Register histological brain sections to BrainGlobe atlases using vision-language and image-generation models.
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正在加载完整 README。 以下为已保存的摘录。
Agent-driven registration of histological brain sections to BrainGlobe atlases.
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 ANTs deformations. It chooses regions and settings and
can use an image model to trace borders where useful.查看完整 README ↗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.
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.
langslice-job, Claude Desktop through MCP, or the built-in agent with
langslice linear run sections/.Tools and options · Tool plugins · File formats · Architecture · Full documentation
Cite the project metadata in CITATION.cff (GitHub's "Cite this
repository" button). BSD-3-Clause; see LICENSE.