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.