 'Time of flight'
+        assert figs[1].canvas.units['x'] == 's'
         assert len(measurement.regions_of_interest) == 1
         roi = measurement.regions_of_interest[0]
-        assert isinstance(roi, RectROI)
+        assert isinstance(roi, RectangleROI)
         assert roi.x_pixel_start == 2
         assert roi.x_pixel_end == 5
         assert roi.y_pixel_start == 2
@@ -1198,6 +1331,58 @@ def test_roi_creator_create_roi_physical_coordinates(self, valid_data_array, plo
         assert roi.y_end == sc.scalar(5, unit='m')
         assert roi._has_physical_coords
 
+    def test_roi_creator_with_existing_roi_both_physical_coords(self, valid_data_array, valid_roi, plot_setup):
+        # When
+        measurement = Measurement(data_array=valid_data_array)
+        measurement.regions_of_interest.append(valid_roi)
+        # Then
+        figs = measurement.roi_creator()
+        # Expect
+        assert figs[1].canvas.ymax == 1.1
+        # The next 2 can only be tested when something is drawn on the plot,
+        # hence this tests that the existing ROI is properly loaded into the plot.
+        assert figs[1].canvas.dims['x'] == 'Time of flight'
+        assert figs[1].canvas.units['x'] == 's'
+
+    def test_roi_creator_with_existing_roi_pixel_coordinates(self, valid_data_array, plot_setup):
+        # When
+        x_pixel_range = (1, 4)
+        y_pixel_range = (2, 5)
+        roi = RectangleROI(
+            x_pixel_range=x_pixel_range,
+            y_pixel_range=y_pixel_range,
+        )
+        measurement = Measurement(data_array=valid_data_array)
+        measurement.regions_of_interest.append(roi)
+        # Then
+        figs = measurement.roi_creator()
+        # Expect
+        assert figs[1].canvas.ymax == 1.1
+        # The next 2 can only be tested when something is drawn on the plot,
+        # hence this tests that the existing ROI is properly loaded into the plot.
+        assert figs[1].canvas.dims['x'] == 'Time of flight'
+        assert figs[1].canvas.units['x'] == 's'
+
+    def test_roi_creator_existing_roi_both_pixel_coords(self, valid_data_array, valid_data_array_no_xy_coords, plot_setup):
+        # When
+        x_pixel_range = (1, 4)
+        y_pixel_range = (2, 5)
+        roi = RectangleROI(
+            x_pixel_range=x_pixel_range,
+            y_pixel_range=y_pixel_range,
+        )
+        valid_data_array_no_xy_coords.data += 0.5
+        measurement = Measurement(data_array=valid_data_array_no_xy_coords)
+        measurement.regions_of_interest.append(roi)
+        # Then
+        figs = measurement.roi_creator()
+        # Expect
+        assert figs[1].canvas.ymax == 0.55
+        # The next 2 can only be tested when something is drawn on the plot,
+        # hence this tests that the existing ROI is properly loaded into the plot.
+        assert figs[1].canvas.dims['x'] == 'Time of flight'
+        assert figs[1].canvas.units['x'] == 's'
+
     def test_roi_creator_create_roi_pixel_coordinates(self, valid_data_array, plot_setup):
         # When
         valid_data_array.coords.pop('x')
@@ -1214,7 +1399,7 @@ def test_roi_creator_create_roi_pixel_coordinates(self, valid_data_array, plot_s
         assert figs[1].canvas.ymax == 1.1
         assert len(measurement.regions_of_interest) == 1
         roi = measurement.regions_of_interest[0]
-        assert isinstance(roi, RectROI)
+        assert isinstance(roi, RectangleROI)
         assert roi.x_pixel_start == 2
         assert roi.x_pixel_end == 5
         assert roi.y_pixel_start == 2
@@ -1229,7 +1414,7 @@ def test_roi_creator_create_roi_pixel_coordinates(self, valid_data_array, plot_s
     # def test_roi_creator_delete_roi_both_physical_coords(self, valid_data_array, plot_setup):
     #     # When
     #     measurement = Measurement(data_array=valid_data_array)
-    #     roi = RectROI(
+    #     roi = RectangleROI(
     #         x_pixel_range=(2, 5),
     #         y_pixel_range=(2, 5),
     #         x_range=(sc.scalar(2.5, unit='m'), sc.scalar(5, unit='m')),
@@ -1261,7 +1446,7 @@ def test_spectrum_valid_with_pixel_roi(self, valid_data_array):
         # When
         valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10])
         measurement = Measurement(data_array=valid_data_array)
-        roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4))
+        roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4))
         # Then
         spectrum = measurement.spectrum(roi=roi)
         # Expect
@@ -1274,12 +1459,13 @@ def test_spectrum_valid_with_physical_roi(self, valid_data_array):
         # When
         valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10])
         measurement = Measurement(data_array=valid_data_array)
-        # Make the physical coordinates different from the pixel coordinates to ensure they are used correctly in the spectrum calculation  # noqa: E501
+        # Make the physical coordinates different from the pixel coordinates
+        # to ensure they are used correctly in the spectrum calculation
         measurement.set_physical_coord_positions(
             x_positions=sc.arange('x', 0, 21, 3, unit='m'),
             y_positions=sc.arange('y', 0, 14, 2, unit='m'),
         )
-        roi = RectROI(
+        roi = RectangleROI(
             x_pixel_range=(1, 6),
             y_pixel_range=(1, 6),
             x_range=(sc.scalar(6, unit='m'), sc.scalar(18, unit='m')),
@@ -1299,10 +1485,10 @@ def test_spectrum_valid_roi_by_name(self, valid_data_array):
         # When
         valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10])
         measurement = Measurement(data_array=valid_data_array)
-        roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi')
+        roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_3')
         # Then
         measurement.regions_of_interest.append(roi)
-        spectrum = measurement.spectrum(roi='test_roi')
+        spectrum = measurement.spectrum(roi='test_roi_3')
         # Expect
         assert isinstance(spectrum, sc.DataArray)
         assert sc.identical(spectrum.coords['tof'], measurement._data_array.coords['tof'])
@@ -1310,10 +1496,11 @@ def test_spectrum_valid_roi_by_name(self, valid_data_array):
         assert sc.identical(spectrum.data, sc.ones(dims=['t'], shape=[10]) * 0.625)
 
