Cucim

🚨 Breaking Changes

- Implement additional deprecations carried out for scikit-image 0.20 ([451](https://github.com/rapidsai/cucim/pull/451)) [grlee77](https://github.com/grlee77)
- improved implementation of ridge filters (bug fixes and reduced memory footprint) ([423](https://github.com/rapidsai/cucim/pull/423)) [grlee77](https://github.com/grlee77)

🐛 Bug Fixes

- pin to cmake !3.25.0 on CI to avoid bug with CUDA+conda during build ([444](https://github.com/rapidsai/cucim/pull/444)) [grlee77](https://github.com/grlee77)
- update incorrect argument and deprecated function for tifffile.TiffWriter ([433](https://github.com/rapidsai/cucim/pull/433)) [JoohyungLee0106](https://github.com/JoohyungLee0106)
- Fix rotate behavior for ndim > 2 ([432](https://github.com/rapidsai/cucim/pull/432)) [grlee77](https://github.com/grlee77)

📖 Documentation

- add whole-slide tiled read/write demos for measuring GPUDirect Storage (GDS) I/O performance ([452](https://github.com/rapidsai/cucim/pull/452)) [grlee77](https://github.com/grlee77)
- Add demo for distance_transform_edt ([394](https://github.com/rapidsai/cucim/pull/394)) [grlee77](https://github.com/grlee77)

🚀 New Features

- Support no-compression method in converter ([443](https://github.com/rapidsai/cucim/pull/443)) [gigony](https://github.com/gigony)
- add three segmentation metrics ([425](https://github.com/rapidsai/cucim/pull/425)) [grlee77](https://github.com/grlee77)
- add isotropic binary morphology functions ([421](https://github.com/rapidsai/cucim/pull/421)) [grlee77](https://github.com/grlee77)
- Add blob feature detectors (blob_dog, blob_log, blob_doh) ([413](https://github.com/rapidsai/cucim/pull/413)) [monzelr](https://github.com/monzelr)

🛠️ Improvements

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

🐛 Bug Fixes

- Correctly use dtype when computing shared memory requirements of separable convolution ([409](https://github.com/rapidsai/cucim/pull/409)) [grlee77](https://github.com/grlee77)
- Forward-merge branch-22.08 to branch-22.10 ([403](https://github.com/rapidsai/cucim/pull/403)) [jakirkham](https://github.com/jakirkham)
- Add missing imports of euler_number and perimeter_crofton ([386](https://github.com/rapidsai/cucim/pull/386)) [grlee77](https://github.com/grlee77)

📖 Documentation

- update pypi CHANGELOG.md for releases 22.08.00 and 22.08.01 ([404](https://github.com/rapidsai/cucim/pull/404)) [grlee77](https://github.com/grlee77)
- Update README.md ([396](https://github.com/rapidsai/cucim/pull/396)) [HesAnEasyCoder](https://github.com/HesAnEasyCoder)

🚀 New Features

- Allow cupy 11 ([399](https://github.com/rapidsai/cucim/pull/399)) [galipremsagar](https://github.com/galipremsagar)
- Add cucim.skimage.feature.match_descriptors ([338](https://github.com/rapidsai/cucim/pull/338)) [grlee77](https://github.com/grlee77)

🛠️ Improvements

- Merge docs and add links ([415](https://github.com/rapidsai/cucim/pull/415)) [jakirkham](https://github.com/jakirkham)
- Add benchmarks for scikit-image functions introduced in 22.08 ([378](https://github.com/rapidsai/cucim/pull/378)) [grlee77](https://github.com/grlee77)

🚨 Breaking Changes

- Stain extraction: use a less strict condition across channels when thresholding ([316](https://github.com/rapidsai/cucim/pull/316)) [grlee77](https://github.com/grlee77)

🐛 Bug Fixes

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

📖 Documentation

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

🚀 New Features

- Add segmentation with the Chan-Vese active contours method ([343](https://github.com/rapidsai/cucim/pull/343)) [grlee77](https://github.com/grlee77)
- Add cucim.skimage.morphology.medial_axis ([342](https://github.com/rapidsai/cucim/pull/342)) [grlee77](https://github.com/grlee77)
- Add cucim.skimage.segmentation.expand_labels ([341](https://github.com/rapidsai/cucim/pull/341)) [grlee77](https://github.com/grlee77)
- Add Euclidean distance transform for images/volumes ([318](https://github.com/rapidsai/cucim/pull/318)) [grlee77](https://github.com/grlee77)

