Dictionary of Functional Modes for brain imaging
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Feb 1, 2021 - HTML
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brain-atlas
Here are 26 public repositories matching this topic...
R package for reading and writing neuroimaging file formats. Not limited to FreeSurfer formats anymore, despite its name.
r research label voxel mri mesh neuroimaging brain surface parcellation dti freesurfer brain-atlas mgh brain-surfaces fileformats curv
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Sep 8, 2026 - R
Search, download, and prepare brain atlas data.
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Mar 10, 2023 - Python
A simple Python-based tool for finding brain atlas regions based on MNI coordinates.
python neuroscience python3 neuroimaging brain-imaging mni brain-regions brain-atlas aal brain-visualization aal3
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Aug 1, 2026 - Python
A neuroanatomy-based augmented reality experience powered by OpenCV. Features 3D visuals of the Atlas Brain Map slices with real-time ArUco marker detection.
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Jun 16, 2021 - Python
Scripts for the paper: Generation of individual whole-brain atlases with resting-state fMRI data using simultaneous graph computation and parcellation.
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Oct 25, 2019 - MATLAB
BBP domains specification (schemas, vocabularies)
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May 18, 2022 - Scala
One-prompt 3D brain-region figures & rotating glow animations from 200+ BrainGlobe atlases (any species), rendered headless in Blender. A low-token Claude Code skill.
blender animation neuroscience data-visualization scientific-visualization 3d-visualization neuroanatomy claude brain-atlas brainglobe claude-code claude-skill
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Jun 24, 2026 - Python
LocareJSON is a collection of JSON schemas for defining geometrical shapes with coordinates in 3D brain atlas coordinate spaces.
neuroscience-methods spatial-search brain-atlas coordinate-reference-systems data-integration-framework
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Oct 24, 2023 - Python
Code repository for automatic retrieval and registration of rodent brain atlases
feature-detection segmentation harris-corners image-registration image-retrieval feature-matching speeded-up-robust-features brain-atlas
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Feb 22, 2019 - Jupyter Notebook
Brain tissue segmentation using several algorithms: EM, Atlas-based methods, nnunet
medical-imaging expectation-maximization segmentation image-segmentation semantic-segmentation brain-atlas brain-tissue-segmentation nnunet
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Jul 25, 2023 - Python
Automatic annotation of cell identities in dense cellular images.
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Jun 23, 2021 - MATLAB
Scripts for the paper: A supervoxel-based method for groupwise whole brain parcellation with resting-state fMRI data.
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Dec 22, 2016 - MATLAB
Use vision-language models to perform alignment and registration of histological brain sections to any BrainGlobe atlas in any orientation plane.
neuroscience image-registration gemma histology tauri brain-atlas vision-language-model brainglobe gemma-4
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Jun 3, 2026 - Python
a web-based 3D tool to register brain MRI volumes to the Marmoset Brain Atlas
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Apr 18, 2023 - TypeScript
a web-based 2D high-resolution brain image viewer
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Dec 22, 2023 - JavaScript
Pairwise Brain Atlas Construction (BAtCh) HTCondor/SLURM workflow
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Jul 20, 2020 - Shell
Brain/MINDS Marmoset Brain Atlas Viewer made using Unity engine
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Oct 7, 2022 - C#
A Python tool for mapping electrophysiology recording sites onto standardized mouse brain coordinates. Supports coronal, axial, and sagittal views with rapid visualization of electrophysiological data and anatomical locations.
python neuroscience data-visualization electrophysiology mouse-brain neurophysiology brain-atlas brain-mapping electrode-localization scientific-tools recording-sites coronal-sections brain-coordinates
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Sep 16, 2025 - Python
Open-source image alignment and brain atlas registration for Fiji / ImageJ2. Review mouse brain microscopy against Allen CCFv3, select anatomical ROIs, and export crops and masks. Supports resumable batch review.
java open-source imagej imagej2 fiji neuroscience roi microscopy image-registration allen-brain-atlas histology image-alignment brain-atlas bioimage-analysis immunofluorescence roi-analysis atlas-registration ccfv3
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Sep 8, 2026 - Java
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