     def test_spectrum_identical_after_rebin(self, valid_data_array):
-        # If the roi is defined such that it includes whole rebinned pixels, then the spectrum should be identical before and after rebinning  # noqa: E501
+        # If the roi is defined such that it includes whole rebinned pixels,
+        # then the spectrum should be identical before and after rebinning
         valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10])
         measurement = Measurement(data_array=valid_data_array)
-        roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4))
+        roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4))
         spectrum_before_rebin = measurement.spectrum(roi=roi)
         # Then
         measurement.rebin(dimensions={'x': 2, 'y': 2})
@@ -1322,10 +1509,11 @@ def test_spectrum_identical_after_rebin(self, valid_data_array):
         assert sc.identical(spectrum_before_rebin, spectrum_after_rebin)
 
     def test_spectrum_not_identical_after_rebin(self, valid_data_array):
-        # If the roi is defined such that it includes partial rebinned pixels, then the spectrum should not be identical before and after rebinning  # noqa: E501
+        # If the roi is defined such that it includes partial rebinned pixels,
+        # then the spectrum should not be identical before and after rebinning
         valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10])
         measurement = Measurement(data_array=valid_data_array)
-        roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 5))
+        roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 5))
         spectrum_before_rebin = measurement.spectrum(roi=roi)
         # Then
         measurement.rebin(dimensions={'x': 2, 'y': 2})
@@ -1347,7 +1535,7 @@ def test_spectrum_roi_with_masked_data(self, valid_data_array, value):
         valid_data_array['x', 2:5]['y', 3:6]['t', 0:10] = sc.zeros(dims=['x', 'y', 't'], shape=[3, 3, 10])
         valid_data_array['x', 3]['y', 3] = sc.full(value=value, dims=['t'], shape=[10])
         measurement = Measurement(data_array=valid_data_array)
-        roi = RectROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4))
+        roi = RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4))
         # Then
         spectrum = measurement.spectrum(roi=roi)
         # Expect
@@ -1361,7 +1549,7 @@ def test_spectrum_invalid_roi_type(self, valid_data_array):
         # When
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
-        with pytest.raises(TypeError, match='roi must be a string, None, or an instance of RectROI.'):
+        with pytest.raises(TypeError, match='roi must be a string, None, or an instance of RectangleROI.'):
             measurement.spectrum(roi=3.4)
 
     def test_spectrum_invalid_roi_name(self, valid_data_array):
@@ -1369,6 +1557,65 @@ def test_spectrum_invalid_roi_name(self, valid_data_array):
         measurement = Measurement(data_array=valid_data_array)
         # Then Expect
         with pytest.raises(
-            KeyError, match="ROI with unique name 'non_existent_roi' not found in the measurement's list of ROIs."
+            KeyError,
+            match="ROI with unique name 'non_existent_roi' not found in the measurement's list of ROIs.",
         ):  # noqa: E501
             measurement.spectrum(roi='non_existent_roi')
+
+    @pytest.mark.parametrize(
+        'roi, expected',
+        [
+            (None, 'entire image'),
+            (RectangleROI(x_pixel_range=(2, 6), y_pixel_range=(2, 4), unique_name='test_roi_2'), "ROI 'test_roi_2'"),
+        ],
+        ids=['no_roi', 'rect_roi'],
+    )
+    def test_spectrum_plot(self, valid_data_array, plot_setup, roi, expected, valid_roi):
+        # When
+        measurement = Measurement(data_array=valid_data_array)
+        measurement.regions_of_interest.append(valid_roi)
+        # Then
+        fig = measurement.spectrum_plot(roi=roi)
+        # Expect
+        assert fig.canvas.dims['x'] == 'tof'
+        assert fig.canvas.units['x'] == 's'
+        assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + expected
+        assert fig.canvas.xlabel == 'Time of flight [s]'
+        assert fig.canvas.ylabel == 'Transmission'
+
+    def test_spectrum_plot_unique_name_roi(self, valid_data_array, plot_setup, valid_roi):
+        # When
+        measurement = Measurement(data_array=valid_data_array)
+        measurement.regions_of_interest.append(valid_roi)
+        roi = valid_roi.unique_name
+        # Then
+        fig = measurement.spectrum_plot(roi=roi)
+        # Expect
+        assert fig.canvas.dims['x'] == 'tof'
+        assert fig.canvas.units['x'] == 's'
+        assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + "ROI '" + roi + "'"
+        assert fig.canvas.xlabel == 'Time of flight [s]'
+        assert fig.canvas.ylabel == 'Transmission'
+
+    def test_spectrum_plot_user_overwrite(self, valid_data_array, plot_setup):
+        # When
+        measurement = Measurement(data_array=valid_data_array)
+        # Then
+        fig = measurement.spectrum_plot(xlabel='Custom X label')
+        # Expect
+        assert fig.canvas.xlabel == 'Custom X label'
+        assert fig.canvas.ylabel == 'Transmission'
+        assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + 'entire image'
+
+    def test_spectrum_plot_automatic_ymax(self, valid_data_array, plot_setup):
+        # When
+        valid_data_array.data *= 10.0  # Scale data to ensure max is above 1.0
+        measurement = Measurement(data_array=valid_data_array)
+        # Then
+        fig = measurement.spectrum_plot()
+        # Expect
+        assert fig.canvas.dims['x'] == 'tof'
+        assert fig.canvas.title == measurement.display_name + ' - Spectrum of ' + 'entire image'
+        assert fig.canvas.xlabel == 'Time of flight [s]'
+        assert fig.canvas.ylabel == 'Transmission'
+        assert fig.canvas.ymax == 3.0
diff --git a/tests/unit_tests/measurement/test_regions.py b/tests/unit/regions_of_interest/test_rectangle_roi.py
similarity index 85%
rename from tests/unit_tests/measurement/test_regions.py
rename to tests/unit/regions_of_interest/test_rectangle_roi.py
index 5fdd122..0cce228 100644
--- a/tests/unit_tests/measurement/test_regions.py
+++ b/tests/unit/regions_of_interest/test_rectangle_roi.py
@@ -1,14 +1,17 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+
 import pytest
 import scipp as sc
 from scipp import UnitError
 
