allencell-segmenter-ml
A plugin to leverage ML segmentation in napari
What is Allen Cell Segmenter ML¶
A napari plugin for deep-learning based segmentation of cellular structures.
- Available at no cost — available on PyPI
- User-friendly — leverage napari as a fast 3D viewer with interactive plugin interface
- Beginner-friendly — new to machine learning? This plugin simplifies the application of machine learning in the segmentation process through the 3 main modules:
- Curation: curate training datasets
- Training: iteratively train custom segmentation model(s) (UNET) to target cellular structure with wide morphological variability
- Prediction & Thresholding: generate segmentation prediction on 2D and 3D cell image data
📰 News¶
- [2024.09.24] :tada: Initial release of the plugin and Megaseg models!
- [2024.05.29] :tada: v1.0.0 Released on PyPi
User Documentation¶
See our full user documentation on our github pages site.
🛠️ Installation¶
System and Data Requirements¶
Please click here to check out our latest System and Data requirements.
Installation Steps¶
Please click here for our latest installation steps.
Models¶
License¶
Distributed under the terms of the Allen Institute Software License.
Issues¶
If you encounter any problems, please file an issue along with a detailed description.
Version:
- 1.0.0
Last updated:
- 29 May 2025
First released:
- 20 September 2024
License:
- Allen Institute Software License – This software license is the 2-clause BSD license plus clause a third clause that prohibits redistribution for commercial purposes without further permission. Copyright © 2024. Allen Institute. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. 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. 3. Redistributions for commercial purposes are not permitted without the Allen Institute’s written permission. For purposes of this license, commercial purposes is the incorporation of the Allen Institute's software into anything for which you will charge fees or other compensation. Contact terms@alleninstitute.org for commercial licensing opportunities. 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: 3
- Forks: 1
- Issues + PRs: 169