Allencell-segmenter-ml

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] 🎉 Initial release of the plugin and Megaseg models!
• [2024.05.29] 🎉 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

More information about the pre-trained models we provide with our plugin, and citation information, can be found here.

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.