-from easyimaging.measurement.regions import RectROI
+from easyimaging.regions_of_interest import RectangleROI
 
 
-class TestRectROI:
+class TestRectangleROI:
     @pytest.fixture
     def roi_basic(self):
-        return RectROI((10, 50), [20, 80])
+        return RectangleROI((10, 50), [20, 80])
 
     @pytest.fixture
     def roi_with_physical_coords(self):
@@ -16,7 +19,14 @@ def roi_with_physical_coords(self):
         x_end = sc.scalar(10.0, unit='m')
         y_start = sc.scalar(0.0, unit='m')
         y_end = sc.scalar(5.0, unit='m')
-        return RectROI((10, 50), (20, 80), (x_start, x_end), (y_start, y_end), unique_name='test_roi', display_name='Test ROI')
+        return RectangleROI(
+            (10, 50),
+            (20, 80),
+            (x_start, x_end),
+            (y_start, y_end),
+            unique_name='test_roi',
+            display_name='Test ROI',
+        )
 
     def test_init_valid_physical_coords(self, roi_with_physical_coords):
         # When Then
@@ -38,8 +48,8 @@ def test_init_valid_pixel_only(self, roi_basic):
         # When Then
         roi = roi_basic
         # Expect
-        assert roi.unique_name.startswith('RectROI_')
-        assert roi.display_name.startswith('RectROI_')
+        assert roi.unique_name.startswith('RectangleROI_')
+        assert roi.display_name.startswith('RectangleROI_')
         assert roi.x_pixel_start == 10
         assert roi.x_pixel_end == 50
         assert roi.y_pixel_start == 20
@@ -52,12 +62,12 @@ def test_init_invalid_single_physical_coords(self):
         x_end = sc.scalar(10.0, unit='m')
         # Then Expect
         with pytest.raises(ValueError, match='Both x_range and y_range must be provided together or not at all.'):
-            RectROI((10, 50), (20, 80), (x_start, x_end))
+            RectangleROI((10, 50), (20, 80), (x_start, x_end))
 
     def test_init_invalid_negative_pixel_indices(self):
         # When Then Expect
         with pytest.raises(ValueError, match='Pixel indices must be non-negative integers.'):
-            RectROI((-10, 50), (20, 80))
+            RectangleROI((-10, 50), (20, 80))
 
     @pytest.mark.parametrize(
         'x_pixel_range',
@@ -72,7 +82,7 @@ def test_init_invalid_negative_pixel_indices(self):
     def test_init_invalid_x_pixel_range_arguments(self, x_pixel_range):
         # When Then Expect
         with pytest.raises(TypeError, match='x_pixel_range must be a tuple or a list of two integers'):
-            RectROI(x_pixel_range, (20, 80))
+            RectangleROI(x_pixel_range, (20, 80))
 
     @pytest.mark.parametrize(
         'x_range, error, message',
@@ -100,12 +110,12 @@ def test_init_invalid_x_pixel_range_arguments(self, x_pixel_range):
             (
                 (sc.scalar(0.0, unit='m'), sc.array(dims=['x'], values=[1.0, 2.0], unit='m')),
                 ValueError,
-                'Physical coordinates must be a scipp scalar \(0-dimensional Variable\).',
+                r'Physical coordinates must be a scipp scalar \(0-dimensional Variable\).',
             ),  # Second element not a scalar  # noqa: E501
             (
                 (sc.scalar(0.0, unit='m'), sc.scalar(1.0, unit='s')),
                 UnitError,
-                "Physical coordinates must be a scipp scalar with a unit of length \(e.g., 'm'\).",
+                r"Physical coordinates must be a scipp scalar with a unit of length \(e.g., 'm'\).",
             ),  # Second element with wrong unit  # noqa: E501
         ],
         ids=[
@@ -120,7 +130,7 @@ def test_init_invalid_x_pixel_range_arguments(self, x_pixel_range):
     def test_init_invalid_x_range_arguments(self, x_range, error, message):
         # When Then Expect
         with pytest.raises(error, match=message):
-            RectROI((10, 50), (20, 80), x_range, (sc.scalar(0.0, unit='m'), sc.scalar(1.0, unit='m')))
+            RectangleROI((10, 50), (20, 80), x_range, (sc.scalar(0.0, unit='m'), sc.scalar(1.0, unit='m')))
 
     def test_set_physical_coord_range(self, roi_basic):
         # When
@@ -182,7 +192,9 @@ def test_pixel_coordinate_setter(self, roi_basic, attribute):
         assert getattr(roi, attribute) == 15
 
