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.
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+https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter.git
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] 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
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:
@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}
}