Register histological brain sections to BrainGlobe atlases.
A VLM estimates position, an image-gen model lays down atlas colors, Elastix warps the rest.

Warning

LangSlice is in-development. Some atlases may produce mixed results; and horizontal and sagittal orientations haven't yet been thoroughly tested. LangSlice does not offer manual registration methods — it is meant to be used in combination with other registration software (ABBA, QUINT, PyNutil, BrainGlobe ecosystem, etc.). Export functions to these tools have not been fully developed yet.

How it works

A VLM agent (default langslice-gemma-4-E4B) inspects the slice, explores candidate atlas planes through tool calls, and submits an AP coordinate. Image generation then produces an atlas-colored target from the histology, and itk-elastix recovers a dense B-spline deformation. Results export to VisuAlign-compatible JSON for QUINT / ABBA.

Quick start

conda env create -f environment.yml
conda activate langslice
pip install -e .
cp .env.example .env  # add AI Studio / Vertex / OpenAI keys

# Position estimation
langslice estimate slice.png

# End-to-end registration at a known atlas position
langslice register slice.png --position 3.9

Full CLI: langslice --help. Pipeline detail: docs/index.md.

Model Hub

LangSlice hosts training/data helpers in shared packages under models/:

• models/langslice-traces/langslice_traces
• models/training-core/langslice_training
• models/data/langslice_data

Training entrypoints are exposed as model-scoped launchers: langslice-gemma-rl and langslice-gemma-sft.

Public model-card metadata for the released variant is in models/langslice-gemma-4/variants/langslice-gemma-4-e4b/README.md.

Links

• Documentation — full pipeline + harness internals
• langslice-gemma-4-E4B — the v1.0 fine-tune
• SliceBench — self-contained position-estimation benchmark
• tauri-gui/ — desktop app

Citation

If you use LangSlice in your work, please cite the project metadata in CITATION.cff. GitHub renders a "Cite this repository" button in the right sidebar from that file.

License

BSD-3-Clause. See LICENSE.