A Napari plugin allowing to detect and segment microglia on fluorescent images.
It consists in:
- Detecting the microglia with a YOLOv5 model.
- Segmenting them with a UNet model.
- Using some morphology to extract metrics such as:
- The total length
- The length of the longest path
- The number of leaves
- The number of vertices
- Area of the convex hull
- Solidity/extent
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
You can install microglia-analyzer via pip:
pip install microglia-analyzer
To install latest development version :
pip install git+https://github.com/MontpellierRessourcesImagerie/microglia-analyzer.git
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the MIT license, "microglia-analyzer" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.