napari-morphodynamics

This plugin offers an interface for the Morphodynamics package which allows to study the shape and intra-cellular dynamics of cells imaged as time-lapses by fluorescence microscopy. The plugin offers a single place to perfrom segmentation, windowing (partition cells into small regions of interests that are tracked over time) and results visualization. The software depends on napari-convpaint a pixel-classifier and/or on cellpose for segmentation.

Installation¶

You can install the plugin via pip with:

pip install napari-morphodynamics

To install latest development version :

pip install git+https://github.com/guiwitz/napari-morphodynamics.git

Contributing¶

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License¶

Distributed under the terms of the BSD-3 license, "napari-morphodynamics" is free and open source software

Authors¶

This plugin has been developed by Guillaume Witz and Ana Stojiljkovic at the Data Science Lab, University of Bern, in collaboration with Lucien Hinderling and Olivier Pertz from the Pertz Lab, University of Bern. Development has been partially funded by a Chan Zuckerberg Initiative grant.

Issues¶

If you encounter any problems, please file an issue along with a detailed description.