Introduction

Cellseg_gsontools is a Python toolset designed to analyze and summarize large cell and tissue segmentation maps created from Whole Slide Images (WSI). The library is built on top of geopandas and libpysal. In other words, the library can process geospatial data with GeoJSON-interface.

NOTE: The library is synergetic with the cellseg_models.pytorch segmentation library which enables you to segment your WSI into GeoJSON format.

Another NOTE: The library expects that the cell type labels are in a field named class_name in your geojson. If not, you should rename that field to class_name.

Installation

pip install cellseg-gsontools

Citation

@misc{cellseg_gsontools2023,
    title={{cellseg_gsontools}: Tools for feature extraction in cell and tissue segmentation maps.},
    author={Oskari Lehtonen},
    howpublished = {\url{https://github.com/okunator/cellseg_gsontools}},
    doi={https://zenodo.org/doi/10.5281/zenodo.10617987},
    year={2023}
}

Contribute

Any suggestions, feature requests, or bug reports are welcome! Please open a new issue on GitHub for those. If you want to contribute to the codebase, please open a pull request.

Licence

This project is distributed under MIT License

If you find this library useful in your project, it is your responsibility to ensure you comply with the conditions of any dependent licenses. Please create an issue if you think something is missing regarding the licenses.