This plugin is still under development. It serves as a toolbox for segmentation and analysis of luminal structures.
The plugin heavily relies on several very useful open source packages and other napari plugins:
- orthogonal view widget: napari multiple viewer widget
- table widget: napari-skimage-regionprops
- geodesic distances: DIPlib
- skeleton analysis: Skan
- local thickness measurements: localthickness
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
You can install napari-lumen-segmentation via pip:
To install latest development version :
pip install git+https://github.com/AnniekStok/napari-lumen-segmentation.git
The 'Orthogonal Views' tab shows the xy and xz views, implementing the napari multiple viewer widget: napari multiple viewer widget
The 'Segmentation' tab aims to offer various tools for segmentation and measuring the size of the objects. The measured properties of the selected label mask can be viewed in the 'Label Plots' tab.
The 'Skeleton Analysis' tab implements skeletonization (skimage.morphology.skeletonize) of the selected label image, and displays skeleton properties (Skan)
The 'Distance Analysis' tab implements geodesic distance measurements from DIPlib, calculating distance maps that reflect the geodesic distance of any pixel on the 'mask' layer to pixels on the 'marker' layer. The marker can be either a Points layer or a Label layer. In case of a Label layer or a single points layer, the geodesic distance map will be added to the viewer. In case of a multi-point Points layer, the euclidean and geodesic distances from each point to each other point are calculated, and visualized in a table and plot.
The 'Calculate local thickness' button serves to run the 'local_thickness' function from localthickness on the selected Labels layer. In the resulting image, the voxel intensity reflects the local thickness of the foreground mask.
Note that voxel anisotropy is NOT taken into account here, and that all measurements are in voxels. Data should therefore be rescaled to isotropic dimensions before using this plugin.
Distributed under the terms of the BSD-3 license, "napari-lumen-segmentation" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.