CellPose Counter
Cell/nuclei counter using cellpose models
Workflow step:
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(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-counterUsage¶
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¶
Version:
- 0.1.0
Last updated:
- 21 November 2024
First released:
- 21 November 2024
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 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Supported data:
- Information not submitted
Plugin type:
GitHub activity:
- Stars: 0
- Forks: 0
- Issues + PRs: 0