cuCIM

RAPIDS cuCIM is an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image processing primitives for N-Dimensional images with a focus on biomedical imaging.

NOTE: For the latest stable README.md ensure you are on the main branch.

• GTC 2021 cuCIM: A GPU Image I/O and Processing Toolkit [S32194]
  • video

Install cuCIM

Conda

Conda (stable)

conda create -n cucim -c rapidsai -c conda-forge/label/cupy_rc -c conda-forge cucim cudatoolkit=<CUDA version>

<CUDA version> should be 11.0+ (e.g., 11.0, 11.2, etc.)

NOTE: The first cuCIM conda package (v0.19.0) would be available on 4/19/2021.

Conda (nightlies)

conda create -n cucim -c rapidsai-nightly -c conda-forge/label/cupy_rc -c conda-forge cucim cudatoolkit=<CUDA version>

<CUDA version> should be 11.0+ (e.g., 11.0, 11.2, etc)

Notebooks

Please check out our Welcome notebook.

Downloading sample images

To download images used in the notebooks, please execute the following commands from the repository root folder to copy sample input images into notebooks/input folder:

(You will need Docker installed in your system)

./run download_testdata

or

mkdir -p notebooks/input
tmp_id=$(docker create gigony/svs-testdata:little-big)
docker cp $tmp_id:/input notebooks
docker rm -v ${tmp_id}

Build/Install from Source

See build instructions.

Contributing Guide

Contributions to cuCIM are more than welcome! Please review the CONTRIBUTING.md file for information on how to contribute code and issues to the project.

Acknowledgments

Without awesome third-party open source software, this project wouldn't exist.

Please find LICENSE-3rdparty.md to see which third-party open source software is used in this project.

License

Apache-2.0 License (see LICENSE file).

Copyright (c) 2020-2021, NVIDIA CORPORATION.