     @pytest.mark.parametrize(
-        'attribute', ['x_pixel_end', 'y_pixel_start', 'y_pixel_end'], ids=['x_pixel_end', 'y_pixel_start', 'y_pixel_end']
+        'attribute',
+        ['x_pixel_end', 'y_pixel_start', 'y_pixel_end'],
+        ids=['x_pixel_end', 'y_pixel_start', 'y_pixel_end'],
     )
     @pytest.mark.parametrize(
         'invalid_value, error, message',
@@ -234,7 +246,9 @@ def test_physical_coordinate_getter(self, roi_with_physical_coords, attribute, s
         assert getattr(roi, attribute) is not getattr(roi, f'_{attribute}')  # Ensure a copy is returned
 
     @pytest.mark.parametrize(
-        'attribute', ['x_start', 'x_end', 'y_start', 'y_end'], ids=['x_start', 'x_end', 'y_start', 'y_end']
+        'attribute',
+        ['x_start', 'x_end', 'y_start', 'y_end'],
+        ids=['x_start', 'x_end', 'y_start', 'y_end'],
     )
     def test_physical_coordinate_setter(self, roi_with_physical_coords, attribute):
         # When
@@ -246,17 +260,24 @@ def test_physical_coordinate_setter(self, roi_with_physical_coords, attribute):
         assert sc.identical(getattr(roi, attribute), new_value)
 
     @pytest.mark.parametrize(
-        'attribute', ['x_start', 'x_end', 'y_start', 'y_end'], ids=['x_start', 'x_end', 'y_start', 'y_end']
+        'attribute',
+        ['x_start', 'x_end', 'y_start', 'y_end'],
+        ids=['x_start', 'x_end', 'y_start', 'y_end'],
     )
     def test_physical_coordinate_setter_setting_single_coordinate(self, roi_basic, attribute):
         # When
         roi = roi_basic
         # Then Expect
-        with pytest.raises(ValueError, match=f'Cannot set {attribute} before setting all physical coordinate ranges.'):
+        with pytest.raises(
+            ValueError,
+            match=f'Cannot set {attribute} before setting all physical coordinate ranges.',
+        ):
             setattr(roi, attribute, sc.scalar(1.0, unit='m'))
 