🛠️ Improvements

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

🚨 Breaking Changes

- Promote small integer types to single rather than double precision ([278](https://github.com/rapidsai/cucim/pull/278)) [grlee77](https://github.com/grlee77)

🐛 Bug Fixes

- Populate correct channel names for RGBA image ([294](https://github.com/rapidsai/cucim/pull/294)) [gigony](https://github.com/gigony)
- Merge branch-22.04 into branch-22.06 ([258](https://github.com/rapidsai/cucim/pull/258)) [jakirkham](https://github.com/jakirkham)

📖 Documentation

- update outdated links to example data ([289](https://github.com/rapidsai/cucim/pull/289)) [grlee77](https://github.com/grlee77)
- Add missing API docs ([275](https://github.com/rapidsai/cucim/pull/275)) [grlee77](https://github.com/grlee77)

🚀 New Features

- add missing `cucim.skimage.segmentation.clear_border` function ([267](https://github.com/rapidsai/cucim/pull/267)) [grlee77](https://github.com/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](https://github.com/rapidsai/cucim/pull/273)) [grlee77](https://github.com/grlee77), [drbeh](https://github.com/drbeh)

🛠️ Improvements

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

🚨 Breaking Changes

- Apply fixes to skimage.transform scheduled for scikit-image 0.19.2 ([208](https://github.com/rapidsai/cucim/pull/208)) [grlee77](https://github.com/grlee77)

🐛 Bug Fixes

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

📖 Documentation

- Update PyPI cuCIM v22.02.01 CHANGELOG.md ([249](https://github.com/rapidsai/cucim/pull/249)) [gigony](https://github.com/gigony)
- Update GTC 2021 Spring video links ([227](https://github.com/rapidsai/cucim/pull/227)) [gigony](https://github.com/gigony)
- Update documents for v22.02.00 ([226](https://github.com/rapidsai/cucim/pull/226)) [gigony](https://github.com/gigony)
- Merge branch-22.02 into branch-22.04 ([220](https://github.com/rapidsai/cucim/pull/220)) [jakirkham](https://github.com/jakirkham)

🛠️ Improvements

- Expose data type of CuImage object for interoperability with NumPy ([246](https://github.com/rapidsai/cucim/pull/246)) [gigony](https://github.com/gigony)
- Temporarily disable new `ops-bot` functionality ([239](https://github.com/rapidsai/cucim/pull/239)) [ajschmidt8](https://github.com/ajschmidt8)
- Add `.github/ops-bot.yaml` config file ([236](https://github.com/rapidsai/cucim/pull/236)) [ajschmidt8](https://github.com/ajschmidt8)
- randomization per image per batch ([231](https://github.com/rapidsai/cucim/pull/231)) [shekhardw](https://github.com/shekhardw)

🚨 Breaking Changes

- Update cucim.skimage API to match scikit-image 0.19 ([190](https://github.com/rapidsai/cucim/pull/190)) [glee77](https://github.com/glee77)

🐛 Bug Fixes

- Fix a bug in [v21.12.01](https://github.com/rapidsai/cucim/wiki/release_notes_v21.12.01) ([#191](https://github.com/rapidsai/cucim/pull/191)) [gigony](https://github.com/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](https://github.com/rapidsai/cucim/pull/214)) [gigony](https://github.com/gigony)

📖 Documentation

- PyPI v21.12.00 release ([182](https://github.com/rapidsai/cucim/pull/182)) [gigony](https://github.com/gigony)

🚀 New Features

- Update cucim.skimage API to match scikit-image 0.19 ([190](https://github.com/rapidsai/cucim/pull/190)) [glee77](https://github.com/glee77)
- Support multi-threads and batch, and support nvJPEG for JPEG-compressed images ([191](https://github.com/rapidsai/cucim/pull/191)) [gigony](https://github.com/gigony)
- Allow CuPy 10 ([195](https://github.com/rapidsai/cucim/pull/195)) [jakikham](https://github.com/jakikham)

🛠️ Improvements

- Add missing imports tests ([183](https://github.com/rapidsai/cucim/pull/183)) [Ethyling](https://github.com/Ethyling)
- Allow installation with CuPy 10 ([197](https://github.com/rapidsai/cucim/pull/197)) [glee77](https://github.com/glee77)
- Upgrade Numpy to 1.18 for Python 3.9 support ([196](https://github.com/rapidsai/cucim/pull/196)) [Ethyling](https://github.com/Ethyling)
- Upgrade Numpy to 1.19 for Python 3.9 support ([203](https://github.com/rapidsai/cucim/pull/203)) [Ethyling](https://github.com/Ethyling)