A simple plugin that implements Nagini3D inference tools 3D biological segmentation.
Project description
nagini3d-napari
A simple plugin that implements Nagini3D inference tools for segmenting 3D biological images.
This napari plugin was generated with copier using the napari-plugin-template (None).
Installation
You can install nagini3d-napari via pip:
pip install nagini3d-napari
If napari is not already installed, you can install nagini3d-napari with napari and Qt via:
pip install "nagini3d-napari[all]"
Installation advice
We recommend installing our plugin on a clean Python environment (Python 3.9 to 3.11 prefered), to avoid any conflict with other packages.
- Create and activate the environment with:
python -m venv <path-to-new-virtual-environment>
source <path-to-new-virtual-environment>/bin/activate
- Download the package in the new env with
pip install "nagini3d-napari[all]"
- Launch Napari
napari
- Activate NAGINI3D in the plugin manager.
Models weights and testing images
An archive containing model weigths trained on different datasets and testing images are available on zenodo at https://zenodo.org/records/17909858.
Documentation
The GitHub project containing all the documentation is available at https://github.com/QuentinRapilly/NAGINI-3D.
Contributing
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.
License
Distributed under the terms of the GNU GPL v3.0 license, "nagini3d-napari" is free and open source software
Issues
If you encounter any problems, please file an issue along with a detailed description.
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