     @pytest.mark.parametrize(
-        'attribute', ['x_start', 'x_end', 'y_start', 'y_end'], ids=['x_start', 'x_end', 'y_start', 'y_end']
+        'attribute',
+        ['x_start', 'x_end', 'y_start', 'y_end'],
+        ids=['x_start', 'x_end', 'y_start', 'y_end'],
     )
     @pytest.mark.parametrize(
         'invalid_value, error, message',
@@ -265,12 +286,12 @@ def test_physical_coordinate_setter_setting_single_coordinate(self, roi_basic, a
             (
                 sc.array(dims=['x'], values=[1.0, 2.0], unit='m'),
                 ValueError,
-                'must be a scipp scalar \(0-dimensional Variable\).',
+                r'must be a scipp scalar \(0-dimensional Variable\).',
             ),  # Not a scalar  # noqa: E501
             (
                 sc.scalar(1.0, unit='s'),
                 UnitError,
-                "must be a scipp scalar with a unit of length \(e.g., 'm'\).",
+                r"must be a scipp scalar with a unit of length \(e.g., 'm'\).",
             ),  # Wrong unit  # noqa: E501
         ],
         ids=['not_scipp_variable', 'not_scalar', 'wrong_unit'],
@@ -318,8 +339,14 @@ def test_to_dict_with_physical_coords(self, roi_with_physical_coords):
         # When Then
         roi_dict = roi_with_physical_coords.to_dict()
         # Expect
-        assert roi_dict['x_pixel_range'] == [roi_with_physical_coords.x_pixel_start, roi_with_physical_coords.x_pixel_end]
-        assert roi_dict['y_pixel_range'] == [roi_with_physical_coords.y_pixel_start, roi_with_physical_coords.y_pixel_end]
+        assert roi_dict['x_pixel_range'] == [
+            roi_with_physical_coords.x_pixel_start,
+            roi_with_physical_coords.x_pixel_end,
+        ]
+        assert roi_dict['y_pixel_range'] == [
+            roi_with_physical_coords.y_pixel_start,
+            roi_with_physical_coords.y_pixel_end,
+        ]
         assert isinstance(roi_dict['x_range'], list) and len(roi_dict['x_range']) == 2
         assert isinstance(roi_dict['y_range'], list) and len(roi_dict['y_range']) == 2
         assert isinstance(roi_dict['x_range'][0], dict) and roi_dict['x_range'][0]['@module'] == 'scipp'
@@ -337,12 +364,12 @@ def test_from_dict_only_pixel_ranges(self):
         # Given
         input_dict = {
             '@module': 'easyimaging.measurement.regions',
-            '@class': 'RectROI',
+            '@class': 'RectangleROI',
             'x_pixel_range': [10, 50],
             'y_pixel_range': [20, 80],
         }
         # When Then
-        roi = RectROI.from_dict(input_dict)
+        roi = RectangleROI.from_dict(input_dict)
         # Expect
         assert roi.x_pixel_start == 10
         assert roi.x_pixel_end == 50
@@ -355,7 +382,7 @@ def test_from_dict_with_physical_coords(self, roi_with_physical_coords):
         roi = roi_with_physical_coords
         input_dict = roi.to_dict(skip='unique_name')  # Skip unique_name to allow auto-generation in from_dict
         # When Then
-        roi_from_dict = RectROI.from_dict(input_dict)
+        roi_from_dict = RectangleROI.from_dict(input_dict)
         # Expect
         assert roi_from_dict.x_pixel_start == roi.x_pixel_start
         assert roi_from_dict.x_pixel_end == roi.x_pixel_end
diff --git a/tools/license_headers.py b/tools/license_headers.py
new file mode 100644
index 0000000..f276ca1
--- /dev/null
+++ b/tools/license_headers.py
@@ -0,0 +1,321 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+"""Add, remove, or check SPDX headers in Python files."""
+
+from __future__ import annotations
+
+import argparse
+import fnmatch
+import tomllib
+from datetime import datetime
+from pathlib import Path
+from typing import Any
+from typing import Optional
+from typing import Union
+
+from git import Repo
+from spdx_headers.core import find_repository_root
+from spdx_headers.core import get_copyright_info
+from spdx_headers.core import has_spdx_header
+from spdx_headers.data import load_license_data
+from spdx_headers.operations import add_header_to_single_file
+from spdx_headers.operations import remove_header_from_single_file
+
+LICENSE_DATABASE = load_license_data()
+
+
+def load_pyproject(repo_path: Union[str, Path]) -> dict[str, Any]:
+    """
+    Load and return parsed ``pyproject.toml`` data for the repository.
+    """
+    repo_root = find_repository_root(repo_path)
+    pyproject_path = repo_root / 'pyproject.toml'
+
+    with pyproject_path.open('rb') as file_handle:
+        return tomllib.load(file_handle)
+
+
+def get_pyproject_value(pyproject_data: dict[str, Any], dotted_key: str) -> Any:
+    """Return a nested ``pyproject.toml`` value from a dotted key."""
+    value: Any = pyproject_data
+    for part in dotted_key.split('.'):
+        if not isinstance(value, dict) or part not in value:
+            raise KeyError(dotted_key)
+        value = value[part]
+    return value
+
+
+def normalize_pattern(pattern: str) -> str:
+    """Normalize an exclude pattern to a POSIX-style relative path."""
+    normalized = Path(pattern).as_posix()
+    if normalized.startswith('./'):
+        normalized = normalized[2:]
+    return normalized.rstrip('/')
+
+
+def get_exclude_patterns(
+    repo_path: Union[str, Path],
+    exclude_values: list[str],
+    exclude_from_pyproject_toml: Optional[str],
+) -> list[str]:
+    """
+    Return normalized exclude patterns from CLI and ``pyproject.toml``.
+    """
+    pyproject_data = load_pyproject(repo_path)
+    patterns: list[str] = []
+
+    if exclude_from_pyproject_toml:
+        value = get_pyproject_value(pyproject_data, exclude_from_pyproject_toml)
+        if not isinstance(value, list) or not all(isinstance(item, str) for item in value):
+            raise ValueError(
+                f'{exclude_from_pyproject_toml} in pyproject.toml must be a list of strings.',
+            )
+        patterns.extend(value)
+
+    for item in exclude_values:
+        try:
+            value = get_pyproject_value(pyproject_data, item)
+        except KeyError:
+            patterns.append(item)
+            continue
+
+        if not isinstance(value, list) or not all(isinstance(entry, str) for entry in value):
+            raise ValueError(f'{item} in pyproject.toml must be a list of strings.')
