Metadata-Version: 2.1
Name: cellpose-counter
Version: 0.1.2
Summary: Cell/nuclei counter using cellpose models
Author: Nicolas Buitrago
Author-email: nsb5@rice.edu
License: 
        Copyright (c) 2024, Szablowski Lab
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of copyright holder nor the names of its
          contributors may be used to endorse or promote products derived from
          this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: qtpy
Requires-Dist: scikit-image
Requires-Dist: napari[all]>=0.5.4
Requires-Dist: cellpose>=3.1.0
Provides-Extra: testing
Requires-Dist: tox; extra == "testing"
Requires-Dist: pytest; extra == "testing"
Requires-Dist: pytest-cov; extra == "testing"
Requires-Dist: pytest-qt; extra == "testing"
Requires-Dist: napari; extra == "testing"
Requires-Dist: pyqt5; extra == "testing"

# cellpose-counter

[![License BSD-3](https://img.shields.io/pypi/l/cellpose-counter.svg?color=green)](https://github.com/szablowskilab/cellpose-counter/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/cellpose-counter.svg?color=green)](https://pypi.org/project/cellpose-counter)
[![Python Version](https://img.shields.io/pypi/pyversions/cellpose-counter.svg?color=green)](https://python.org)
[![tests](https://github.com/szablowskilab/cellpose-counter/workflows/tests/badge.svg)](https://github.com/szablowskilab/cellpose-counter/actions)
[![codecov](https://codecov.io/gh/szablowskilab/cellpose-counter/branch/main/graph/badge.svg)](https://codecov.io/gh/szablowskilab/cellpose-counter)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/cellpose-counter)](https://napari-hub.org/plugins/cellpose-counter)

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

----------------------------------

## Installation

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

Option 2: via [pip](https://pip.pypa.io/en/stable/)(or pip alternatives like
[uv](https://docs.astral.sh/uv/)):

```bash
# 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:

```bitex
@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](./LICENSE)
