Release 1.1.0

[1.1.0] - 2026-06-30

Added

• Managed Server mode: A brand-new Managed Server mode lets the CopilotJ Bridge plugin install, configure, and launch the Core Server automatically in the background. Getting CopilotJ running is now just a few clicks from inside Fiji — no manual Python server to set up, dramatically simplifying installation.
  • In the plugin dialog's Managed Server tab, Install downloads Python, creates a virtual environment, and installs all dependencies automatically; Start launches the server.
  • Open the chat UI straight from the dialog (Open copilotj.chat) and reach your CopilotJ home folder via Open Resources.
  • Removing the managed environment offers a keep-data vs delete-all choice, so you can uninstall without losing your data.
• Install the plugin from the ImageJ Updater: The CopilotJ Bridge plugin is now published on a Fiji/ImageJ update site, so it installs and updates through the ImageJ Updater — no manual JAR placement.
  • Add the CopilotJ update site (https://sites.imagej.net/CopilotJ/) under Help → Update… → Manage Update Sites, then Apply Changes.
  • Smaller download — StarDist model weights and other heavy assets are fetched on demand instead of being bundled in the plugin.
• Web frontend & onboarding: copilotj.chat is now the recommended hosted frontend (no need to run it yourself), and a new first-time setup wizard lets users start using it directly in the browser and point it at their local CopilotJ server.
  • Use CopilotJ directly at copilotj.chat — the hosted frontend is now the recommended path instead of self-hosting.
  • A new setup wizard walks first-time users through configuring the server connection and their model provider/keys; the wizard and Settings dialogs share unified components.
• Agent runtime & reliability: Reliability improvements to the multi-agent run loop.
  • Auto-retry on 429 rate limits with visible frontend feedback, so transient rate limits no longer fail a run.
  • Stop now aborts in-flight runs promptly, including mid-retry.
  • Expanded provider support: Added support for more providers, including Anthropic via the native SDK, Google Gemini via the native SDK, OpenRouter with OpenAI-compatible APIs, and more. Also introduced a unified model discovery API and a revamped provider settings UI.
  • Stronger knowledge-bank execution validation and error checks.
  • Script/macro execution timeout is enforced via a new ScriptRequest timeout field — protection against runaway scripts.
• Privacy & consent:
  • Added a User Agreement and Vision notice so users consent before any vision/VLM feature is used.
  • A vision_enabled flag disables vision features; the preference no longer resets to the server default on reload.
• Java-based MCP server: CopilotJ can expose itself as an MCP server so external MCP clients (e.g. Claude Desktop, Cline) can drive ImageJ; loaded via an isolated child-first ClassLoader, ensuring compatibility with both Java 8 and Java 17+ Fiji.
• Batch QC: new batch quality-control capability integrated with the workflow tools.
• Usage logging: per-request token usage (prompt, completion, and cache-hit tokens) is now logged for every provider, so operators can monitor consumption and verify that prompt caching is actually hitting.

Changed

• Prompt caching: enabled for Anthropic and Qwen to reduce latency and cost.
• Docs: the user manual was restructured with troubleshooting FAQs and is rendered at build time via a Vite plugin.

Fixed

• Notable fixes: Fiji-Quit hang from a leaked EDT context ClassLoader; emoji-encoding crash on GBK stdout in managed mode; broken MCP-unavailable manual deep-link.

Security

• Merged a large batch of dependency updates (~50) across the Python, Java, JavaScript, and CI stacks — including security-relevant libraries (tornado, cryptography, aiohttp, urllib3) — to keep CopilotJ on current, patched versions.