+        patterns.extend(value)
+
+    normalized_patterns: list[str] = []
+    seen: set[str] = set()
+    for pattern in patterns:
+        normalized = normalize_pattern(pattern)
+        if normalized and normalized not in seen:
+            normalized_patterns.append(normalized)
+            seen.add(normalized)
+
+    return normalized_patterns
+
+
+def get_file_creation_year(file_path: Union[str, Path]) -> str:
+    """Return the year the file was first added to Git history.
+
+    If the year cannot be determined, fall back to the current year.
+    """
+    file_path = Path(file_path)
+
+    repo = Repo(file_path, search_parent_directories=True)
+    root = Path(repo.working_tree_dir).resolve()
+    rel_path = file_path.resolve().relative_to(root)
+
+    rel_path_git = rel_path.as_posix()
+
+    log_output = repo.git.log(
+        '--follow',
+        '--diff-filter=A',
+        '--reverse',
+        '--format=%ad',
+        '--date=format:%Y',
+        '--',
+        rel_path_git,
+    ).strip()
+
+    year = log_output.splitlines()[0].strip() if log_output else ''
+
+    return year or str(datetime.now().year)
+
+
+def get_org_url(repo_path: Union[str, Path]) -> str:
+    """
+    Return the organization URL derived from the repository source URL.
+    """
+    pyproject_data = load_pyproject(repo_path)
+    repo_url = pyproject_data['project']['urls']['Source Code']
+    return repo_url.rsplit('/', 1)[0]
+
+
+def get_project_license(repo_path: Union[str, Path]) -> str:
+    """Return the project license value from ``pyproject.toml``."""
+    pyproject_data = load_pyproject(repo_path)
+    return pyproject_data['project']['license']
+
+
+def get_copyright_holder(repo_path: Union[str, Path]) -> str:
+    """Return the repository copyright holder name."""
+    _, name, _ = get_copyright_info(repo_path)
+    return name
+
+
+def add_spdx_header(
+    target_file: Union[str, Path],
+    *,
+    license_key: str,
+    copyright_holder: str,
+    org_url: str,
+) -> None:
+    """Add SPDX headers to one file."""
+    year = get_file_creation_year(target_file)
+
+    add_header_to_single_file(
+        filepath=target_file,
+        license_key=license_key,
+        license_data=LICENSE_DATABASE,
+        year=year,
+        name=copyright_holder,
+        email=org_url,
+    )
+
+
+def is_excluded(relative_path: str, exclude_patterns: list[str]) -> bool:
+    """Return whether a relative path should be excluded."""
+    for pattern in exclude_patterns:
+        if fnmatch.fnmatch(relative_path, pattern):
+            return True
+        if relative_path == pattern:
+            return True
+        if relative_path.startswith(f'{pattern}/'):
+            return True
+    return False
+
+
+def iter_python_files(
+    paths: list[str],
+    *,
+    repo_root: Path,
+    exclude_patterns: list[str],
+    parser: argparse.ArgumentParser,
+) -> list[Path]:
+    """Collect Python files under the given paths after exclusions."""
+    files: list[Path] = []
+    seen: set[Path] = set()
+
+    for base_dir in paths:
+        base_path = Path(base_dir)
+        if not base_path.exists():
+            parser.error(f'Path does not exist: {base_dir}')
+
+        if base_path.is_file():
+            candidates = [base_path] if base_path.suffix == '.py' else []
+        else:
+            candidates = sorted(base_path.rglob('*.py'))
+
+        for py_file in candidates:
+            resolved = py_file.resolve()
+            try:
+                relative_path = resolved.relative_to(repo_root).as_posix()
+            except ValueError:
+                relative_path = py_file.as_posix()
+
+            if is_excluded(relative_path, exclude_patterns):
+                continue
+
+            if resolved not in seen:
+                files.append(py_file)
+                seen.add(resolved)
+
+    return files
+
+
+def run_add(
+    files: list[Path],
+    *,
+    license_key: str,
+    copyright_holder: str,
+    org_url: str,
+) -> int:
+    """Add SPDX headers to all selected files."""
+    for py_file in files:
+        add_spdx_header(
+            py_file,
+            license_key=license_key,
+            copyright_holder=copyright_holder,
+            org_url=org_url,
+        )
+    return 0
+
+
+def run_remove(files: list[Path]) -> int:
+    """Remove SPDX headers from all selected files."""
+    for py_file in files:
+        remove_header_from_single_file(py_file)
+    return 0
+
+
+def run_check(files: list[Path]) -> int:
+    """Check SPDX headers in all selected files."""
+    missing_files = [py_file for py_file in files if not has_spdx_header(py_file)]
+
+    if not missing_files:
+        print('✓ All Python files have valid SPDX headers.')
+        return 0
+
+    print('✗ The following files are missing SPDX headers:')
+    for py_file in missing_files:
+        print(f'  - {py_file.as_posix()}')
+    print(f'\nFound {len(missing_files)} files without SPDX headers.')
+    return 1
+
+
+def build_parser() -> argparse.ArgumentParser:
+    """Build the CLI argument parser."""
+    parser = argparse.ArgumentParser(
+        description='Add, remove, or check SPDX headers in Python files.',
+    )
+    subparsers = parser.add_subparsers(dest='command', required=True)
+
+    for command_name in ('check', 'remove', 'add'):
+        command_parser = subparsers.add_parser(command_name)
+        command_parser.add_argument(
+            'paths',
+            nargs='+',
+            help='Relative paths to scan (e.g. src tests)',
+        )
+        command_parser.add_argument(
+            '--exclude',
+            nargs='*',
+            default=[],
+            help='Exclude paths, glob patterns, or pyproject dotted keys.',
+        )
+        command_parser.add_argument(
+            '--exclude-from-pyproject-toml',
+            help='Read exclude patterns from a dotted key in pyproject.toml.',
+        )
+
+    return parser
+
+
+def main(argv: Optional[list[str]] = None) -> int:
+    """Run the SPDX header CLI."""
+    parser = build_parser()
+    args = parser.parse_args(argv)
+
+    repo_path = Path('.').resolve()
