├── .circleci └── config.yml ├── .dockerignore ├── .git-blame-ignore-revs ├── .github ├── dependabot.yml └── workflows │ ├── ci.yml │ └── codespell.yml ├── .gitignore ├── .pre-commit-config.yaml ├── AUTHORS.rst ├── CMakeLists.txt ├── CONTRIBUTING.rst ├── Dockerfile ├── Dockerfile-wheels ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.rst ├── codecov.yml ├── docs ├── Makefile ├── api-docs.rst ├── authors.rst ├── conf.py ├── contributing.rst ├── examples.rst ├── examples │ ├── annotation_database_backup_and_sql_parser.ipynb │ ├── annotations_to_object_segmentation_masks.ipynb │ ├── annotations_to_semantic_segmentation_masks.ipynb │ ├── color_deconvolution.ipynb │ ├── color_normalization_and_augmentation.ipynb │ ├── create_classifier.ipynb │ ├── creating_gallery_images_review.ipynb │ ├── doc_files │ │ ├── ModifiedHTTAnnotationProtocol.pdf │ │ ├── ModifiedNucleusAnnotationProtocol.pdf │ │ └── NucleiClassification │ │ │ ├── inputmodel-fie.png │ │ │ ├── nucleiClass-panel.png │ │ │ ├── nucleiFeature-extraction.png │ │ │ ├── results.png │ │ │ └── submit button.png │ ├── introducing_the_girder_api.rst │ ├── nuclei_classification.md │ ├── nuclei_segmentation.ipynb │ ├── polygon_merger_from_tiled_masks.ipynb │ ├── polygon_merger_using_rtree.ipynb │ ├── positive_pixel_count.ipynb │ ├── procedure_for_typical_annotation_project.rst │ ├── segmentation_masks_to_annotations.ipynb │ ├── semantic_segmentation_color_thresholding_approach.ipynb │ ├── semantic_segmentation_superpixel_approach.ipynb │ ├── simple_tissue_detection.ipynb │ ├── tips_for_scalable_annotation_rendering.rst │ ├── using_large_image.ipynb │ └── workflows.ipynb ├── favicon.ico ├── histomicstk.annotations_and_masks.annotation_and_mask_utils.rst ├── histomicstk.annotations_and_masks.annotation_database_parser.rst ├── histomicstk.annotations_and_masks.annotations_to_object_segmentation_masks.rst ├── histomicstk.annotations_and_masks.annotations_to_semantic_segmentation_masks.rst ├── histomicstk.annotations_and_masks.masks_to_annotations_handler.rst ├── histomicstk.annotations_and_masks.polygon_merger.rst ├── histomicstk.annotations_and_masks.review_gallery.rst ├── histomicstk.annotations_and_masks.rst ├── histomicstk.features.rst ├── histomicstk.filters.edge.rst ├── histomicstk.filters.rst ├── histomicstk.filters.shape.rst ├── histomicstk.preprocessing.augmentation.rst ├── histomicstk.preprocessing.color_conversion.rst ├── histomicstk.preprocessing.color_deconvolution.rst ├── histomicstk.preprocessing.color_normalization.rst ├── histomicstk.preprocessing.rst ├── histomicstk.rst ├── histomicstk.saliency.cellularity_detection_superpixels.rst ├── histomicstk.saliency.cellularity_detection_thresholding.rst ├── histomicstk.saliency.rst ├── histomicstk.saliency.tissue_detection.rst ├── histomicstk.segmentation.label.rst ├── histomicstk.segmentation.level_set.rst ├── histomicstk.segmentation.nuclear.rst ├── histomicstk.segmentation.positive_pixel_count.rst ├── histomicstk.segmentation.rst ├── histomicstk.utils.rst ├── histomicstk.workflows.rst ├── histomicstk.workflows.specific_workflows.rst ├── histomicstk.workflows.workflow_runner.rst ├── histomicstk_mark.png ├── histomicstk_mark.svg ├── index.rst ├── installation.rst ├── make.bat └── make_docs.sh ├── histomicstk ├── __init__.py ├── annotations_and_masks │ ├── __init__.py │ ├── annotation_and_mask_utils.py │ ├── annotation_database_parser.py │ ├── annotations_to_masks_handler.py │ ├── annotations_to_object_mask_handler.py │ ├── masks_to_annotations_handler.py │ ├── polygon_merger.py │ ├── polygon_merger_v2.py │ ├── pyrtree │ │ ├── __init__.py │ │ ├── rect.py │ │ └── rtree.py │ ├── review_gallery.py │ └── tests │ │ ├── test_annotation_and_mask_utils.py │ │ ├── test_annotation_database_parser.py │ │ ├── test_annotations_to_masks_handler.py │ │ ├── test_annotations_to_object_mask_handler.py │ │ ├── test_masks_to_annotations_handler.py │ │ ├── test_polygon_merger.py │ │ └── test_review_gallery.py ├── cli │ ├── BackgroundIntensity │ │ ├── BackgroundIntensity.py │ │ ├── BackgroundIntensity.xml │ │ └── __init__.py │ ├── ColorDeconvolution │ │ ├── ColorDeconvolution.py │ │ ├── ColorDeconvolution.xml │ │ └── __init__.py │ ├── ComputeNucleiFeatures │ │ ├── ComputeNucleiFeatures.py │ │ ├── ComputeNucleiFeatures.xml │ │ ├── README.md │ │ └── __init__.py │ ├── NucleiClassification │ │ ├── NucleiClassification.py │ │ ├── NucleiClassification.xml │ │ └── __init__.py │ ├── NucleiDetection │ │ ├── NucleiDetection.py │ │ ├── NucleiDetection.xml │ │ └── __init__.py │ ├── PositivePixelCount │ │ ├── PositivePixelCount.py │ │ ├── PositivePixelCount.xml │ │ └── __init__.py │ ├── SeparateStainsMacenkoPCA │ │ ├── SeparateStainsMacenkoPCA.py │ │ ├── SeparateStainsMacenkoPCA.xml │ │ └── __init__.py │ ├── SeparateStainsXuSnmf │ │ ├── SeparateStainsXuSnmf.py │ │ ├── SeparateStainsXuSnmf.xml │ │ └── __init__.py │ ├── SuperpixelSegmentation │ │ ├── SuperpixelSegmentation.py │ │ ├── SuperpixelSegmentation.xml │ │ └── __init__.py │ ├── __init__.py │ ├── __main__.py │ ├── dask_config.yaml │ ├── docker-entrypoint.sh │ ├── slicer_cli_list.json │ └── utils.py ├── features │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _compute_marginal_glcm_probs_cython.pyx │ ├── compute_fsd_features.py │ ├── compute_global_cell_graph_features.py │ ├── compute_gradient_features.py │ ├── compute_haralick_features.py │ ├── compute_intensity_features.py │ ├── compute_morphometry_features.py │ ├── compute_nuclei_features.py │ └── graycomatrixext.py ├── filters │ ├── __init__.py │ ├── edge │ │ ├── __init__.py │ │ └── gaussian_grad.py │ └── shape │ │ ├── __init__.py │ │ ├── cdog.py │ │ ├── clog.py │ │ ├── glog.py │ │ └── vesselness.py ├── preprocessing │ ├── __init__.py │ ├── augmentation │ │ ├── __init__.py │ │ └── color_augmentation.py │ ├── color_conversion │ │ ├── __init__.py │ │ ├── lab_mean_std.py │ │ ├── lab_to_rgb.py │ │ ├── od_to_rgb.py │ │ ├── rgb_to_hsi.py │ │ ├── rgb_to_lab.py │ │ ├── rgb_to_od.py │ │ ├── rgb_to_sda.py │ │ └── sda_to_rgb.py │ ├── color_deconvolution │ │ ├── __init__.py │ │ ├── _linalg.py │ │ ├── color_convolution.py │ │ ├── color_deconvolution.py │ │ ├── complement_stain_matrix.py │ │ ├── find_stain_index.py │ │ ├── rgb_separate_stains_macenko_pca.py │ │ ├── rgb_separate_stains_xu_snmf.py │ │ ├── separate_stains_macenko_pca.py │ │ ├── separate_stains_xu_snmf.py │ │ └── stain_color_map.py │ ├── color_normalization │ │ ├── __init__.py │ │ ├── background_intensity.py │ │ ├── deconvolution_based_normalization.py │ │ ├── reinhard.py │ │ └── reinhard_stats.py │ └── tests │ │ └── test_normalization_and_augmentation.py ├── saliency │ ├── __init__.py │ ├── cellularity_detection_superpixels.py │ ├── cellularity_detection_thresholding.py │ ├── tests │ │ └── test_saliency.py │ └── tissue_detection.py ├── segmentation │ ├── __init__.py │ ├── embed_boundaries.py │ ├── label │ │ ├── CMakeLists.txt │ │ ├── __init__.py │ │ ├── _trace_object_boundaries_cython.pyx │ │ ├── area_open.py │ │ ├── compact.py │ │ ├── condense.py │ │ ├── delete.py │ │ ├── delete_border.py │ │ ├── delete_overlap.py │ │ ├── dilate_xor.py │ │ ├── perimeter.py │ │ ├── remove_overlap_nuclei.py │ │ ├── shuffle.py │ │ ├── split.py │ │ ├── trace_object_boundaries.py │ │ └── width_open.py │ ├── level_set │ │ ├── __init__.py │ │ ├── chan_vese.py │ │ └── reg_edge.py │ ├── nuclear │ │ ├── CMakeLists.txt │ │ ├── __init__.py │ │ ├── _max_clustering_cython.pyx │ │ ├── detect_nuclei_kofahi.py │ │ ├── detect_tile_nuclei.py │ │ ├── gaussian_voting.py │ │ ├── gvf_tracking.py │ │ ├── max_clustering.py │ │ └── min_model.py │ ├── positive_pixel_count.py │ ├── rag.py │ ├── rag_add_layer.py │ └── rag_color.py ├── utils │ ├── __init__.py │ ├── compute_tile_foreground_fraction.py │ ├── convert_image_to_matrix.py │ ├── convert_matrix_to_image.py │ ├── del2.py │ ├── eigen.py │ ├── exclude_nonfinite.py │ ├── fit_poisson_mixture.py │ ├── general_utils.py │ ├── girder_convenience_utils.py │ ├── gradient_diffusion.py │ ├── hessian.py │ ├── merge_colinear.py │ ├── sample_pixels.py │ ├── simple_mask.py │ └── tests │ │ └── test_girder_convenience_utils.py └── workflows │ ├── __init__.py │ ├── specific_workflows.py │ ├── tests │ └── test_workflow_runner.py │ └── workflow_runner.py ├── pyproject.toml ├── requirements-dev.txt ├── ruff.toml ├── test_wheels.py ├── tests ├── .dockerignore ├── Dockerfile-gc-tests ├── __init__.py ├── datastore.py ├── docker-compose.yml ├── docker_setup.py ├── htk_test_utilities.py ├── test_blob_detection_filters.py ├── test_cli_common.py ├── test_cli_results.py ├── test_cli_xml.py ├── test_color_conversion.py ├── test_color_deconvolution.py ├── test_color_normalization.py ├── test_feature_extraction.py ├── test_files │ ├── Easy1_nuclei_fsd_features.csv │ ├── Easy1_nuclei_gradient_features.csv │ ├── Easy1_nuclei_gradient_features_v2.csv │ ├── Easy1_nuclei_haralick_features.csv │ ├── Easy1_nuclei_intensity_features.csv │ ├── Easy1_nuclei_morphometry_features.csv │ ├── Easy1_nuclei_morphometry_features_v2.csv │ ├── annotations_and_masks │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-59206_top-33505_mag-BASE.png │ │ ├── img │ │ │ ├── polygon_merger_merged.JPG │ │ │ └── polygon_merger_unmerged.JPG │ │ ├── polygon_merger_roi_masks │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44350_top-43750_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44350_top-44262_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44350_top-44774_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44350_top-45286_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44350_top-45798_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44862_top-43750_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44862_top-44262_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44862_top-44774_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44862_top-45286_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-44862_top-45798_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45374_top-43750_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45374_top-44262_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45374_top-44774_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45374_top-45286_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45374_top-45798_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45886_top-43750_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45886_top-44262_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45886_top-44774_mag-BASE.png │ │ │ ├── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45886_top-45286_mag-BASE.png │ │ │ └── TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_left-45886_top-45798_mag-BASE.png │ │ └── sample_contours_df.tsv │ ├── saliency_GTcodes.csv │ └── sample_GTcodes.csv ├── test_glcm.py ├── test_global_cell_graph_features.py ├── test_nuclei_segmentation.py └── test_segmentation_label.py └── tox.ini /.circleci/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DigitalSlideArchive/HistomicsTK/HEAD/.circleci/config.yml 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