cucim

v23.10.0

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. For more information about how to use this package see README

Latest version published 1 year ago

License: Apache-2.0

PyPI

GitHub

Package Health Score

58 / 100

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Security review needed
popularity
Small
maintenance
Inactive
community
Active

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GitHub Stars: 362
Forks: 61
Contributors: 30

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Security

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Security and license risk for latest version

Release Date: Oct 17, 2023
Direct Vulnerabilities: 0
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Indirect Vulnerabilities: 0
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License

Apache-2.0

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Maintenance

Inactive

Commit Frequency

Open Issues: 108
Open PR: 5
Last Release: 1 year ago
Last Commit: 9 days ago

Further analysis of the maintenance status of cucim based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Inactive.

An important project maintenance signal to consider for cucim is that it hasn't seen any new versions released to PyPI in the past 12 months, and could be considered as a discontinued project, or that which receives low attention from its maintainers.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 30
Funding: No

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Package

Python Versions Compatibility: >= 3.6

Age: 4 years
Latest Release: 1 year ago
Dependencies: 3 Direct / 7 Total
Versions: 31
Maintainers: 0
Wheels: Linux

Readme

cuCIM

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:

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 ensure you are on the main branch.

GTC 2022 Accelerating Storage IO to GPUs with Magnum IO [S41347]
- cuCIM's GDS API examples:
SciPy 2021 cuCIM - A GPU image I/O and processing library
- video
GTC 2021 cuCIM: A GPU Image I/O and Processing Toolkit [S32194]
- video

Developer Page

Blogs

Webinars

cuCIM: a GPU Image IO and Processing Library

Documentation

Release notes are available on our wiki page.

Install cuCIM

Conda

Conda (stable)

> conda create -n cucim -c rapidsai -c conda-forge cucim cudatoolkit=``

`` should be 11.0+ (e.g., 11.0, 11.2, etc.)

Conda (nightlies)

> conda create -n cucim -c rapidsai-nightly -c conda-forge cucim cudatoolkit=``

`` should be 11.0+ (e.g., 11.0, 11.2, etc)

PyPI

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 notebook (NBViewer)

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

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).

cuCIM 23.10.00 (11 Oct 2023)

🐛 Bug Fixes

Use conda mambabuild not mamba mambabuild (#607) @bdice

📖 Documentation

minor updates to release 23.08 changelog (#605) @grlee77

🛠️ Improvements

Update image names (#609) @AyodeAwe
Use copy-pr-bot (#606) @ajschmidt8

cuCIM 23.08.00 (9 Aug 2023)

🚨 Breaking Changes

Sync cuCIM API with scikit-image 0.21 (#573) @grlee77
The random_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) @grlee77
The existing function cucim.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

🐛 Bug Fixes

Remove libwebp-base upper bound. (#599) @bdice
Fix ignore_run_exports_from. (#596) @bdice
Add ignore_run_exports for CUDA 11 (#593) @raydouglass
Use linalg & inline _get_manders_overlap_coeff (#578) @jakirkham
Fix canny and butterworth (recent CuPy and NumPy compatibility) (#574) @grlee77
A bug was fixed in 2D shear calculations for AffineTransform. (#573) @grlee77
A bug was fixed in the energy calculation of cucim.skimage.segmentation.chan_vese. This fix may result in different output from previous versions. (#573) @grlee77

🛠️ Improvements

The formerly private function _invariant_denoise has been renamed denoise_invariant and is now part of the public cucim.skimage.restoration API (#573) @grlee77
A new return_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) @grlee77
Added support for y-axis shear to the 2D AffineTransform. (#573) @grlee77
Postponed the assessment of GPU memory for testing (#601) @gigony
Do not use x86_64 GDS binaries for aarch64 (#590) @gigony
remove checks for versions of scikit-image that are no longer supported (#587) @grlee77
Allow scikit-image 0.21.0 (#580) @jakirkham
Drop unneeded selector on libwebp-base (#579) @jakirkham
switch from bundled lazy loading code to the public lazy_loader package (#575) @grlee77
Sync cuCIM API with scikit-image 0.21 (#573) @grlee77
cuCIM: Build CUDA 12 packages (#572) @jakirkham
use rapids-upload-docs script (#570) @AyodeAwe
Remove documentation build scripts for Jenkins (#567) @ajschmidt8

cuCIM 23.06.00 (7 Jun 2023)

