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A plugin to automatically count lung organoids

Project description

Napari Organoid Counter - Version 0.2 is out!

stability-stable DOI License PyPI Python Version tests codecov napari hub

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

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


You can install napari-organoid-counter via pip:

pip install napari-organoid-counter

To install latest development version :

pip install git+

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

pip install -e .  

For installing on a Windows machine via napari, follow the instuctions here.

What's new in v2?

Checkout our What's New in v2 here.

How to use?

After installing, you can start napari (either by typing napari in your terminal or by launching the application) and select the plugin from the drop down menu.

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


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.


Distributed under the terms of the MIT license, "napari-organoid-counter" is free and open source software


napari-organoid-counter uses the napari-aicsimageio[1] [2] plugin for reading and processing CZI images.

[1] Eva Maxfield Brown, Dan Toloudis, Jamie Sherman, Madison Swain-Bowden, Talley Lambert, AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub.

[2] Eva Maxfield Brown, Talley Lambert, Peter Sobolewski, Napari-AICSImageIO Contributors (2021). Napari-AICSImageIO: Image Reading in Napari using AICSImageIO [Computer software]. GitHub.


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


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

Christina Bukas, Harshavardhan Subramanian, & Marie Piraud. (2023). HelmholtzAI-Consultants-Munich/napari-organoid-counter: v0.2.0 (v0.2.0). Zenodo.


  author       = {Christina Bukas, Harshavardhan Subramanian, & Marie Piraud},
  title        = {{HelmholtzAI-Consultants-Munich/napari-organoid- 
                   counter: second release of the napari plugin for lung
                   organoid counting}},
  month        = apr,
  year         = 2023,
  publisher    = {Zenodo},
  version      = {v0.2.0},
  doi          = {10.5281/zenodo.7859571},
  url          = {}

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