napari-maskel

Simon Wittmann, Dominik Pysch, Stefan Uderhardt, David B. Blumenthal, Anna Möller

napari plugin for maskel: skeletonization and graph-based feature extraction for branching biological structures — vasculature, fibers, neurites, and other network-like objects — with interactive visualization of branches and node features.

Quick start

1. Install napari itself first if you haven't, with a Qt backend (e.g. pip install "napari[all]"), then the plugin: pip install napari-maskel (this also installs maskel).
2. In napari, open a segmentation mask (2D or 3D) and convert it to a labels layer.
3. Run Analyze mask (Maskel) from the Plugins menu, pick that layer as the input, and configure the extraction/cleanup parameters.
4. Click Analyze mask to add the resulting branches/nodes/summary/radius layers to the viewer, and inspect them with napari's built-in feature table widget.

See the full documentation for every configurable parameter, the 2D multi-label workflow, and sharing recipes with the maskel CLI for batch processing.

License

napari-maskel is released under the MIT License. See LICENSE for details.