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.
