napari-organoid-counter 0.2.0

A plugin to automatically count lung organoids

Napari Organoid Counter - Version 0.2 is out!

A napari plugin to automatically count lung organoids from microscopy imaging data. Note that this only works for one channel grayscale images.

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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

For the dev branch you can clone this repo and install with:

pip install -e .  

Then run napari on your terminal.

What's new in v2?

Checkout our What's New in v2 here.

How to use?

For more information on this plugin, its' intended audience, as well as Quickstart guide go to our Quickstart guide.

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}
}