🚨 Breaking Changes

Support Python 3.9 build/tests (#547) @shwina

🐛 Bug Fixes

Fix SHA256 check failure in test suite (#564) @grlee77
Handle space character in ./run download_testdata (#556) @gigony
Fix return_error='always' behavior in phase_cross_correlation (#549) @grlee77
Only load versioned libcufile (#548) @jakirkham
add a 20 minute timeout for pytest runs on CI (#545) @grlee77
protect against possible out of bounds memory access in 2D distance transform (#540) @grlee77

📖 Documentation

Fix doc building via run build_package (#553) @grlee77
update changelog for release 23.04.00 and 23.04.01 (#552) @grlee77

🛠️ Improvements

Allow numpy 1.24. (#563) @bdice
run docs nightly too (#560) @AyodeAwe
Update cupy dependency (#558) @vyasr
Remove libjpeg dependency (#557) @gigony
Enable sccache hits from local builds (#551) @AyodeAwe
Revert shared workflows branch (#550) @ajschmidt8
Support Python 3.9 build/tests (#547) @shwina
Remove usage of rapids-get-rapids-version-from-git (#546) @jjacobelli
Use ARC V2 self-hosted runners for GPU jobs (#538) @jjacobelli
Remove underscore in build string. (#528) @bdice

cuCIM 23.04.01 (14 Apr 2023)

🛠️ Improvements

Pin libwebp-base (#541) @ajschmidt8

cuCIM 23.04.00 (6 Apr 2023)

🚨 Breaking Changes

Fix inefficiency in handling clipping of image range in resize and other transforms (#516) @grlee77

🐛 Bug Fixes

Fix bug in median filter with non-uniform footprint (#521) @grlee77
use cp.around instead of cp.round for CuPy 10.x compatiblity (#508) @grlee77
Fix error in LZ4-compressed Zarr writing demo (#506) @grlee77
Normalize whitespace. (#474) @bdice

🛠️ Improvements

allow scikit-image 0.20 as well (#536) @grlee77
Pass AWS_SESSION_TOKEN and SCCACHE_S3_USE_SSL vars to conda build (#525) @ajschmidt8
Update aarch64 to GCC 11 (#524) @bdice
Update to GCC 11 (#522) @bdice
Upgrade dockcross and pybind11 (#519) @gigony
Binary morphology: omit weights array when possible (#517) @grlee77
Fix inefficiency in handling clipping of image range in resize and other transforms (#516) @grlee77
Fix GHA build workflow (#515) @AjayThorve
Reduce error handling verbosity in CI tests scripts (#511) @AjayThorve
Update shared workflow branches (#510) @ajschmidt8
Remove gpuCI scripts. (#505) @bdice
Move date to build string in conda recipe (#497) @ajschmidt8

cuCIM 23.02.00 (9 Feb 2023)

🚨 Breaking Changes

Add disambiguation option to phase_cross_correlation (skimage 0.20 feature) (#486) @grlee77

🐛 Bug Fixes

apply bug fix to vendored ndimage code (#494) @grlee77
Closes #490 -- fixes bug in hue jitter (#491) @benlansdell
Fix random seed used in test_3d_similarity_estimation (#472) @grlee77

📖 Documentation

Fix documentation author (#475) @bdice

🚀 New Features

Add colocalization measures (#488) @grlee77
Add disambiguation option to phase_cross_correlation (skimage 0.20 feature) (#486) @grlee77

🛠️ Improvements

Update shared workflow branches (#501) @ajschmidt8
Update isort version to 5.12.0 (#492) @ajschmidt8
Improve rank filtering performance by removing use of footprint kernel when possible (#485) @grlee77
use vendored version of cupy.pad with added performance optimizations (#482) @grlee77
add docs builds to Github Actions (#481) @AjayThorve
Update numpy version specifier (#480) @ajschmidt8
Build CUDA 11.8 and Python 3.10 Packages (#476) @ajschmidt8
Add GitHub Actions Workflows. (#471) @bdice
Fix conflicts in "Forward-merge branch-22.12 to branch-23.02" (#468) @jakirkham
Enable copy_prs. (#465) @bdice

cuCIM 22.12.00 (8 Dec 2022)

🚨 Breaking Changes

Implement additional deprecations carried out for scikit-image 0.20 (#451) @grlee77
improved implementation of ridge filters (bug fixes and reduced memory footprint) (#423) @grlee77

🐛 Bug Fixes

pin to cmake !3.25.0 on CI to avoid bug with CUDA+conda during build (#444) @grlee77
update incorrect argument and deprecated function for tifffile.TiffWriter (#433) @JoohyungLee0106
Fix rotate behavior for ndim > 2 (#432) @grlee77