+    repo_root = find_repository_root(repo_path).resolve()
+    exclude_patterns = get_exclude_patterns(
+        repo_path,
+        args.exclude,
+        args.exclude_from_pyproject_toml,
+    )
+    files = iter_python_files(
+        args.paths,
+        repo_root=repo_root,
+        exclude_patterns=exclude_patterns,
+        parser=parser,
+    )
+
+    if args.command == 'check':
+        return run_check(files)
+
+    if args.command == 'remove':
+        return run_remove(files)
+
+    license_key = get_project_license(repo_path)
+    copyright_holder = get_copyright_holder(repo_path)
+    org_url = get_org_url(repo_path)
+    return run_add(
+        files,
+        license_key=license_key,
+        copyright_holder=copyright_holder,
+        org_url=org_url,
+    )
+
+
+if __name__ == '__main__':
+    raise SystemExit(main())
diff --git a/tools/update_docs_assets.py b/tools/update_docs_assets.py
new file mode 100644
index 0000000..fa31665
--- /dev/null
+++ b/tools/update_docs_assets.py
@@ -0,0 +1,91 @@
+"""
+Update documentation assets from the assets-branding repository.
+
+This script fetches branding assets (logos, icons, images) from the
+easyscience/assets-branding GitHub repository and copies them to the
+appropriate locations in the documentation directory.
+"""
+
+import shutil
+from pathlib import Path
+
+import pooch
+
+# Configuration: Define what to fetch and where to copy
+GITHUB_REPO = 'easyscience/assets-branding'
+GITHUB_BRANCH = 'master'
+BASE_URL = f'https://raw.githubusercontent.com/{GITHUB_REPO}/refs/heads/{GITHUB_BRANCH}'
+PROJECT_NAME = 'easyimaging'
+
+# Mapping of source files to destination paths
+# Format: "source_path_in_repo": "destination_path_in_project"
+ASSETS_MAP = {
+    # Logos
+    f'{PROJECT_NAME}/logos/dark.svg': 'docs/docs/assets/images/logo_dark.svg',
+    f'{PROJECT_NAME}/logos/light.svg': 'docs/docs/assets/images/logo_light.svg',
+    # Favicon
+    f'{PROJECT_NAME}/icons/color.png': 'docs/docs/assets/images/favicon.png',
+    # Icon overrides
+    f'{PROJECT_NAME}/icons/bw.svg': f'docs/overrides/.icons/{PROJECT_NAME}.svg',
+    'easyscience-org/icons/eso-icon_bw.svg': 'docs/overrides/.icons/easyscience.svg',
+}
+
+
+def fetch_and_copy_asset(
+    source_path: str,
+    dest_path: str,
+    cache_dir: Path,
+) -> None:
+    """
+    Fetch an asset from GitHub and copy it to the destination.
+
+    Args:
+        source_path: Path to the file in the GitHub repository
+        dest_path: Destination path in the project
+        cache_dir: Directory to cache downloaded files
+    """
+    url = f'{BASE_URL}/{source_path}'
+
+    # Create a unique cache filename based on source path
+    cache_filename = source_path.replace('/', '_')
+
+    # Download file using pooch
+    file_path = pooch.retrieve(
+        url=url,
+        known_hash=None,  # Skip hash verification
+        path=cache_dir,
+        fname=cache_filename,
+    )
+
+    # Create destination directory if it doesn't exist
+    dest = Path(dest_path)
+    dest.parent.mkdir(parents=True, exist_ok=True)
+
+    # Copy the file to destination
+    shutil.copy2(file_path, dest)
+    print(f'Copied {file_path} -> {dest_path}')
+
+
+def main():
+    """Main function to update all documentation assets."""
+    print('📥 Updating documentation assets...')
+    print(f'   Repository: {GITHUB_REPO}')
+    print(f'   Branch: {GITHUB_BRANCH}\n')
+
+    # Use a temporary cache directory
+    cache_dir = Path.home() / '.cache' / GITHUB_REPO
+    cache_dir.mkdir(parents=True, exist_ok=True)
+
+    # Fetch and copy each asset
+    for source_path, dest_path in ASSETS_MAP.items():
+        try:
+            fetch_and_copy_asset(source_path, dest_path, cache_dir)
+            print()
+        except Exception as e:
+            print(f'❌ Failed to fetch {source_path}: {e}')
+
+    print('\n✅ Documentation assets updated successfully!')
+
+
+if __name__ == '__main__':
+    main()
diff --git a/tools/update_github_labels.py b/tools/update_github_labels.py
new file mode 100644
index 0000000..84de575
--- /dev/null
+++ b/tools/update_github_labels.py
@@ -0,0 +1,341 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
+# SPDX-License-Identifier: BSD-3-Clause
+"""Set/update GitHub labels for current or specified easyscience
+repository.
+
+Requires:
+  - gh CLI installed
+  - gh auth login completed
+
+Usage:
+  python update_github_labels.py
+  python update_github_labels.py --dry-run
+  python update_github_labels.py --repo easyscience/my-repo
+  python update_github_labels.py --repo easyscience/my-repo --dry-run
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import shlex
+import subprocess  # noqa: S404
+import sys
+from dataclasses import dataclass
+
+EASYSCIENCE_ORG = 'easyscience'
+
+
+# Data structures
+
+
+@dataclass(frozen=True)
+class Label:
+    """A GitHub label with name, color, and description."""
+
+    name: str
+    color: str
+    description: str = ''
+
+
+@dataclass(frozen=True)
+class LabelRename:
+    """Mapping from old label name to new label name."""
+
+    old: str
+    new: str
+
+
+class Colors:
+    """Hex color codes for label groups."""
+
+    SCOPE = 'd73a4a'
+    MAINTAINER = '0e8a16'
+    PRIORITY = 'fbca04'
+    BOT = '5319e7'
+
+
+LABEL_RENAMES = [
+    # Default GitHub labels to rename (if they exist)
+    LabelRename('bug', '[scope] bug'),
+    LabelRename('documentation', '[scope] documentation'),
+    LabelRename('duplicate', '[maintainer] duplicate'),
+    LabelRename('enhancement', '[scope] enhancement'),
+    LabelRename('good first issue', '[maintainer] good first issue'),
+    LabelRename('help wanted', '[maintainer] help wanted'),
+    LabelRename('invalid', '[maintainer] invalid'),
+    LabelRename('question', '[maintainer] question'),
+    LabelRename('wontfix', '[maintainer] wontfix'),
+    # Custom label renames (if they exist)
+    LabelRename('[bot] pull request', '[bot] release'),
+]
+
+LABELS = [
+    # Scope labels
+    Label(
+        '[scope] bug',
+        Colors.SCOPE,
+        'Bug report or fix (major.minor.PATCH)',
+    ),
+    Label(
+        '[scope] documentation',
+        Colors.SCOPE,
+        'Documentation only changes (major.minor.patch.POST)',
