napari-cupy-image-processing

napari-cupy-image-processing

GPU-accelerated image processing using CUDA

Workflow step:
Image segmentationConnected-component analysis
Image correctionIllumination correction
Image correction
Image reconstructionImage denoising
Image enhancementImage denoising
Image segmentationImage thresholding
Image segmentation
Image enhancementSmoothing
Morphological operations
Image segmentationSemi-automatic segmentation
Image feature detectionEdge detection
Morphological operationsTop-hat transform
Morphological operationsClosing
Morphological operationsDilation
Morphological operationsOpening
Morphological operationsErosion
Image enhancement

License PyPI Python Version tests codecov Development Status napari hub

GPU-accelerated image processing using cupy and CUDA

Usage

This napari plugin adds some menu entries to the Tools menu. You can recognize them with their suffix (n-cupy) in brackets. 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.

img.png

You can also call operations from python, e.g. as shown in this demo notebook.

Installation

Follow the instructions for installing cupy on your computer first.

conda install -c conda-forge cupy

Afterwards, you can install napari-cupy-image-processing via pip:

pip install napari-cupy-image-processing

A more detailed example for installation (change 11.2 to your desired CUDA version):

conda create --name cupy_p39 python=3.9
conda activate cupy_p39
conda install -c conda-forge cupy cudatoolkit=11.2 napari
pip install napari-cupy-image-processing

Contributing

Contributions are very welcome. Adding cupy ndimage functions is quite easy as you can see in the implementation of the current operations. If you need another function in napari, just send a PR. Please make sure the tests pass locally before submitting a PR.

pip install pytest-cov pytest-qt
pytest --cov=napari_cupy_image_processing

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

License

Distributed under the terms of the MIT license, "napari-cupy-image-processing" is free and open source software

Issues

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

Version:

  • 0.3.1

Last updated:

  • 27 August 2022

First released:

  • 22 October 2021

License:

  • MIT

Supported data:

Plugin type:

GitHub activity:

  • Stars: 17
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • numpy
  • toolz
  • cupy
  • napari-tools-menu
  • scikit-image
  • napari-time-slicer (>=0.4.8)
  • napari-skimage-regionprops
  • napari-assistant
  • stackview (>=0.3.2)

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