📖 Documentation

add whole-slide tiled read/write demos for measuring GPUDirect Storage (GDS) I/O performance (#452) @grlee77
Add demo for distance_transform_edt (#394) @grlee77

🚀 New Features

Support no-compression method in converter (#443) @gigony
add three segmentation metrics (#425) @grlee77
add isotropic binary morphology functions (#421) @grlee77
Add blob feature detectors (blob_dog, blob_log, blob_doh) (#413) @monzelr

🛠️ Improvements

additional minor updates (skimage 0.20) (#455) @grlee77
Implement additional deprecations carried out for scikit-image 0.20 (#451) @grlee77
Faster hessian_matrix_* and structure_tensor_eigvals via analytical eigenvalues for the 3D case (#434) @grlee77
use fused kernels to reduce overhead in corner detector implementations (#426) @grlee77
Misc updates for consistency with scikit-image 0.20 (#424) @grlee77
improved implementation of ridge filters (bug fixes and reduced memory footprint) (#423) @grlee77
analytical moments computations, support pixel spacings in moments and regionprops (#422) @grlee77
Forward merge branch-22.10 to branch-22.12 (#420) @grlee77
Support sampling kwarg for distance_transform_edt (take pixel/voxel sizes into account) (#407) @grlee77
Improve performance of Euclidean distance transform (#406) @grlee77

cuCIM 22.10.00 (12 Oct 2022)

🐛 Bug Fixes

Correctly use dtype when computing shared memory requirements of separable convolution (#409) @grlee77
Forward-merge branch-22.08 to branch-22.10 (#403) @jakirkham
Add missing imports of euler_number and perimeter_crofton (#386) @grlee77

📖 Documentation

update pypi CHANGELOG.md for releases 22.08.00 and 22.08.01 (#404) @grlee77
Update README.md (#396) @HesAnEasyCoder

🚀 New Features

Allow cupy 11 (#399) @galipremsagar
Add cucim.skimage.feature.match_descriptors (#338) @grlee77

🛠️ Improvements

Merge docs and add links (#415) @jakirkham
Add benchmarks for scikit-image functions introduced in 22.08 (#378) @grlee77

cuCIM 22.08.00 (17 Aug 2022)

🚨 Breaking Changes

Stain extraction: use a less strict condition across channels when thresholding (#316) @grlee77

🐛 Bug Fixes

create SimilarityTransform using CuPy 9.x-compatible indexing (#365) @grlee77
Add __init__.py in cucim.core (#359) @jakirkham
Stain extraction: use a less strict condition across channels when thresholding (#316) @grlee77
Incorporate bug fixes from skimage 0.19.3 (#312) @grlee77
fix RawKernel bug for canny filter when quantiles are used (#310) @grlee77

📖 Documentation

Defer loading of custom.js (#383) @galipremsagar
add cucim.core.morphology to API docs + other docstring fixes (#367) @grlee77
Update README.md (#361) @HesAnEasyCoder
remove unimplemented functions from See Also and fix version numbers in deprecation warnings (#356) @grlee77
Forward-merge branch-22.06 to branch-22.08 (#344) @grlee77
Update README.md (#315) @HesAnEasyCoder
Update index.rst (#314) @HesAnEasyCoder
Update PyPI package documentation for v22.06.00 (#311) @gigony

🚀 New Features

Add segmentation with the Chan-Vese active contours method (#343) @grlee77
Add cucim.skimage.morphology.medial_axis (#342) @grlee77
Add cucim.skimage.segmentation.expand_labels (#341) @grlee77
Add Euclidean distance transform for images/volumes (#318) @grlee77

🛠️ Improvements

Revert "Allow CuPy 11" (#362) @galipremsagar
Fix issues with day & night modes in python docs (#360) @galipremsagar
Allow CuPy 11 (#357) @jakirkham
more efficient separable convolution (#355) @grlee77
Support resolution and spacing metadata (#349) @gigony
Performance optimizations to morphological segmentation functions (#340) @grlee77
benchmarks: avoid use of deprecated pandas API (#339) @grlee77
Reduce memory overhead and improve performance of normalize_colors_pca (#328) @grlee77
Protect against obscure divide by zero error in edge case of normalize_colors_pca (#327) @grlee77
complete parametrization of cucim.skimage benchmarks (#324) @grlee77
parameterization of filters and features benchmarks (v2) (#322) @grlee77
Add a fast histogram-based median filter (#317) @grlee77
Remove custom compiler environment variables (#307) @ajschmidt8

cuCIM 22.06.00 (7 Jun 2022)

