napari-morphodynamics 0.1.2
Interface to run the morphodynamics package.
License: BSD-3-Clause
Requires Python: >=3.9

# napari-morphodynamics

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This plugin offers an interface for the [Morphodynamics](https://github.com/guiwitz/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](https://github.com/guiwitz/napari-convpaint) a pixel-classifier and/or on [cellpose](https://cellpose.readthedocs.io/en/latest/index.html) 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](https://chanzuckerberg.com/science/programs-resources/imaging/napari/napari-morphodynamics-a-plugin-to-quantify-cellular-dynamics/).

## Issues

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

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[file an issue]: https://github.com/guiwitz/napari-morphodynamics/issues

[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/