LangSlice

LangSlice gives a vision-language agent tools to register a stack of histology sections to a BrainGlobe atlas. The agent inspects the anatomy, sets positions and cutting angles, aligns sections in-plane, and optionally fits SyN deformations. It chooses regions and settings and can use an image model to trace borders where useful.

Source images stay unchanged. Work is checkpointed and undoable, with coordinate and label maps, registration.json, and QuickNII / VisuAlign exports. Coronal sections of the Allen mouse atlas are the most tested case.

Install

Download and extract the source, open a terminal in the folder with environment.yml, then:

conda env create -f environment.yml
conda activate langslice
langslice login        # ChatGPT sign-in; or set OPENAI_API_KEY / GEMINI_API_KEY (see .env.example)

On Windows, run the same conda env create and conda activate commands in Miniforge Prompt or PowerShell with conda initialized. Python 3.11 on Windows is tested in CI. Atlases are downloaded by BrainGlobe on first use into the user's .brainglobe folder. Python 3.11 or newer is required; the environment includes the deformable engine (FireANTs on torch), the Claude Desktop server and the ABBA launcher.

Use LangSlice

• Getting started: install LangSlice and connect the AI app you already use (Codex, Antigravity or Claude Code).
• Agents, CLI and MCP: Claude Code, Antigravity or Codex through langslice-job, Claude Desktop through MCP, or the built-in agent with langslice linear run sections/.
• ABBA: register selected sections through the Fiji connector and review changes in ABBA.
• Python: coding agents can open a job and write their own workflows using the same tools.

Tools and options · Tool plugins · File formats · Architecture · Full documentation

Citation and license

Cite the project metadata in CITATION.cff (GitHub's "Cite this repository" button). BSD-3-Clause; see LICENSE.