napari-imagegrains

An interactive napari plugin for the ImageGrains software.

Installation

We recommend to install the plugin in an isolated environment as provided by conda. For conda create an appropriate environment with (do not use Python more recent than 3.11):

conda create -n napari-imagegrains -c conda-forge python=3.11 napari pyqt
conda activate napari-imagegrains
pip install napari-imagegrains

To install latest development version :

pip install git+https://github.com/guiwitz/napari-imagegrains.git

Or if you want to contribute to the plugin, fork the repository, clone it locally and install it in editable mode:

pip install -e .

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 BSD-3 license, "napari-imagegrains" is free and open source software

Issues

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

Authors

The original software ImageGrain was developed by David Mair, Institute of Geological Sciences, University of Bern. The current plugin, a user-interface for the ImageGrains software, was developed by Guillaume Witz and Michael Horn, Data Science Lab, University of Bern in collaboration with David Mair.

Citation

If you use this software, please cite the following publication: Mair, D., Witz, G., Do Prado, A.H., Garefalakis, P. & Schlunegger, F. (2023) Automated detecting, segmenting and measuring of grains in images of fluvial sediments: The potential for large and precise data from specialist deep learning models and transfer learning. Earth Surface Processes and Landforms, 1–18. https://doi.org/10.1002/esp.5755.