napari-organoid-counter

A napari plugin to automatically count lung organoids from microscopy imaging data. The original implementation can be found in the Organoid-Counting repository, which has been adapted here to work as a napari plugin.

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This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-organoid-counter via pip:

pip install napari-organoid-counter

To install latest development version :

pip install git+https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter.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 MIT license, "napari-organoid-counter" is free and open source software

Dependencies

napari-organoid-counter uses the napari-aicsimageio^[1] plugin for reading and processing CZI images.

[1] AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio

Issues

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

Citing

If you use this plugin for your work, please cite it using the following:

@software{christina_bukas_2022_6457904,
  author       = {Christina Bukas},
  title        = {{HelmholtzAI-Consultants-Munich/napari-organoid- 
                   counter: first release of napari plugin for lung
                   organoid counting}},
  month        = apr,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v0.1.0-beta},
  doi          = {10.5281/zenodo.6457904},
  url          = {https://doi.org/10.5281/zenodo.6457904}
}