+    ),
+    Label(
+        '[scope] enhancement',
+        Colors.SCOPE,
+        'Adds/improves features (major.MINOR.patch)',
+    ),
+    Label(
+        '[scope] maintenance',
+        Colors.SCOPE,
+        'Code/tooling cleanup, no feature or bugfix (major.minor.PATCH)',
+    ),
+    Label(
+        '[scope] significant',
+        Colors.SCOPE,
+        'Breaking or major changes (MAJOR.minor.patch)',
+    ),
+    Label(
+        '[scope] ⚠️ label needed',
+        Colors.SCOPE,
+        'Automatically added to issues and PRs without a [scope] label',
+    ),
+    # Maintainer labels
+    Label(
+        '[maintainer] duplicate',
+        Colors.MAINTAINER,
+        'Already reported or submitted',
+    ),
+    Label(
+        '[maintainer] good first issue',
+        Colors.MAINTAINER,
+        'Good entry-level issue for newcomers',
+    ),
+    Label(
+        '[maintainer] help wanted',
+        Colors.MAINTAINER,
+        'Needs additional help to resolve or implement',
+    ),
+    Label(
+        '[maintainer] invalid',
+        Colors.MAINTAINER,
+        'Invalid, incorrect or outdated',
+    ),
+    Label(
+        '[maintainer] question',
+        Colors.MAINTAINER,
+        'Needs clarification, discussion, or more information',
+    ),
+    Label(
+        '[maintainer] wontfix',
+        Colors.MAINTAINER,
+        'Will not be fixed or continued',
+    ),
+    # Priority labels
+    Label(
+        '[priority] lowest',
+        Colors.PRIORITY,
+        'Very low urgency',
+    ),
+    Label(
+        '[priority] low',
+        Colors.PRIORITY,
+        'Low importance',
+    ),
+    Label(
+        '[priority] medium',
+        Colors.PRIORITY,
+        'Normal/default priority',
+    ),
+    Label(
+        '[priority] high',
+        Colors.PRIORITY,
+        'Should be prioritized soon',
+    ),
+    Label(
+        '[priority] highest',
+        Colors.PRIORITY,
+        'Urgent. Needs attention ASAP',
+    ),
+    Label(
+        '[priority] ⚠️ label needed',
+        Colors.PRIORITY,
+        'Automatically added to issues without a [priority] label',
+    ),
+    # Bot label
+    Label(
+        '[bot] release',
+        Colors.BOT,
+        'Automated release PR. Excluded from changelog/versioning',
+    ),
+    Label(
+        '[bot] backmerge',
+        Colors.BOT,
+        'Automated backmerge master → develop failed due to conflicts',
+    ),
+]
+
+
+# Helpers
+
+
+@dataclass(frozen=True)
+class CmdResult:
+    """Result of a shell command execution."""
+
+    returncode: int
+    stdout: str
+    stderr: str
+
+
+def run_cmd(
+    args: list[str],
+    *,
+    dry_run: bool,
+    check: bool = True,
+) -> CmdResult:
+    """Run a command (or print it in dry-run mode)."""
+    cmd_str = ' '.join(shlex.quote(a) for a in args)
+
+    if dry_run:
+        print(f'  [dry-run] {cmd_str}')
+        return CmdResult(0, '', '')
+
+    proc = subprocess.run(
+        args=args,
+        text=True,
+        capture_output=True,
+    )
+    result = CmdResult(
+        proc.returncode,
+        proc.stdout.strip(),
+        proc.stderr.strip(),
+    )
+
+    if check and proc.returncode != 0:
+        raise RuntimeError(f'Command failed ({proc.returncode}): {cmd_str}\n{result.stderr}')
+
+    return result
+
+
+def get_current_repo() -> str:
+    """Get the current repository name in 'owner/repo' format."""
+    result = subprocess.run(
+        args=[
+            'gh',
+            'repo',
+            'view',
+            '--json',
+            'nameWithOwner',
+        ],
+        text=True,
+        capture_output=True,
+        check=True,
+    )
+    data = json.loads(result.stdout)
+    name_with_owner = data.get('nameWithOwner', '')
+
+    if '/' not in name_with_owner:
+        raise RuntimeError('Could not determine current repository name')
+
+    return name_with_owner
+
+
+def rename_label(
+    repo: str,
+    rename: LabelRename,
+    *,
+    dry_run: bool,
+) -> None:
+    """Rename a label, silently skipping if it doesn't exist."""
+    result = run_cmd(
+        args=[
+            'gh',
+            'label',
+            'edit',
+            rename.old,
+            '--name',
+            rename.new,
+            '--repo',
+            repo,
+        ],
+        dry_run=dry_run,
+        check=False,
+    )
+
+    if dry_run or result.returncode == 0:
+        print(f'  Rename: {rename.old!r} → {rename.new!r}')
+    else:
+        print(f'  Skip (not found): {rename.old!r}')
+
+
+def upsert_label(
+    repo: str,
+    label: Label,
+    *,
+    dry_run: bool,
+) -> None:
+    """Create or update a label."""
+    run_cmd(
+        [
+            'gh',
+            'label',
+            'create',
+            label.name,
+            '--color',
+            label.color,
+            '--description',
+            label.description,
+            '--force',
+            '--repo',
+            repo,
+        ],
+        dry_run=dry_run,
+    )
+    print(f'  Upsert: {label.name!r}')
+
+
+# Main
+
+
+def main() -> int:
+    """Entry point: parse arguments and sync labels."""
+    parser = argparse.ArgumentParser(description='Sync GitHub labels for easyscience repos')
+    parser.add_argument(
+        '--repo',
+        help='Target repository (owner/name)',
+    )
+    parser.add_argument(
+        '--dry-run',
+        action='store_true',
+        help='Print actions without applying changes',
+    )
+    args = parser.parse_args()
+
+    repo = args.repo or get_current_repo()
+    org = repo.split('/')[0]
+
+    if org.lower() != EASYSCIENCE_ORG:
+        print(f"Error: repository '{repo}' is not under '{EASYSCIENCE_ORG}'", file=sys.stderr)
+        return 2
+
+    print(f'Repository: {repo}')
+    if args.dry_run:
+        print('Mode: DRY-RUN (no changes will be made)\n')
+
+    print('\nRenaming default labels...')
+    for rename in LABEL_RENAMES:
+        rename_label(repo, rename, dry_run=args.dry_run)
+
+    print('\nUpserting labels...')
+    for label in LABELS:
+        upsert_label(repo, label, dry_run=args.dry_run)
+
+    print('\nDone.')
+    return 0
+
+
+if __name__ == '__main__':
+    raise SystemExit(main())