bioimage-cpp

Image processing and segmentation functionality in C++ with light-weight python bindings through nanobind and minimal dependencies to enable distribution via pip.

The package includes dependency-free triangle-mesh extraction from 3D volumes and segmentation masks, plus Laplacian mesh smoothing, under bioimage_cpp.mesh. It also includes exact masked-grid Dijkstra paths under bioimage_cpp.distance and binary-forest plus semantic multi-label 3D TEASAR skeletonization under bioimage_cpp.skeleton.

The bioimage_cpp python library can be installed via pip:

pip install bioimage-cpp

Or via conda-forge:

conda install -c conda-forge bioimage-cpp

Please refer to the documentation for details.

Disclaimer: The functionality of this library was implemented mainly by coding agents (Claude Code and OpenAI Codex). We have made our best efforts to test the implementations thoroughly and are already using it heavily in our day-to-day research and have integrated with other software tools. Nevertheless, it may contain bugs or unintended behavior (as most software does). If you find such a problem, please open an issue on github. We are committed to improving and mainting this software.