napari-deepmeta

Mice lungs and metastases segmentation tool. This tool is a demo tool for DeepMeta network.

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-deepmeta via pip:

pip install napari-deepmeta

To install latest development version :

pip install git+https://github.com/EdgarLefevre/napari-deepmeta.git

Usage

This plugin is designed to process your mouse MRI images with our dataset. It comes with a demo, including one of our test images.

By opening the deepmeta demo plugin, you will see an interface with one unique button, by clicking on it, it will load an image, run prediction and then draw the masks contours on each slice.

If you open the deepmeta plugin, you will see an interface with one button and 3 checkboxes. By checking the checkboxes, you add steps to the pipeline (enhance contrast, do postprocessing, segment metastases). Once everything is setup, just click on the button and wait (the waiting time depends on your computer performance.)

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 MIT license, "napari-deepmeta" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.