What's Changed

• Add AWT window and component node node by @yzx9 in #5
• Fix demo width by @yzx9 in #3
• Update the branch trigger of GitHub Action by @yzx9 in #4
• Add support for bold ReAct keywords by @yzx9 in #7
• docs: Improve manual by @yzx9 in #8
• Add release action to CI workflow by @yzx9 in #13
• Improve the CopilotJ user experience by @ctrueden in #9
• Improve the Contribution Guidelines Document by @yzx9 in #15
• Update the PolyU logo by @yzx9 in #17
• Support more GPT models and improve performance by @ctrueden in #16
• Fix dependency path by @yzx9 in #20
• fix: configure separate base url for vlm by @00JackLu in #24
• Add just recipe for creating worktrees with direnv and deps setup by @yzx9 in #19
• Add disclaimer about CopilotJ affiliation by @00JackLu in #25
• Fix worktree deps install using subshells to avoid cd side effects by @yzx9 in #27
• Redirect root path to /chat or /home based on VITE_DISABLE_CHAT by @yzx9 in #28
• Format code by @yzx9 in #33
• Update trace context with current session ID in _Thread class by @00JackLu in #34
• Bump vite from 6.4.1 to 6.4.2 in /web by @dependabot[bot] in #38
• Bump nltk from 3.9.1 to 3.9.4 by @dependabot[bot] in #40
• Bump ujson from 5.11.0 to 5.12.1 by @dependabot[bot] in #41
• Bump unstructured from 0.18.14 to 0.18.18 by @dependabot[bot] in #39
• Bump aiohttp from 3.12.15 to 3.13.4 by @dependabot[bot] in #44
• Bump urllib3 from 2.5.0 to 2.7.0 by @dependabot[bot] in #43
• Bump pypdf from 6.0.0 to 6.10.2 by @dependabot[bot] in #46
• Bump cryptography from 45.0.6 to 46.0.7 by @dependabot[bot] in #45
• Bump orjson from 3.11.3 to 3.11.6 by @dependabot[bot] in #48
• Bump tornado from 6.5.2 to 6.5.5 by @dependabot[bot] in #47
• Bump protobuf from 5.29.5 to 5.29.6 by @dependabot[bot] in #49
• Bump lxml from 6.0.1 to 6.1.0 by @dependabot[bot] in #50
• Bump pyasn1 from 0.6.1 to 0.6.3 by @dependabot[bot] in #53
• Bump filelock from 3.19.1 to 3.20.3 by @dependabot[bot] in #54
• Improve worktree management: env copy and cleanup script by @yzx9 in #35
• Fix for Dereferenced variable may be null by @yzx9 in #61
• Fix for Dereferenced variable may be null by @yzx9 in #60
• Fix for Unused import by @yzx9 in #59
• Fix for Empty except by @00JackLu in #62
• Fix for Empty except by @yzx9 in #63
• Add missing @OverRide annotations by @yzx9 in #58
• Fix for Inefficient String constructor by @yzx9 in #56
• Fix for Boxed variable is never null by @yzx9 in #57
• Fix for Inconsistent equals and hashCode by @yzx9 in #55
• Bump langfuse from v3 to v4 by @yzx9 in #36
• Add agent document, skill and hook by @yzx9 in #64
• Configurable api base by @yzx9 in #29
• Fix dev-plugin failing without prior compile by @yzx9 in #66
• Update agent avatar display in ChatboxReactPosts component by @00JackLu in #32
• Remove detailed numbers by @yzx9 in #31
• Generalize cleanup script to scan all local branches by @yzx9 in #69
• Default GitHub Pages to the homepage and update Home page hero buttons by @yzx9 in #70
• Add local RAG system builder and updater script by @00JackLu in #67
• Install and run the server using the CopilotJ plugin via Appose by @yzx9 in #37
• Bump uuid from 11.1.0 to 14.0.0 in /web by @dependabot[bot] in #72
• Fix final answer output by @00JackLu in #76
• Improve workflow module and enhance execution and validation by @00JackLu in #65
• Configure all entries in the frontend and add setup wizard by @yzx9 in #74
• Disable napari pytest plugin to avoid cache PermissionError by @yzx9 in https://github.com/neurogeom/Copilo...

v1.0.0

The CopilotJ Docker image is too large (~14 GB) to be uploaded to GitHub and is instead provided at copilotj.cvcd.xyz. Users are recommended to build it locally, following the simple instructions in the user manual.