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cuCIM - 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.
RAPIDS 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:
cuCIM supports the following formats:
NOTE: For the latest stable README.md ensure you are on the main
branch.
Blogs
Webinars
Release notes are available on our wiki page.
conda create -n cucim -c rapidsai -c conda-forge cucim cudatoolkit=
<CUDA version>
<CUDA version>
should be 11.0+ (e.g., 11.0
, 11.2
, etc.)
conda create -n cucim -c rapidsai-nightly -c conda-forge cucim cudatoolkit=
<CUDA version>
<CUDA version>
should be 11.0+ (e.g., 11.0
, 11.2
, etc)
pip install cucim
# Install dependencies for `cucim.skimage` (assuming that CUDA 11.0 is used for CuPy)
pip install scipy scikit-image cupy-cuda110
Please check out our Welcome notebook (NBViewer)
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}
See build instructions.
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.
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.
Apache-2.0 License (see LICENSE file).
Copyright (c) 2020-2022, NVIDIA CORPORATION.
copy-pr-bot
(#606) @ajschmidt8random_state
argument of medial_axis and unsupervised_wiener is now deprecated and will be removed in the future. The new argument name, seed
, should be used instead. (#573) @grlee77cucim.skimage.color.get_xyz_coords
has been renamed cucim.skimage.color.xyz_tristimulus_values
. The former function name is deprecated and will be removed in the future. (#573) @grlee77_get_manders_overlap_coeff
(#578) @jakirkhamcucim.skimage.segmentation.chan_vese
. This fix may result in different output from previous versions. (#573) @grlee77_invariant_denoise
has been renamed denoise_invariant
and is now part of the public cucim.skimage.restoration
API (#573) @grlee77return_mapping
option was added to cucim.skimage.segmentation.join_segmentations
. This provides an additional output with a mapping between the labels in the joined segmentation and the original ones. (#573) @grlee77libwebp-base
(#579) @jakirkhamreturn_error='always'
behavior in phase_cross_correlation (#549) @grlee77libcufile
(#548) @jakirkhamrun build_package
(#553) @grlee77AWS_SESSION_TOKEN
and SCCACHE_S3_USE_SSL
vars to conda build (#525) @ajschmidt8resize
and other transforms (#516) @grlee77conda
recipe (#497) @ajschmidt8isort
version to 5.12.0 (#492) @ajschmidt8numpy
version specifier (#480) @ajschmidt811.8
and Python 3.10
Packages (#476) @ajschmidt8hessian_matrix_*
and structure_tensor_eigvals
via analytical eigenvalues for the 3D case (#434) @grlee77sampling
kwarg for distance_transform_edt
(take pixel/voxel sizes into account) (#407) @grlee77__init__.py
in cucim.core
(#359) @jakirkhamcustom.js
(#383) @galipremsagarnormalize_colors_pca
(#327) @grlee77filters
and features
benchmarks (v2) (#322) @grlee77cucim.skimage.segmentation.clear_border
function (#267) @grlee77cucim.core.operations.color.stain_extraction_pca
and cucim.core.operations.color.normalize_colors_pca
for digital pathology H&E stain extraction and normalization (#273) @grlee77, @drbehops-bot
functionality (#239) @ajschmidt8.github/ops-bot.yaml
config file (#236) @ajschmidt8device='cuda'
parameter is used in read_region
method).conda
recipes for Enhanced Compatibility effort by (#164) [@ajschmidt8](https://github.com/ajschmidt8](https://github.com/ajschmidt8))branch-21.12
(#156) [@ajschmidt8](https://github.com/ajschmidt8](https://github.com/ajschmidt8))isort
hook to 5.6.4 (#73) @charlesbluca21.08
forward-merge conflicts (#57) @ajschmidt8update-version.sh
(#42) @ajschmidt8cuda_version
(#43) @ajschmidt8FAQs
cuCIM - 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.
We found that cucim demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago.Β It has 4 open source maintainers collaborating on the project.
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