napari-roxas-ai 0.1.1

A plugin that integrates the ROXAS AI analysis methods for quantitative wood anatomy in the napari platform

napari-roxas-ai

A plugin that integrates the ROXAS AI analysis methods for quantitative wood anatomy in the napari platform

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This napari plugin was generated with copier using the napari-plugin-template.

Installation

Environment setup

It's recommended to create a dedicated Python environment for napari-roxas-ai:

1. Install Miniconda if you don't have it already: Miniconda Installation Guide

2. Create a new environment:

conda create -n roxas-ai python=3.12
conda activate roxas-ai

Installation

Install napari-roxas-ai via pip:

pip install napari-roxas-ai

Launching the plugin

Once installed, you can launch napari with the roxas-ai plugin:

napari

Verifying installation

To check if the plugin is working correctly:

1. Go to File > Open Sample > ROXAS AI in the napari interface.
2. The first time you open a sample, it may take some time as sample data and model weights are being downloaded. Progress will be logged in the terminal.
3. After the downloads, a sample made of three layers should open in the viewer

GPU Support

If you want to use GPU acceleration for model inference:

1. Ensure you have the proper GPU drivers and CUDA installed for your system:

   • NVIDIA CUDA Installation Guide Linux
   • NVIDIA CUDA Installation Guide Windows

2. Enable GPU support in the napari-roxas-ai settings within the napari interface.

3. You may need to reinstall PyTorch with CUDA support for your specific hardware: Visit the PyTorch Installation Guide to find the appropriate installation command for your setup.

Contributing

Contributions are very welcome. Tests are automatically run with tox, please ensure the coverage at least stays the same before you submit a pull request.

Contributor Installation

In order to contribute to the development of the plugin the installation can be done as follows:

1. Create an environment

conda create -n roxas-ai python=3.12
conda activate roxas-ai

2. In the cloned / forked plugin directory, install the plugin dependencies

pip install -e .

3. Install the testing dependencies, as well as the napari plugin engine

pip install -e ".[testing]"
pip install npe2

4. Install pre-commit for quality checks

pip install pre-commit
pre-commit install

Documentation: Plugin Template and Development

You can find more information on the plugin template on the napari-plugin-template repository. You can find more information on plugin contributions and how to create plugins on the plugins section of the napari documentation.

License

Distributed under the terms of the GNU GPL v3.0 license, "napari-roxas-ai" is free and open source software

Issues

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