🚨 Breaking Changes

Promote small integer types to single rather than double precision (#278) @grlee77

🐛 Bug Fixes

Populate correct channel names for RGBA image (#294) @gigony
Merge branch-22.04 into branch-22.06 (#258) @jakirkham

📖 Documentation

update outdated links to example data (#289) @grlee77
Add missing API docs (#275) @grlee77

🚀 New Features

add missing cucim.skimage.segmentation.clear_border function (#267) @grlee77
add cucim.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, @drbeh

🛠️ Improvements

Update to use DLPack v0.6 (#295) @gigony
Remove plugin-related messages temporarily (#291) @gigony
Simplify recipes (#286) @Ethyling
Use cupy.fuse to improve efficiency hessian_matrix_eigvals (#280) @grlee77
Promote small integer types to single rather than double precision (#278) @grlee77
improve efficiency of histogram-based thresholding functions (#276) @grlee77
Remove unused dependencies in GPU tests job (#268) @Ethyling
Enable footprint decomposition for morphology (#274) @grlee77
Use conda compilers (#232) @Ethyling
Build packages using mambabuild (#216) @Ethyling

cuCIM 22.04.00 (6 Apr 2022)

🚨 Breaking Changes

Apply fixes to skimage.transform scheduled for scikit-image 0.19.2 (#208) @grlee77

🐛 Bug Fixes

Fix ImportError from vendored code (#252) @grlee77
Fix wrong dimension in metadata (#248) @gigony
Handle file descriptor ownership and update documents for GDS (#234) @gigony
Check nullptr of handler in CuFileDriver::close() (#229) @gigony
Fix docs builds (#218) @ajschmidt8
Apply fixes to skimage.transform scheduled for scikit-image 0.19.2 (#208) @grlee77

📖 Documentation

Update PyPI cuCIM v22.02.01 CHANGELOG.md (#249) @gigony
Update GTC 2021 Spring video links (#227) @gigony
Update documents for v22.02.00 (#226) @gigony
Merge branch-22.02 into branch-22.04 (#220) @jakirkham

🛠️ Improvements

Expose data type of CuImage object for interoperability with NumPy (#246) @gigony
Temporarily disable new ops-bot functionality (#239) @ajschmidt8
Add .github/ops-bot.yaml config file (#236) @ajschmidt8
randomization per image per batch (#231) @shekhardw

cuCIM 22.02.00 (2 Feb 2022)

🚨 Breaking Changes

Update cucim.skimage API to match scikit-image 0.19 (#190) @glee77

🐛 Bug Fixes

Fix a bug in v21.12.01 (#191) @gigony
- Fix GPU memory leak when using nvJPEG API (when device='cuda' parameter is used in read_region method).
Fix segfault for preferred_memory_capacity in Python 3.9+ (#214) @gigony

📖 Documentation

PyPI v21.12.00 release (#182) @gigony

🚀 New Features

Update cucim.skimage API to match scikit-image 0.19 (#190) @glee77
Support multi-threads and batch, and support nvJPEG for JPEG-compressed images (#191) @gigony
Allow CuPy 10 (#195) @jakikham

🛠️ Improvements

Add missing imports tests (#183) @Ethyling
Allow installation with CuPy 10 (#197) @glee77
Upgrade Numpy to 1.18 for Python 3.9 support (#196) @Ethyling
Upgrade Numpy to 1.19 for Python 3.9 support (#203) @Ethyling

cuCIM 21.12.00 (9 Dec 2021)

🚀 New Features

Support Aperio SVS with CPU LZW and jpeg2k decoder (#141) [@gigony](https://github.com/gigony](https://github.com/gigony))
Add NVTX support for performance analysis (#144) [@gigony](https://github.com/gigony](https://github.com/gigony))
Normalize operation (#150) [@shekhardw](https://github.com/shekhardw](https://github.com/shekhardw))

🐛 Bug Fixes

Load libcufile.so with RTLD_NODELETE flag (#177) [@gigony](https://github.com/gigony](https://github.com/gigony))
Remove rmm/nvcc dependencies to fix cudaErrorUnsupportedPtxVersion error (#175) [@gigony](https://github.com/gigony](https://github.com/gigony))
Do not compile code with nvcc if no CUDA kernel exists (#171) [@gigony](https://github.com/gigony](https://github.com/gigony))
Fix a segmentation fault due to unloaded libcufile (#158) [@gigony](https://github.com/gigony](https://github.com/gigony))
Fix thread contention in Cache (#145) [@gigony](https://github.com/gigony](https://github.com/gigony))
Build with NumPy 1.17 (#148) [@jakirkham](https://github.com/jakirkham](https://github.com/jakirkham))

