From a65daf5a41ee261cb8b2f406c825f61a16cf2e58 Mon Sep 17 00:00:00 2001 From: gpuCI <38199262+GPUtester@users.noreply.github.com> Date: Wed, 12 Oct 2022 14:45:49 +0000 Subject: [PATCH] REL v22.10.00 release --- python/cucim/README.md | 114 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 113 insertions(+), 1 deletion(-) mode change 120000 => 100644 python/cucim/README.md diff --git a/python/cucim/README.md b/python/cucim/README.md deleted file mode 120000 index fe8400541..000000000 --- a/python/cucim/README.md +++ /dev/null @@ -1 +0,0 @@ -../../README.md \ No newline at end of file diff --git a/python/cucim/README.md b/python/cucim/README.md new file mode 100644 index 000000000..b4e6ffc79 --- /dev/null +++ b/python/cucim/README.md @@ -0,0 +1,113 @@ +#
 cuCIM
+ +[RAPIDS](https://rapids.ai) cuCIM is an open-source, accelerated computer vision and image processing software library for multidimensional images used in biomedical, geospatial, material and life science, and remote sensing use cases. + +cuCIM offers: + +- Enhanced Image Processing Capabilities for large and n-dimensional tag image file format (TIFF) files +- Accelerated performance through Graphics Processing Unit (GPU)-based image processing and computer vision primitives +- A Straightforward Pythonic Interface with Matching Application Programming Interface (API) for Openslide + +cuCIM supports the following formats: + +- Aperio ScanScope Virtual Slide (SVS) +- Philips TIFF +- Generic Tiled, Multi-resolution RGB TIFF files with the following compression schemes: + - No Compression + - JPEG + - JPEG2000 + - Lempel-Ziv-Welch (LZW) + - Deflate + +**NOTE:** For the latest stable [README.md](https://github.com/rapidsai/cucim/blob/main/README.md) ensure you are on the `main` branch. + +- [GTC 2022 Accelerating Storage IO to GPUs with Magnum IO [S41347]](https://events.rainfocus.com/widget/nvidia/gtcspring2022/sessioncatalog/session/1634960000577001Etxp) + - cuCIM's GDS API examples: +- [SciPy 2021 cuCIM - A GPU image I/O and processing library](https://www.scipy2021.scipy.org/) + - [video](https://youtu.be/G46kOOM9xbQ) +- [GTC 2021 cuCIM: A GPU Image I/O and Processing Toolkit [S32194]](https://www.nvidia.com/en-us/on-demand/search/?facet.mimetype[]=event%20session&layout=list&page=1&q=cucim&sort=date) + - [video](https://www.nvidia.com/en-us/on-demand/session/gtcspring21-s32194/) + +**[Developer Page](https://developer.nvidia.com/multidimensional-image-processing)** + +**Blogs** +- [Enhanced Image Analysis with Multidimensional Image Processing](https://developer.nvidia.com/blog/enhanced-image-analysis-with-multidimensional-image-processing/) +- [Accelerating Scikit-Image API with cuCIM: n-Dimensional Image Processing and IO on GPUs](https://developer.nvidia.com/blog/cucim-rapid-n-dimensional-image-processing-and-i-o-on-gpus/) +- [Accelerating Digital Pathology Pipelines with NVIDIA Clara™ Deploy](https://developer.nvidia.com/blog/accelerating-digital-pathology-pipelines-with-nvidia-clara-deploy-2/) + +**Webinars** + +- [cuCIM: a GPU Image IO and Processing Library](https://www.youtube.com/watch?v=G46kOOM9xbQ) + +**[Documentation](https://docs.rapids.ai/api/cucim/stable)** + +**Release notes** are available on our [wiki page](https://github.com/rapidsai/cucim/wiki/Release-Notes). + +## Install cuCIM + +### Conda + +#### [Conda (stable)](https://anaconda.org/rapidsai/cucim) + +> conda create -n cucim -c rapidsai -c conda-forge cucim cudatoolkit=`` + +`` should be 11.0+ (e.g., `11.0`, `11.2`, etc.) + +#### [Conda (nightlies)](https://anaconda.org/rapidsai-nightly/cucim) + +> conda create -n cucim -c rapidsai-nightly -c conda-forge cucim cudatoolkit=`` + +`` should be 11.0+ (e.g., `11.0`, `11.2`, etc) + +### [PyPI](https://pypi.org/project/cucim/) + +```bash +pip install cucim + +# Install dependencies for `cucim.skimage` (assuming that CUDA 11.0 is used for CuPy) +pip install scipy scikit-image cupy-cuda110 +``` + +### Notebooks + +Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-22.10/notebooks/Welcome.ipynb)) + +#### 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](https://www.docker.com/) installed in your system) + +```bash +./run download_testdata +``` +or + +```bash +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.md#setting-up-your-build-environment). + +## Contributing Guide + +Contributions to cuCIM are more than welcome! +Please review the [CONTRIBUTING.md](https://github.com/rapidsai/cucim/blob/main/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](LICENSE-3rdparty.md) to see which third-party open source software +is used in this project. + +## License + +Apache-2.0 License (see [LICENSE](LICENSE) file). + +Copyright (c) 2020-2022, NVIDIA CORPORATION.