napari-morphodynamics

napari-morphodynamics

Interface to run the morphodynamics package.

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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.

Version:

  • 0.1.2

Last updated:

  • 22 January 2024

First released:

  • 08 November 2023

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 3
  • Forks: 1
  • Issues + PRs: 4

Python versions supported:

Operating system:

Requirements:

  • morphodynamics
  • napari-convpaint
  • napari-guitils
  • napari-matplotlib

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