3D Tissue Map Tools

a python toolkit to create 3D Tissue Maps

🚧The library is still under development, breaking changes may occur! 🚧

tissue-map-tools is a python toolkit to create scalable 3D Tissue Maps from 3D OME-NGFF volumes and segmentation masks, and 3D SpatialData objects.

• Fast ⚡, building upon scalable and adaptive data formats like OME-NGFF and the Neuroglancer Precomputed Format, the mesh representation is fast and reliable.
• Interactive, users can view results of the toolkit from the browser using Vitessce.
• Adaptive, users can adapt parameters like the sharding, chunking and spatial indexing factors to their needs.
• Reproducible, our pipeline is fully deterministic delivering the same results for every run.

Contact us

Feedback or collaborations are very welcome! Please open a GitHub issue or contact us via direct message in the scverse Zulip.

Install

pip install tissue-map-tools

Usage

Please see the examples folder.

License

The project is licensed under BSD 3-Clause License. Please note that one of the optional dependencies, igneous-pipeline, is licensed under GPL-3.0. This implies that if you use igneous-pipeline as part of your workflow, you are required to comply with both the terms of the BSD 3-Clause License and the GPL-3.0 license.

The code from igneous-pipeline is used for certain meshing operations and exposed in a detached module igneous_converter. If GPL-3.0 is not compatible with your use case, you can still use the rest of the tissue-map-tools package without any restrictions, and replace the meshing functionality with your own implementation.

Development

Editable install

uv venv
source .venv/bin/activate
# install with specific dependency groups
uv sync --group examples --group dev --group test
# note: calling `uv sync` is equivalent to the above since
# `tool.uv.default-groups = ["examples", "dev", "test"]` in `pyproject.toml`

Adding/removing packages

uv add <package_name>
uv remove <package_name>
# to add/remove to a group
uv add --group <group_name> <package_name>
# shortcut to add/remove to the dev group
uv add --dev <package_name>

Building the package for distribution

uv build

Using pre-commit.

# install
pre-commit install

# pre-commit are run automatically on commit; you can run on request with
pre-commit run --all-files

# to commit without running pre-commit hooks
git commit --no-verify