├── .clang-format ├── .editorconfig ├── .git-blame-ignore-revs ├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── documentation-request.md │ ├── feature_request.md │ └── submit-question.md ├── PULL_REQUEST_TEMPLATE.md ├── copy-pr-bot.yaml ├── ops-bot.yaml ├── release.yml └── workflows │ ├── build.yaml │ ├── pr.yaml │ ├── test.yaml │ └── trigger-breaking-change-alert.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── 3rdparty ├── LICENSE.CLI11 ├── LICENSE.Catch2 ├── LICENSE.NVTX ├── LICENSE.StainTools ├── LICENSE.abseil-cpp ├── LICENSE.aicsimageio ├── LICENSE.benchmark ├── LICENSE.boost ├── LICENSE.click ├── LICENSE.cuda ├── LICENSE.cupy ├── LICENSE.dask ├── LICENSE.dask-cuda ├── LICENSE.dlpack ├── LICENSE.dockcross ├── LICENSE.fmt ├── LICENSE.folly ├── LICENSE.googletest ├── LICENSE.gputil ├── LICENSE.json ├── LICENSE.libcuckoo ├── LICENSE.libdeflate ├── LICENSE.libjpeg-turbo ├── LICENSE.libspng ├── LICENSE.libtiff ├── LICENSE.numpy ├── LICENSE.nvjpeg ├── LICENSE.nvjpeg2000 ├── LICENSE.opencv-contrib-python ├── LICENSE.openjpeg ├── LICENSE.openslide ├── LICENSE.pba+ ├── LICENSE.psutil ├── LICENSE.pugixml ├── LICENSE.pybind11 ├── LICENSE.pybind11_json ├── LICENSE.pytest ├── LICENSE.pytest-lazy-fixtures ├── LICENSE.pytorch ├── LICENSE.rmm ├── LICENSE.scifio ├── LICENSE.scikit-image ├── LICENSE.spdlog ├── LICENSE.taskflow ├── LICENSE.tifffile └── LICENSE.zarr-python ├── CHANGELOG.md ├── CMakeLists.txt ├── CONTRIBUTING.md ├── LICENSE ├── LICENSE-3rdparty.md ├── LICENSES └── LicenseRef-Berkeley-lzw.txt ├── README.md ├── VERSION ├── benchmarks ├── CMakeLists.txt ├── config.h ├── main.cpp ├── primitives.cpp └── skimage │ ├── _image_bench.py │ ├── bench_convolve.py │ ├── cucim_color_bench.py │ ├── cucim_exposure_bench.py │ ├── cucim_feature_bench.py │ ├── cucim_filters_bench.py │ ├── cucim_measure_bench.py │ ├── cucim_metrics_bench.py │ ├── cucim_morphology_bench.py │ ├── cucim_registration_bench.py │ ├── cucim_restoration_bench.py │ ├── cucim_segmentation_bench.py │ ├── cucim_transform_bench.py │ ├── cupyx_scipy_ndimage_filter_bench.py │ ├── cupyx_scipy_ndimage_fourier_bench.py │ ├── cupyx_scipy_ndimage_interp_bench.py │ ├── cupyx_scipy_ndimage_measurements_bench.py │ ├── cupyx_scipy_ndimage_morphology_bench.py │ ├── requirements-bench.txt │ ├── run-all.sh │ ├── run-nv-bench-color.sh │ ├── run-nv-bench-exposure.sh │ ├── run-nv-bench-feature.sh │ ├── run-nv-bench-filters.sh │ ├── run-nv-bench-measure.sh │ ├── run-nv-bench-metrics.sh │ ├── run-nv-bench-morphology.sh │ ├── run-nv-bench-registration.sh │ ├── run-nv-bench-restoration.sh │ ├── run-nv-bench-segmentation.sh │ └── run-nv-bench-transform.sh ├── ci ├── build_cpp.sh ├── build_docs.sh ├── build_python.sh ├── build_wheel.sh ├── check_style.sh ├── rapids-configure-conda-channels ├── release │ └── update-version.sh ├── test_python.sh ├── test_wheel.sh └── validate_wheel.sh ├── conda ├── environments │ ├── all_cuda-129_arch-aarch64.yaml │ ├── all_cuda-129_arch-x86_64.yaml │ ├── all_cuda-130_arch-aarch64.yaml │ └── all_cuda-130_arch-x86_64.yaml └── recipes │ ├── cucim │ ├── build.sh │ ├── conda_build_config.yaml │ └── meta.yaml │ └── libcucim │ ├── build.sh │ ├── conda_build_config.yaml │ └── meta.yaml ├── cpp ├── CMakeLists.txt ├── cmake │ ├── cucim-config.cmake.in │ ├── deps │ │ ├── abseil.cmake │ │ ├── boost-header-only.cmake │ │ ├── boost-header-only.patch │ │ ├── boost.cmake │ │ ├── catch2.cmake │ │ ├── cli11.cmake │ │ ├── fmt.cmake │ │ ├── googlebenchmark.cmake │ │ ├── googletest.cmake │ │ ├── json.cmake │ │ ├── libcuckoo.cmake │ │ ├── libcuckoo.patch │ │ ├── nvimgcodec.cmake │ │ ├── nvtx3.cmake │ │ ├── openslide.cmake │ │ ├── pybind11.cmake │ │ ├── pybind11_pr4857_4877.patch │ │ └── taskflow.cmake │ └── modules │ │ ├── CuCIMUtils.cmake │ │ └── SuperBuildUtils.cmake ├── include │ └── cucim │ │ ├── 3rdparty │ │ └── dlpack │ │ │ ├── dlpack.h │ │ │ └── dlpackcpp.h │ │ ├── cache │ │ ├── cache_type.h │ │ ├── image_cache.h │ │ ├── image_cache_config.h │ │ └── image_cache_manager.h │ │ ├── codec │ │ ├── base64.h │ │ ├── hash_function.h │ │ └── methods.h │ │ ├── concurrent │ │ └── threadpool.h │ │ ├── config │ │ └── config.h │ │ ├── core │ │ ├── framework.h │ │ ├── interface.h │ │ ├── plugin.h │ │ ├── plugin_util.h │ │ └── version.h │ │ ├── cpp20 │ │ └── find_if.h │ │ ├── cuimage.h │ │ ├── dynlib │ │ └── helper.h │ │ ├── filesystem │ │ ├── cufile_driver.h │ │ ├── file_handle.h │ │ └── file_path.h │ │ ├── io │ │ ├── device.h │ │ ├── device_type.h │ │ └── format │ │ │ └── image_format.h │ │ ├── loader │ │ ├── batch_data_processor.h │ │ ├── thread_batch_data_loader.h │ │ └── tile_info.h │ │ ├── logger │ │ ├── logger.h │ │ └── timer.h │ │ ├── macros │ │ ├── api_header.h │ │ └── defines.h │ │ ├── memory │ │ ├── dlpack.h │ │ └── memory_manager.h │ │ ├── plugin │ │ ├── image_format.h │ │ └── plugin_config.h │ │ ├── profiler │ │ ├── nvtx3.h │ │ ├── profiler.h │ │ └── profiler_config.h │ │ └── util │ │ ├── cuda.h │ │ ├── file.h │ │ └── platform.h ├── plugins │ ├── cucim.kit.cumed │ │ ├── .clang-format │ │ ├── .editorconfig │ │ ├── .gitignore │ │ ├── .idea │ │ │ ├── .gitignore │ │ │ ├── .name │ │ │ ├── codeStyles │ │ │ │ ├── Project.xml │ │ │ │ └── codeStyleConfig.xml │ │ │ ├── cucim.kit.cumed.iml │ │ │ ├── fileTemplates │ │ │ │ ├── includes │ │ │ │ │ ├── NVIDIA_CMAKE_HEADER.cmake │ │ │ │ │ └── NVIDIA_C_HEADER.h │ │ │ │ └── internal │ │ │ │ │ ├── C Header File.h │ │ │ │ │ ├── C Source File.c │ │ │ │ │ ├── C++ Class Header.h │ │ │ │ │ ├── C++ Class.cc │ │ │ │ │ └── CMakeLists.txt.cmake │ │ │ ├── misc.xml │ │ │ └── vcs.xml │ │ ├── CMakeLists.txt │ │ ├── benchmarks │ │ │ ├── CMakeLists.txt │ │ │ ├── config.h │ │ │ └── main.cpp │ │ ├── cmake │ │ │ ├── cucim.kit.cumed-config.cmake.in │ │ │ ├── deps │ │ │ │ ├── catch2.cmake │ │ │ │ ├── cli11.cmake │ │ │ │ ├── fmt.cmake │ │ │ │ ├── googlebenchmark.cmake │ │ │ │ └── googletest.cmake │ │ │ └── modules │ │ │ │ ├── CuCIMUtils.cmake │ │ │ │ └── SuperBuildUtils.cmake │ │ ├── src │ │ │ └── cumed │ │ │ │ ├── cumed.cpp │ │ │ │ └── cumed.h │ │ ├── test_data │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── config.h │ │ │ ├── main.cpp │ │ │ └── test_basic.cpp │ ├── cucim.kit.cuslide │ │ ├── .clang-format │ │ ├── .editorconfig │ │ ├── .gitignore │ │ ├── .idea │ │ │ ├── .gitignore │ │ │ ├── .name │ │ │ ├── codeStyles │ │ │ │ ├── Project.xml │ │ │ │ └── codeStyleConfig.xml │ │ │ ├── cucim.kit.cuslide.iml │ │ │ ├── fileTemplates │ │ │ │ ├── includes │ │ │ │ │ ├── NVIDIA_CMAKE_HEADER.cmake │ │ │ │ │ └── NVIDIA_C_HEADER.h │ │ │ │ └── internal │ │ │ │ │ ├── C Header File.h │ │ │ │ │ ├── C Source File.c │ │ │ │ │ ├── C++ Class Header.h │ │ │ │ │ ├── C++ Class.cc │ │ │ │ │ └── CMakeLists.txt.cmake │ │ │ ├── misc.xml │ │ │ └── vcs.xml │ │ ├── .vscode │ │ │ └── settings.json │ │ ├── CMakeLists.txt │ │ ├── benchmarks │ │ │ ├── CMakeLists.txt │ │ │ ├── config.h │ │ │ └── main.cpp │ │ ├── cmake │ │ │ ├── cucim.kit.cuslide-config.cmake.in │ │ │ ├── deps │ │ │ │ ├── boost.cmake │ │ │ │ ├── catch2.cmake │ │ │ │ ├── cli11.cmake │ │ │ │ ├── fmt.cmake │ │ │ │ ├── googlebenchmark.cmake │ │ │ │ ├── googletest.cmake │ │ │ │ ├── json.cmake │ │ │ │ ├── libdeflate.cmake │ │ │ │ ├── libjpeg-turbo-policies-fix.cmake │ │ │ │ ├── libjpeg-turbo.cmake │ │ │ │ ├── libjpeg-turbo.patch │ │ │ │ ├── libopenjpeg.cmake │ │ │ │ ├── libopenjpeg.patch │ │ │ │ ├── libtiff-policies-fix.cmake │ │ │ │ ├── libtiff.cmake │ │ │ │ ├── libtiff.patch │ │ │ │ ├── openslide.cmake │ │ │ │ └── pugixml.cmake │ │ │ └── modules │ │ │ │ ├── CuCIMUtils.cmake │ │ │ │ └── SuperBuildUtils.cmake │ │ ├── cuslide.map │ │ ├── src │ │ │ └── cuslide │ │ │ │ ├── cuslide.cpp │ │ │ │ ├── cuslide.h │ │ │ │ ├── deflate │ │ │ │ ├── deflate.cpp │ │ │ │ └── deflate.h │ │ │ │ ├── jpeg │ │ │ │ ├── libjpeg_turbo.cpp │ │ │ │ ├── libjpeg_turbo.h │ │ │ │ ├── libnvjpeg.cpp │ │ │ │ └── libnvjpeg.h │ │ │ │ ├── jpeg2k │ │ │ │ ├── color_conversion.cpp │ │ │ │ ├── color_conversion.h │ │ │ │ ├── color_table.h │ │ │ │ ├── gen_color_table.py │ │ │ │ ├── libopenjpeg.cpp │ │ │ │ └── libopenjpeg.h │ │ │ │ ├── loader │ │ │ │ ├── nvjpeg_processor.cpp │ │ │ │ └── nvjpeg_processor.h │ │ │ │ ├── lzw │ │ │ │ ├── lzw.cpp │ │ │ │ ├── lzw.h │ │ │ │ ├── lzw_libtiff.cpp │ │ │ │ └── lzw_libtiff.h │ │ │ │ ├── raw │ │ │ │ ├── raw.cpp │ │ │ │ └── raw.h │ │ │ │ ├── srctest.h │ │ │ │ └── tiff │ │ │ │ ├── ifd.cpp │ │ │ │ ├── ifd.h │ │ │ │ ├── tiff.cpp │ │ │ │ ├── tiff.h │ │ │ │ └── types.h │ │ ├── test_data │ │ └── tests │ │ │ ├── CMakeLists.txt │ │ │ ├── config.h │ │ │ ├── main.cpp │ │ │ ├── test_philips_tiff.cpp │ │ │ ├── test_read_rawtiff.cpp │ │ │ └── test_read_region.cpp │ └── cucim.kit.cuslide2 │ │ ├── .clang-format │ │ ├── .editorconfig │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── benchmarks │ │ ├── CMakeLists.txt │ │ ├── config.h │ │ └── main.cpp │ │ ├── cmake │ │ ├── cucim.kit.cuslide2-config.cmake.in │ │ ├── deps │ │ │ └── nvimgcodec.cmake │ │ └── modules │ │ │ └── CuCIMUtils.cmake │ │ ├── cuslide.map │ │ ├── src │ │ ├── cuslide │ │ │ ├── cuslide.cpp │ │ │ ├── cuslide.h │ │ │ ├── nvimgcodec │ │ │ │ ├── nvimgcodec_decoder.cpp │ │ │ │ ├── nvimgcodec_decoder.h │ │ │ │ ├── nvimgcodec_tiff_parser.cpp │ │ │ │ └── nvimgcodec_tiff_parser.h │ │ │ └── tiff │ │ │ │ ├── ifd.cpp │ │ │ │ ├── ifd.h │ │ │ │ ├── tiff.cpp │ │ │ │ ├── tiff.h │ │ │ │ ├── tiff_constants.h │ │ │ │ └── types.h │ │ └── nvimgcodec_dynlink │ │ │ ├── nvimgcodec.h │ │ │ ├── nvimgcodec_stubs_generated.cc │ │ │ ├── nvimgcodec_version.h │ │ │ └── nvimgcodec_wrap.cc │ │ ├── test_data │ │ └── tests │ │ ├── CMakeLists.txt │ │ ├── config.h │ │ ├── main.cpp │ │ ├── test_philips_tiff.cpp │ │ ├── test_read_rawtiff.cpp │ │ └── test_read_region.cpp ├── src │ ├── cache │ │ ├── cache_type.cpp │ │ ├── image_cache.cpp │ │ ├── image_cache_config.cpp │ │ ├── image_cache_empty.cpp │ │ ├── image_cache_empty.h │ │ ├── image_cache_manager.cpp │ │ ├── image_cache_per_process.cpp │ │ ├── image_cache_per_process.h │ │ ├── image_cache_shared_memory.cpp │ │ └── image_cache_shared_memory.h │ ├── codec │ │ └── base64.cpp │ ├── concurrent │ │ └── threadpool.cpp │ ├── config │ │ └── config.cpp │ ├── core │ │ ├── cucim_framework.cpp │ │ ├── cucim_framework.h │ │ ├── cucim_plugin.cpp │ │ ├── cucim_plugin.h │ │ ├── framework.cpp │ │ ├── plugin_manager.cpp │ │ ├── plugin_manager.h │ │ └── version.inl │ ├── cuimage.cpp │ ├── filesystem │ │ ├── cufile_driver.cpp │ │ └── file_handle.cpp │ ├── io │ │ ├── device.cpp │ │ ├── device_type.cpp │ │ └── format │ │ │ └── image_format.cpp │ ├── loader │ │ ├── batch_data_processor.cpp │ │ └── thread_batch_data_loader.cpp │ ├── logger │ │ ├── logger.cpp │ │ └── timer.cpp │ ├── memory │ │ └── memory_manager.cpp │ ├── plugin │ │ ├── image_format.cpp │ │ └── plugin_config.cpp │ ├── profiler │ │ ├── profiler.cpp │ │ └── profiler_config.cpp │ └── util │ │ ├── file.cpp │ │ └── platform.cpp └── tests │ ├── CMakeLists.txt │ ├── config.h │ ├── main.cpp │ ├── test_cufile.cpp │ ├── test_metadata.cpp │ └── test_read_region.cpp ├── cucim.code-workspace ├── dependencies.yaml ├── docs ├── Makefile ├── README.md ├── adr │ ├── README.md │ └── example.md ├── make.bat ├── references.css ├── requirement.txt └── source │ ├── _static │ └── EMPTY │ ├── api.rst │ ├── conf.py │ ├── ext │ └── doi_role.py │ └── index.rst ├── examples ├── cpp │ ├── CMakeLists.txt │ ├── CMakeLists.txt.examples.release.in │ └── tiff_image │ │ └── main.cpp └── python │ ├── distance_transform_edt_demo.py │ ├── gds_whole_slide │ ├── README.md │ ├── benchmark_read.py │ ├── benchmark_round_trip.py │ ├── benchmark_zarr_write.py │ ├── benchmark_zarr_write_lz4_via_dask.py │ ├── demo_implementation.py │ └── lz4_nvcomp.py │ └── tiff_image │ └── main.py ├── experiments ├── Supporting_Aperio_SVS_Format │ └── benchmark.py └── Using_Cache │ └── benchmark.py ├── gds ├── CMakeLists.txt ├── include │ └── cufile_stub.h └── src │ └── cufile_stub.cpp ├── notebooks ├── Accessing_File_with_GDS.ipynb ├── Basic_Usage.ipynb ├── File-access_Experiments_on_TIFF.ipynb ├── Multi-thread_and_Multi-process_Tests.ipynb ├── Supporting_Aperio_SVS_Format.ipynb ├── Using_Cache.ipynb ├── Welcome.ipynb ├── Working_with_Albumentation.ipynb ├── Working_with_DALI.ipynb ├── gabor_example.ipynb ├── input │ └── README.md ├── random_walker_example.ipynb ├── static_images │ ├── File-access_Experiments_on_TIFF_FileFormat.png │ ├── File-access_Experiments_on_TIFF_FileFormat2.png │ ├── File-access_Experiments_on_TIFF_HDD.png │ ├── File-access_Experiments_on_TIFF_NVMe.png │ ├── File-access_Experiments_on_TIFF_SSD.png │ └── Multi-thread_and_Multi-process_Tests_Alignment.png └── vesselness_example.ipynb ├── python ├── .clang-format ├── .editorconfig ├── .gitignore ├── .idea │ ├── .gitignore │ ├── .name │ ├── codeStyles │ │ ├── Project.xml │ │ └── codeStyleConfig.xml │ ├── dataSources.xml │ ├── fileTemplates │ │ ├── includes │ │ │ ├── NVIDIA_CMAKE_HEADER.cmake │ │ │ └── NVIDIA_C_HEADER.h │ │ └── internal │ │ │ ├── C Header File.h │ │ │ ├── C Source File.c │ │ │ ├── C++ Class Header.h │ │ │ ├── C++ Class.cc │ │ │ └── CMakeLists.txt.cmake │ ├── misc.xml │ ├── pycucim.iml │ ├── python.iml │ └── vcs.xml ├── .vscode │ └── settings.json ├── CMakeLists.txt ├── cmake │ ├── deps │ │ ├── fmt.cmake │ │ ├── json.cmake │ │ ├── pybind11.cmake │ │ ├── pybind11_json.cmake │ │ └── pybind11_pr4857_4877.patch │ └── modules │ │ ├── CuCIMUtils.cmake │ │ └── SuperBuildUtils.cmake ├── cucim │ ├── .coveragerc │ ├── .editorconfig │ ├── CHANGELOG.md │ ├── CONTRIBUTING.md │ ├── LICENSE │ ├── LICENSE-3rdparty.md │ ├── MANIFEST.in │ ├── README.md │ ├── VERSION │ ├── pyproject.toml │ ├── setup.py │ ├── src │ │ ├── cucim │ │ │ ├── VERSION │ │ │ ├── __init__.py │ │ │ ├── __init__.pyi │ │ │ ├── __main__.py │ │ │ ├── _misc.py │ │ │ ├── _version.py │ │ │ ├── clara │ │ │ │ ├── __init__.py │ │ │ │ ├── cache │ │ │ │ │ └── __init__.py │ │ │ │ ├── cli.py │ │ │ │ ├── converter │ │ │ │ │ └── tiff.py │ │ │ │ ├── filesystem │ │ │ │ │ └── __init__.py │ │ │ │ └── io │ │ │ │ │ └── __init__.py │ │ │ ├── core │ │ │ │ ├── __init__.py │ │ │ │ └── operations │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── color │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── jitter.py │ │ │ │ │ ├── kernel │ │ │ │ │ │ └── cuda_kernel_source.py │ │ │ │ │ ├── stain_normalizer.py │ │ │ │ │ └── tests │ │ │ │ │ │ └── test_color_jitter.py │ │ │ │ │ ├── expose │ │ │ │ │ ├── tests │ │ │ │ │ │ └── test_expose.py │ │ │ │ │ └── transform.py │ │ │ │ │ ├── intensity │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── kernel │ │ │ │ │ │ └── cuda_kernel_source.py │ │ │ │ │ ├── normalize.py │ │ │ │ │ ├── scaling.py │ │ │ │ │ ├── tests │ │ │ │ │ │ ├── normalized.png │ │ │ │ │ │ ├── normalized_atan.png │ │ │ │ │ │ ├── scaled.png │ │ │ │ │ │ ├── test_normalize.py │ │ │ │ │ │ ├── test_rand_zoom.py │ │ │ │ │ │ ├── test_scaling.py │ │ │ │ │ │ ├── test_zoom.py │ │ │ │ │ │ ├── zoomed.png │ │ │ │ │ │ └── zoomout_padded.png │ │ │ │ │ └── zoom.py │ │ │ │ │ ├── morphology │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── _distance_transform.py │ │ │ │ │ ├── _pba_2d.py │ │ │ │ │ ├── _pba_3d.py │ │ │ │ │ ├── cuda │ │ │ │ │ │ ├── pba_kernels_2d.h │ │ │ │ │ │ └── pba_kernels_3d.h │ │ │ │ │ └── tests │ │ │ │ │ │ └── test_distance_transform.py │ │ │ │ │ └── spatial │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── rotate_and_flip.py │ │ │ │ │ └── tests │ │ │ │ │ ├── flipped.png │ │ │ │ │ ├── rotated.png │ │ │ │ │ ├── test_flip.py │ │ │ │ │ ├── test_random_flip.py │ │ │ │ │ ├── test_random_rotate90.py │ │ │ │ │ └── test_rotate90.py │ │ │ ├── py.typed │ │ │ ├── skimage │ │ │ │ ├── __init__.py │ │ │ │ ├── __init__.pyi │ │ │ │ ├── _shared │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── _dependency_checks.py │ │ │ │ │ ├── _gradient.py │ │ │ │ │ ├── _warnings.py │ │ │ │ │ ├── compat.py │ │ │ │ │ ├── coord.py │ │ │ │ │ ├── distance.py │ │ │ │ │ ├── fft.py │ │ │ │ │ ├── filters.py │ │ │ │ │ ├── testing.py │ │ │ │ │ ├── tests │ │ │ │ │ │ ├── test_coord.py │ │ │ │ │ │ ├── test_utils.py │ │ │ │ │ │ └── test_warnings.py │ │ │ │ │ ├── utils.py │ │ │ │ │ └── version_requirements.py │ │ │ │ ├── _vendored │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── _internal.py │ │ │ │ │ ├── _ndimage_filters.py │ │ │ │ │ ├── _ndimage_filters_core.py │ │ │ │ │ ├── _ndimage_interp_kernels.py │ │ │ │ │ ├── _ndimage_interpolation.py │ │ │ │ │ ├── _ndimage_measurements.py │ │ │ │ │ ├── _ndimage_morphology.py │ │ │ │ │ ├── _ndimage_spline_kernel_weights.py │ │ │ │ │ ├── _ndimage_spline_prefilter_core.py │ │ │ │ │ ├── _ndimage_util.py │ │ │ │ │ ├── _pearsonr.py │ │ │ │ │ ├── _signaltools_core.py │ │ │ │ │ ├── _texture.py │ │ │ │ │ ├── ndimage.py │ │ │ │ │ ├── pad.py │ │ │ │ │ ├── pad_elementwise.py │ │ │ │ │ ├── signaltools.py │ │ │ │ │ ├── tests │ │ │ │ │ │ └── test_morphology.py │ │ │ │ │ └── time.py │ │ │ │ ├── color │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── adapt_rgb.py │ │ │ │ │ ├── colorconv.py │ │ │ │ │ ├── colorlabel.py │ │ │ │ │ ├── delta_e.py │ │ │ │ │ ├── rgb_colors.