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| 1 | +# <div align="left"><img src="https://rapids.ai/assets/images/rapids_logo.png" width="90px"/> cuCIM</div> |
| 2 | + |
| 3 | +[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. |
| 4 | + |
| 5 | +cuCIM offers: |
| 6 | + |
| 7 | +- Enhanced Image Processing Capabilities for large and n-dimensional tag image file format (TIFF) files |
| 8 | +- Accelerated performance through Graphics Processing Unit (GPU)-based image processing and computer vision primitives |
| 9 | +- A Straightforward Pythonic Interface with Matching Application Programming Interface (API) for Openslide |
| 10 | + |
| 11 | +cuCIM supports the following formats: |
| 12 | + |
| 13 | +- Aperio ScanScope Virtual Slide (SVS) |
| 14 | +- Philips TIFF |
| 15 | +- Generic Tiled, Multi-resolution RGB TIFF files with the following compression schemes: |
| 16 | + - No Compression |
| 17 | + - JPEG |
| 18 | + - JPEG2000 |
| 19 | + - Lempel-Ziv-Welch (LZW) |
| 20 | + - Deflate |
| 21 | + |
| 22 | +**NOTE:** For the latest stable [README.md](https://github.com/rapidsai/cucim/blob/main/README.md) ensure you are on the `main` branch. |
| 23 | + |
| 24 | +- [GTC 2022 Accelerating Storage IO to GPUs with Magnum IO [S41347]](https://events.rainfocus.com/widget/nvidia/gtcspring2022/sessioncatalog/session/1634960000577001Etxp) |
| 25 | + - cuCIM's GDS API examples: <https://github.com/NVIDIA/MagnumIO/tree/main/gds/readers/cucim-gds> |
| 26 | +- [SciPy 2021 cuCIM - A GPU image I/O and processing library](https://www.scipy2021.scipy.org/) |
| 27 | + - [video](https://youtu.be/G46kOOM9xbQ) |
| 28 | +- [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) |
| 29 | + - [video](https://www.nvidia.com/en-us/on-demand/session/gtcspring21-s32194/) |
| 30 | + |
| 31 | +**[Developer Page](https://developer.nvidia.com/multidimensional-image-processing)** |
| 32 | + |
| 33 | +**Blogs** |
| 34 | +- [Enhanced Image Analysis with Multidimensional Image Processing](https://developer.nvidia.com/blog/enhanced-image-analysis-with-multidimensional-image-processing/) |
| 35 | +- [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/) |
| 36 | +- [Accelerating Digital Pathology Pipelines with NVIDIA Clara™ Deploy](https://developer.nvidia.com/blog/accelerating-digital-pathology-pipelines-with-nvidia-clara-deploy-2/) |
| 37 | + |
| 38 | +**Webinars** |
| 39 | + |
| 40 | +- [cuCIM: a GPU Image IO and Processing Library](https://www.youtube.com/watch?v=G46kOOM9xbQ) |
| 41 | + |
| 42 | +**[Documentation](https://docs.rapids.ai/api/cucim/stable)** |
| 43 | + |
| 44 | +**Release notes** are available on our [wiki page](https://github.com/rapidsai/cucim/wiki/Release-Notes). |
| 45 | + |
| 46 | +## Install cuCIM |
| 47 | + |
| 48 | +### Conda |
| 49 | + |
| 50 | +#### [Conda (stable)](https://anaconda.org/rapidsai/cucim) |
| 51 | + |
| 52 | +> conda create -n cucim -c rapidsai -c conda-forge cucim cudatoolkit=`<CUDA version>` |
| 53 | +
|
| 54 | +`<CUDA version>` should be 11.0+ (e.g., `11.0`, `11.2`, etc.) |
| 55 | + |
| 56 | +#### [Conda (nightlies)](https://anaconda.org/rapidsai-nightly/cucim) |
| 57 | + |
| 58 | +> conda create -n cucim -c rapidsai-nightly -c conda-forge cucim cudatoolkit=`<CUDA version>` |
| 59 | +
|
| 60 | +`<CUDA version>` should be 11.0+ (e.g., `11.0`, `11.2`, etc) |
| 61 | + |
| 62 | +### [PyPI](https://pypi.org/project/cucim/) |
| 63 | + |
| 64 | +```bash |
| 65 | +pip install cucim |
| 66 | + |
| 67 | +# Install dependencies for `cucim.skimage` (assuming that CUDA 11.0 is used for CuPy) |
| 68 | +pip install scipy scikit-image cupy-cuda110 |
| 69 | +``` |
| 70 | + |
| 71 | +### Notebooks |
| 72 | + |
| 73 | +Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-22.10/notebooks/Welcome.ipynb)) |
| 74 | + |
| 75 | +#### Downloading sample images |
| 76 | + |
| 77 | +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: |
| 78 | + |
| 79 | +(You will need [Docker](https://www.docker.com/) installed in your system) |
| 80 | + |
| 81 | +```bash |
| 82 | +./run download_testdata |
| 83 | +``` |
| 84 | +or |
| 85 | + |
| 86 | +```bash |
| 87 | +mkdir -p notebooks/input |
| 88 | +tmp_id=$(docker create gigony/svs-testdata:little-big) |
| 89 | +docker cp $tmp_id:/input notebooks |
| 90 | +docker rm -v ${tmp_id} |
| 91 | +``` |
| 92 | + |
| 93 | +## Build/Install from Source |
| 94 | + |
| 95 | +See build [instructions](CONTRIBUTING.md#setting-up-your-build-environment). |
| 96 | + |
| 97 | +## Contributing Guide |
| 98 | + |
| 99 | +Contributions to cuCIM are more than welcome! |
| 100 | +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. |
| 101 | + |
| 102 | +## Acknowledgments |
| 103 | + |
| 104 | +Without awesome third-party open source software, this project wouldn't exist. |
| 105 | + |
| 106 | +Please find [LICENSE-3rdparty.md](LICENSE-3rdparty.md) to see which third-party open source software |
| 107 | +is used in this project. |
| 108 | + |
| 109 | +## License |
| 110 | + |
| 111 | +Apache-2.0 License (see [LICENSE](LICENSE) file). |
| 112 | + |
| 113 | +Copyright (c) 2020-2022, NVIDIA CORPORATION. |
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