Process images using the Hydra Image Processor and CUDA-compatible graphics cards in napari
Filters provided by this napari plugin can be found in the Tools menu.
You can recognize them with their suffix (n-HIP).
Furthermore, it can be used from the napari-assistant graphical user interface.
Therefore, just click the menu Tools > Utilities > Assistant (na) or run naparia from the command line.
All filters implemented in this napari plugin are also demonstrated in this notebook.
You can install napari-hydra-image-processor via using mamba/conda and pip.
If you have never used conda before, please go through this tutorial first.
mamba create --name napari_hip_env python=3.9 cudatoolkit=11.2 napari -c conda-forge
conda activate napari_hip_env
pip install napari-hydra-image-processor
There are other napari plugins with similar functionality for processing images and extracting features:
- napari-skimage-regionprops
- napari-cupy-image-processing
- napari-simpleitk-image-processing
- napari-pyclesperanto-assistant
- napari-allencell-segmenter
- RedLionfish
- bbii-decon
- napari-segment-blobs-and-things-with-membranes
Contributions are very welcome.
Distributed under the terms of the BSD-3 license, "napari-hydra-image-processor" is free and open source software
This napari plugin uses the HIP infrastructure published in this paper:
Wait, E., Winter, M. & Cohen, A. R. Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers. Bioinformatics (2019). doi:10.1093/bioinformatics/btz523
If you encounter any problems, please file an issue along with a detailed description.