📖 Documentation

Add Jupyter notebook for SVS Support (#147) [@gigony](https://github.com/gigony](https://github.com/gigony))
Update change log for v21.10.01 (#142) [@gigony](https://github.com/gigony](https://github.com/gigony))
update docs theme to pydata-sphinx-theme (#138) [@quasiben](https://github.com/quasiben](https://github.com/quasiben))
Update Github links in README.md through script (#132) [@gigony](https://github.com/gigony](https://github.com/gigony))
Fix GDS link in Jupyter notebook (#131) [@gigony](https://github.com/gigony](https://github.com/gigony))
Update notebook for the interoperability with DALI (#127) [@gigony](https://github.com/gigony](https://github.com/gigony))

🛠️ Improvements

Update conda recipes for Enhanced Compatibility effort by (#164) [@ajschmidt8](https://github.com/ajschmidt8](https://github.com/ajschmidt8))
Fix Changelog Merge Conflicts for branch-21.12 (#156) [@ajschmidt8](https://github.com/ajschmidt8](https://github.com/ajschmidt8))
Add cucim.kit.cumed plugin with skeleton (#129) [@gigony](https://github.com/gigony](https://github.com/gigony))
Update initial cpp unittests (#128) [@gigony](https://github.com/gigony](https://github.com/gigony))
Optimize zoom out implementation with separate padding kernel (#125) [@chirayuG-nvidia](https://github.com/chirayuG-nvidia](https://github.com/chirayuG-nvidia))
Do not force install linux-64 version of openslide-python (#124) [@Ethyling](https://github.com/Ethyling](https://github.com/Ethyling))

cuCIM 21.10.00 (7 Oct 2021)

🐛 Bug Fixes

fix failing regionprops test cases (#110) @grlee77

📖 Documentation

Forward-merge branch-21.08 to branch-21.10 (#88) @jakirkham
Update PyPI cuCIM v21.08.01 README.md and CHANGELOG.md (#87) @gigony

🚀 New Features

Support raw RGB tiled TIFF (#108) @gigony
Add a mechanism for user to know the availability of cucim.CuImage (#107) @gigony
Enable GDS and Support Runtime Context (enter, exit) for CuFileDriver and CuImage (#106) @gigony
Add transforms for Digital Pathology (#100) @shekhardw

🛠️ Improvements

ENH Replace gpuci_conda_retry with gpuci_mamba_retry (#69) @dillon-cullinan

cuCIM 21.08.00 (4 Aug 2021)

🐛 Bug Fixes

Remove int-type bug on Windows in skimage.measure.label (#72) @grlee77
Fix missing array interface for associated_image() (#65) @gigony
Handle zero-padding version string (#59) @gigony
Remove invalid conda environment activation (#58) @ajschmidt8

📖 Documentation

Fix a typo in cache document (#66) @gigony

🚀 New Features

Pin isort hook to 5.6.4 (#73) @charlesbluca
Add skimage.morphology.thin (#27) @grlee77

🛠️ Improvements

Add SciPy 2021 to README (#79) @jakirkham
Use more descriptive ElementwiseKernel names in cucim.skimage (#75) @grlee77
Add initial Python unit/performance tests for TIFF loader module (#62) @gigony
Fix 21.08 forward-merge conflicts (#57) @ajschmidt8

cuCIM 21.06.00 (9 Jun 2021)

🐛 Bug Fixes

Update update-version.sh (#42) @ajschmidt8

🛠️ Improvements

Update environment variable used to determine cuda_version (#43) @ajschmidt8
Update version script to remove bump2version dependency (#41) @gigony
Update changelog (#40) @ajschmidt8
Update docs build script (#39) @ajschmidt8

cuCIM 0.19.0 (15 Apr 2021)

Initial release of cuCIM including cuClaraImage and cupyimg.

cucim dependencies

click lazy-loader numpy

FAQs

What is cucim?

cuCIM - an extensible toolkit designed to provide GPU accelerated I/O, computer vision & image processing primitive... Visit Snyk Advisor to see a full health score report for cucim, including popularity, security, maintenance & community analysis.

Is cucim popular?

The python package cucim receives a total of 2,719 weekly downloads. As such, cucim popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is cucim well maintained?

We found indications that cucim is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is cucim safe to use?

While scanning the latest version of cucim, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 20 December-2024, at 08:07 (UTC).

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