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── ciede2000_test_data.txt │ │ │ │ │ │ ├── data │ │ │ │ │ │ ├── lab_array_a_10.npy │ │ │ │ │ │ ├── lab_array_a_2.npy │ │ │ │ │ │ ├── lab_array_a_r.npy │ │ │ │ │ │ ├── lab_array_b_10.npy │ │ │ │ │ │ ├── lab_array_b_2.npy │ │ │ │ │ │ ├── lab_array_b_r.npy │ │ │ │ │ │ ├── lab_array_c_10.npy │ │ │ │ │ │ ├── lab_array_c_2.npy │ │ │ │ │ │ ├── lab_array_c_r.npy │ │ │ │ │ │ ├── lab_array_d50_10.npy │ │ │ │ │ │ ├── lab_array_d50_2.npy │ │ │ │ │ │ ├── lab_array_d50_r.npy │ │ │ │ │ │ ├── lab_array_d55_10.npy │ │ │ │ │ │ ├── lab_array_d55_2.npy │ │ │ │ │ │ ├── lab_array_d55_r.npy │ │ │ │ │ │ ├── lab_array_d65_10.npy │ │ │ │ │ │ ├── lab_array_d65_2.npy │ │ │ │ │ │ ├── lab_array_d65_r.npy │ │ │ │ │ │ ├── lab_array_d75_10.npy │ │ │ │ │ │ ├── lab_array_d75_2.npy │ │ │ │ │ │ ├── lab_array_e_2.npy │ │ │ │ │ │ ├── luv_array_a_10.npy │ │ │ │ │ │ ├── luv_array_a_2.npy │ │ │ │ │ │ ├── luv_array_a_r.npy │ │ │ │ │ │ ├── luv_array_b_10.npy │ │ │ │ │ │ ├── luv_array_b_2.npy │ │ │ │ │ │ ├── luv_array_b_r.npy │ │ │ │ │ │ ├── luv_array_c_10.npy │ │ │ │ │ │ ├── luv_array_c_2.npy │ │ │ │ │ │ ├── luv_array_c_r.npy │ │ │ │ │ │ ├── luv_array_d50_10.npy │ │ │ │ │ │ ├── luv_array_d50_2.npy │ │ │ │ │ │ ├── luv_array_d50_r.npy │ │ │ │ │ │ ├── luv_array_d55_10.npy │ │ │ │ │ │ ├── luv_array_d55_2.npy │ │ │ │ │ │ ├── luv_array_d55_r.npy │ │ │ │ │ │ ├── luv_array_d65_10.npy │ │ │ │ │ │ ├── luv_array_d65_2.npy │ │ │ │ │ │ ├── luv_array_d65_r.npy │ │ │ │ │ │ ├── luv_array_d75_10.npy │ │ │ │ │ │ ├── luv_array_d75_2.npy │ │ │ │ │ │ └── luv_array_e_2.npy │ │ │ │ │ │ ├── test_adapt_rgb.py │ │ │ │ │ │ ├── test_colorconv.py │ │ │ │ │ │ ├── test_colorlabel.py │ │ │ │ │ │ └── test_delta_e.py │ │ │ │ ├── data │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _binary_blobs.py │ │ │ │ │ └── tests │ │ │ │ │ │ └── test_data.py │ │ │ │ ├── exposure │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _adapthist.py │ │ │ │ │ ├── exposure.py │ │ │ │ │ ├── histogram_matching.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── test_exposure.py │ │ │ │ │ │ └── test_histogram_matching.py │ │ │ │ ├── feature │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _basic_features.py │ │ │ │ │ ├── _canny.py │ │ │ │ │ ├── _daisy.py │ │ │ │ │ ├── _hessian_det_appx.py │ │ │ │ │ ├── blob.py │ │ │ │ │ ├── corner.py │ │ │ │ │ ├── cuda │ │ │ │ │ │ ├── _hessian_det_appx.cu │ │ │ │ │ │ └── blob.cu │ │ │ │ │ ├── match.py │ │ │ │ │ ├── peak.py │ │ │ │ │ ├── template.py │ │ │ │ │ ├── tests │ │ │ │ │ │ ├── test_basic_features.py │ │ │ │ │ │ ├── test_blob.py │ │ │ │ │ │ ├── test_canny.py │ │ │ │ │ │ ├── test_corner.py │ │ │ │ │ │ ├── test_daisy.py │ │ │ │ │ │ ├── test_match.py │ │ │ │ │ │ ├── test_peak.py │ │ │ │ │ │ └── test_template.py │ │ │ │ │ └── util.py │ │ │ │ ├── filters │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _fft_based.py │ │ │ │ │ ├── _gabor.py │ │ │ │ │ ├── _gaussian.py │ │ │ │ │ ├── _median.py │ │ │ │ │ ├── _median_hist.py │ │ │ │ │ ├── _rank_order.py │ │ │ │ │ ├── _separable_filtering.py │ │ │ │ │ ├── _sparse.py │ │ │ │ │ ├── _unsharp_mask.py │ │ │ │ │ ├── _window.py │ │ │ │ │ ├── cuda │ │ │ │ │ │ └── histogram_median.cu │ │ │ │ │ ├── edges.py │ │ │ │ │ ├── lpi_filter.py │ │ │ │ │ ├── ridges.py │ │ │ │ │ ├── tests │ │ │ │ │ │ ├── test_correlate.py │ │ │ │ │ │ ├── test_edges.py │ │ │ │ │ │ ├── test_fft_based.py │ │ │ │ │ │ ├── test_gabor.py │ │ │ │ │ │ ├── test_gaussian.py │ │ │ │ │ │ ├── test_lpi_filter.py │ │ │ │ │ │ ├── test_median.py │ │ │ │ │ │ ├── test_rank_order.py │ │ │ │ │ │ ├── test_ridges.py │ │ │ │ │ │ ├── test_separable_filtering.py │ │ │ │ │ │ ├── test_thresholding.py │ │ │ │ │ │ ├── test_unsharp_mask.py │ │ │ │ │ │ └── test_window.py │ │ │ │ │ └── thresholding.py │ │ │ │ ├── measure │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _blur_effect.py │ │ │ │ │ ├── _colocalization.py │ │ │ │ │ ├── _label.py │ │ │ │ │ ├── _label_kernels.py │ │ │ │ │ ├── _moments.py │ │ │ │ │ ├── _moments_analytical.py │ │ │ │ │ ├── _polygon.py │ │ │ │ │ ├── _regionprops.py │ │ │ │ │ ├── _regionprops_gpu.py │ │ │ │ │ ├── _regionprops_gpu_basic_kernels.py │ │ │ │ │ ├── _regionprops_gpu_convex.py │ │ │ │ │ ├── _regionprops_gpu_intensity_kernels.py │ │ │ │ │ ├── _regionprops_gpu_misc_kernels.py │ │ │ │ │ ├── _regionprops_gpu_moments_kernels.py │ │ │ │ │ ├── _regionprops_gpu_utils.py │ │ │ │ │ ├── _regionprops_utils.py │ │ │ │ │ ├── block.py │ │ │ │ │ ├── entropy.py │ │ │ │ │ ├── profile.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── test_block.py │ │ │ │ │ │ ├── test_blur_effect.py │ │ │ │ │ │ ├── test_ccomp.py │ │ │ │ │ │ ├── test_colocalization.py │ │ │ │ │ │ ├── test_entropy.py │ │ │ │ │ │ ├── test_moments.py │ │ │ │ │ │ ├── test_polygon.py │ │ │ │ │ │ ├── test_profile.py │ │ │ │ │ │ ├── test_regionprops.py │ │ │ │ │ │ └── test_regionprops_gpu_kernels.py │ │ │ │ ├── metrics │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _adapted_rand_error.py │ │ │ │ │ ├── _contingency_table.py │ │ │ │ │ ├── _structural_similarity.py │ │ │ │ │ ├── _variation_of_information.py │ │ │ │ │ ├── simple_metrics.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── test_segmentation_metrics.py │ │ │ │ │ │ ├── test_simple_metrics.py │ │ │ │ │ │ └── test_structural_similarity.py │ │ │ │ ├── morphology │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── _medial_axis_lookup.py │ │ │ │ │ ├── _skeletonize.py │ │ │ │ │ ├── ball_decompositions.npy │ │ │ │ │ ├── binary.py │ │ │ │ │ ├── convex_hull.py │ │ │ │ │ ├── disk_decompositions.npy │ │ │ │ │ ├── footprints.py │ │ │ │ │ ├── gray.py │ │ │ │ │ ├── grayreconstruct.py │ │ │ │ │ ├── isotropic.py │ │ │ │ │ ├── misc.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── test_binary.py │ │ │ │ │ │ ├── test_convex_hull.py │ │ │ │ │ │ ├── test_footprints.py │ │ │ │ │ │ ├── test_gray.py │ │ │ │ │ │ ├── test_isotropic.py │ │ │ │ │ │ ├── test_misc.py │ │ │ │ │ │ ├── test_reconstruction.py │ │ │ │ │ │ └── test_skeletonize.py │ │ │ │ ├── registration │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _masked_phase_cross_correlation.py │ │ │ │ │ ├── _optical_flow.py │ │ │ │ │ ├── _optical_flow_utils.py │ │ │ │ │ ├── _phase_cross_correlation.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── data │ │ │ │ │ │ ├── OriginalX-130Y130.png │ │ │ │ │ │ ├── OriginalX130Y130.png │ │ │ │ │ │ ├── OriginalX75Y75.png │ │ │ │ │ │ ├── TransformedX-130Y130.png │ │ │ │ │ │ ├── TransformedX130Y130.png │ │ │ │ │ │ └── TransformedX75Y75.png │ │ │ │ │ │ ├── test_ilk.py │ │ │ │ │ │ ├── test_masked_phase_cross_correlation.py │ │ │ │ │ │ ├── test_phase_cross_correlation.py │ │ │ │ │ │ └── test_tvl1.py │ │ │ │ ├── restoration │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _denoise.py │ │ │ │ │ ├── deconvolution.py │ │ │ │ │ ├── j_invariant.py │ │ │ │ │ ├── tests │ │ │ │ │ │ ├── test_denoise.py │ │ │ │ │ │ ├── test_j_invariant.py │ │ │ │ │ │ └── test_restoration.py │ │ │ │ │ └── uft.py │ │ │ │ ├── segmentation │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── _chan_vese.py │ │ │ │ │ ├── _clear_border.py │ │ │ │ │ ├── _expand_labels.py │ │ │ │ │ ├── _join.py │ │ │ │ │ ├── boundaries.py │ │ │ │ │ ├── morphsnakes.py │ │ │ │ │ ├── random_walker_segmentation.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── test_boundaries.py │ │ │ │ │ │ ├── test_chan_vese.py │ │ │ │ │ │ ├── test_clear_border.py │ │ │ │ │ │ ├── test_expand_labels.py │ │ │ │ │ │ ├── test_join.py │ │ │ │ │ │ ├── test_morphsnakes.py │ │ │ │ │ │ └── test_random_walker.py │ │ │ │ ├── transform │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __init__.pyi │ │ │ │ │ ├── _geometric.py │ │ │ │ │ ├── _warps.py │ │ │ │ │ ├── integral.py │ │ │ │ │ ├── pyramids.py │ │ │ │ │ └── tests │ │ │ │ │ │ ├── test_geometric.py │ │ │ │ │ │ ├── test_integral.py │ │ │ │ │ │ ├── test_pyramids.py │ │ │ │ │ │ └── test_warps.py │ │ │ │ └── util │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── _invert.py │ │ │ │ │ ├── _map_array.py │ │ │ │ │ ├── _montage.py │ │ │ │ │ ├── arraycrop.py │ │ │ │ │ ├── compare.py │ │ │ │ │ ├── dtype.py │ │ │ │ │ ├── noise.py │ │ │ │ │ ├── shape.py │ │ │ │ │ └── tests │ │ │ │ │ ├── test_arraycrop.py │ │ │ │ │ ├── test_compare.py │ │ │ │ │ ├── test_dtype.py │ │ │ │ │ ├── test_invert.py │ │ │ │ │ ├── test_map_array.py │ │ │ │ │ ├── test_montage.py │ │ │ │ │ ├── test_random_noise.py │ │ │ │ │ └── test_shape.py │ │ │ └── time.py │ │ └── localtest.py │ └── tests │ │ ├── __init__.py │ │ ├── conftest.py │ │ ├── fixtures │ │ └── testimage.py │ │ ├── integration │ │ ├── __init__.py │ │ └── clara │ │ │ └── __init__.py │ │ ├── performance │ │ ├── __init__.py │ │ └── clara │ │ │ ├── __init__.py │ │ │ └── test_read_region_memory_usage.py │ │ ├── test_cucim.py │ │ ├── unit │ │ ├── __init__.py │ │ ├── clara │ │ │ ├── __init__.py │ │ │ ├── converter │ │ │ │ └── test_converter.py │ │ │ ├── test_image_cache.py │ │ │ ├── test_load_image.py │ │ │ ├── test_load_image_metadata.py │ │ │ └── test_tiff_read_region.py │ │ ├── core │ │ │ └── test_stain_normalizer.py │ │ ├── test_init.py │ │ └── test_version.py │ │ └── util │ │ ├── gen_image.py │ │ ├── gen_tiff.py │ │ └── io.py └── pybind11 │ ├── cache │ ├── cache_py.cpp │ ├── cache_py.h │ ├── cache_pydoc.h │ ├── image_cache_py.cpp │ ├── image_cache_py.h │ └── image_cache_pydoc.h │ ├── cucim_py.cpp │ ├── cucim_py.h │ ├── cucim_pydoc.h │ ├── filesystem │ ├── cufile_py.cpp │ ├── cufile_py.h │ ├── cufile_pydoc.h │ ├── filesystem_py.cpp │ ├── filesystem_py.h │ └── filesystem_pydoc.h │ ├── io │ ├── device_py.cpp │ ├── device_pydoc.h │ ├── io_py.cpp │ ├── io_py.h │ └── io_pydoc.h │ ├── macros.h │ ├── memory │ ├── memory_py.cpp │ ├── memory_py.h │ └── memory_pydoc.h │ └── profiler │ ├── profiler_py.cpp │ ├── profiler_py.h │ └── profiler_pydoc.h ├── run ├── scripts ├── debug_python ├── test_aperio_svs.py ├── test_philips_tiff.py └── verify_cuslide2_infrastructure.py └── test_data ├── .gitignore ├── Dockerfile ├── README.md ├── gen_images.sh ├── input ├── LICENSE-3rdparty └── README.md └── push_testdata.sh /.clang-format: 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