ROXAS AI
A plugin that integrates the ROXAS AI analysis methods for quantitative wood anatomy in the napari platform
A plugin that integrates the ROXAS AI analysis methods for quantitative wood anatomy in the napari platform
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:
-
Install Miniconda if you don't have it already: Miniconda Installation Guide
-
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:
- Go to
File > Open Sample > ROXAS AIin the napari interface. - 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.
- 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:
-
Ensure you have the proper GPU drivers and CUDA installed for your system:
-
Enable GPU support in the napari-roxas-ai settings within the napari interface.
-
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:
- Create an environment
conda create -n roxas-ai python=3.12
conda activate roxas-ai
- In the cloned / forked plugin directory, install the plugin dependencies
pip install -e .
- Install the testing dependencies, as well as the napari plugin engine
pip install -e ".[testing]"
pip install npe2
- 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.
Version:
- 0.1.2
Last updated:
- 2025-06-19
First released:
- 2025-05-17
License:
- GNU GENERAL PUBLIC LICENSE ...
Supported data:
- Information not submitted
Plugin type:
Save extension:
Operating system:
- Information not submitted
Requirements:
- magicgui==0.10.0
- napari[all]==0.5.6
- numpy<=2.1.3,>=2.0.2
- opencv-contrib-python-headless==4.11.0.86
- qtpy==2.4.3
- rasterio==1.4.3
- scikit-image<=0.25.2,>=0.24.0
- matplotlib<=3.10.1,>=3.9.4
- torch<2.7.0,>=2.2.0; sys_platform == "linux" and platform_machine == "x86_64"
- torchvision==0.21.0; sys_platform == "linux" and platform_machine == "x86_64"
- torch<2.7.0,>=2.2.0; sys_platform == "win32" and platform_machine == "AMD64"
- torchvision==0.21.0; sys_platform == "win32" and platform_machine == "AMD64"
- torch<2.7.0,>=2.4.0; sys_platform == "darwin" or platform_machine == "arm64"
- torchvision==0.21.0; sys_platform == "darwin" or platform_machine == "arm64"
- pytorch-lightning==2.5.1
- segmentation-models-pytorch==0.4.0
- albumentations==2.0.5
- hydra-core==1.3.2
- tox==4.25.0; extra == "testing"
- pytest==8.3.5; extra == "testing"
- pytest-cov==6.0.0; extra == "testing"
- pytest-qt==4.4.0; extra == "testing"
- napari==0.5.6; extra == "testing"
- pyqt5==5.15.11; extra == "testing"