cellpose-counter 0.1.1

Cell/nuclei counter using cellpose models

cellpose-counter

A Napari plugin for cell/nuclei counting from a region or interest using cellpose models.

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Installation

Option 1: Install in Napari directly under the plugins tab and select cellpose-counter.

Option 2: via pip(or pip alternatives like uv):

# install napari and cellpose-counter plugin
pip install napari[all] cellpose-counter

# or if you prefer uv
uv add "napari[all]" cellpose-counter

Usage

To start, napari, run the cli using napari -w cellpose-counter

Contributing

All contributions are welcome. Please submit an issue for feedback or bugs.

Citations

This plugin is built on top of the Cellpose segmentation and denoising models. If you use this plugin, please cite the following paper:

@article{stringer2021cellpose,
title={Cellpose: a generalist algorithm for cellular segmentation},
author={Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius},
journal={Nature Methods},
volume={18},
number={1},
pages={100--106},
year={2021},
publisher={Nature Publishing Group}
}

License

BSD-3