AUTHORS.rst
CMakeLists.txt
CONTRIBUTING.rst
LICENSE
NOTICE
README.rst
pyproject.toml
requirements-dev.txt
setup.py
histomicstk/__init__.py
histomicstk/annotations_and_masks/__init__.py
histomicstk/annotations_and_masks/annotation_and_mask_utils.py
histomicstk/annotations_and_masks/annotation_database_parser.py
histomicstk/annotations_and_masks/annotations_to_masks_handler.py
histomicstk/annotations_and_masks/annotations_to_object_mask_handler.py
histomicstk/annotations_and_masks/masks_to_annotations_handler.py
histomicstk/annotations_and_masks/polygon_merger.py
histomicstk/annotations_and_masks/polygon_merger_v2.py
histomicstk/annotations_and_masks/review_gallery.py
histomicstk/annotations_and_masks/pyrtree/__init__.py
histomicstk/annotations_and_masks/pyrtree/rect.py
histomicstk/annotations_and_masks/pyrtree/rtree.py
histomicstk/annotations_and_masks/tests/test_annotation_and_mask_utils.py
histomicstk/annotations_and_masks/tests/test_annotation_database_parser.py
histomicstk/annotations_and_masks/tests/test_annotations_to_masks_handler.py
histomicstk/annotations_and_masks/tests/test_annotations_to_object_mask_handler.py
histomicstk/annotations_and_masks/tests/test_masks_to_annotations_handler.py
histomicstk/annotations_and_masks/tests/test_polygon_merger.py
histomicstk/annotations_and_masks/tests/test_review_gallery.py
histomicstk/cli/__init__.py
histomicstk/cli/__main__.py
histomicstk/cli/dask_config.yaml
histomicstk/cli/docker-entrypoint.sh
histomicstk/cli/slicer_cli_list.json
histomicstk/cli/utils.py
histomicstk/cli/BackgroundIntensity/BackgroundIntensity.py
histomicstk/cli/BackgroundIntensity/BackgroundIntensity.xml
histomicstk/cli/BackgroundIntensity/__init__.py
histomicstk/cli/ColorDeconvolution/ColorDeconvolution.py
histomicstk/cli/ColorDeconvolution/ColorDeconvolution.xml
histomicstk/cli/ColorDeconvolution/__init__.py
histomicstk/cli/ComputeNucleiFeatures/ComputeNucleiFeatures.py
histomicstk/cli/ComputeNucleiFeatures/ComputeNucleiFeatures.xml
histomicstk/cli/ComputeNucleiFeatures/README.md
histomicstk/cli/ComputeNucleiFeatures/__init__.py
histomicstk/cli/NucleiClassification/NucleiClassification.py
histomicstk/cli/NucleiClassification/NucleiClassification.xml
histomicstk/cli/NucleiClassification/__init__.py
histomicstk/cli/NucleiDetection/NucleiDetection.py
histomicstk/cli/NucleiDetection/NucleiDetection.xml
histomicstk/cli/NucleiDetection/__init__.py
histomicstk/cli/PositivePixelCount/PositivePixelCount.py
histomicstk/cli/PositivePixelCount/PositivePixelCount.xml
histomicstk/cli/PositivePixelCount/__init__.py
histomicstk/cli/SeparateStainsMacenkoPCA/SeparateStainsMacenkoPCA.py
histomicstk/cli/SeparateStainsMacenkoPCA/SeparateStainsMacenkoPCA.xml
histomicstk/cli/SeparateStainsMacenkoPCA/__init__.py
histomicstk/cli/SeparateStainsXuSnmf/SeparateStainsXuSnmf.py
histomicstk/cli/SeparateStainsXuSnmf/SeparateStainsXuSnmf.xml
histomicstk/cli/SeparateStainsXuSnmf/__init__.py
histomicstk/cli/SuperpixelSegmentation/SuperpixelSegmentation.py
histomicstk/cli/SuperpixelSegmentation/SuperpixelSegmentation.xml
histomicstk/cli/SuperpixelSegmentation/__init__.py
histomicstk/features/CMakeLists.txt
histomicstk/features/__init__.py
histomicstk/features/_compute_marginal_glcm_probs_cython.pyx
histomicstk/features/compute_fsd_features.py
histomicstk/features/compute_global_cell_graph_features.py
histomicstk/features/compute_gradient_features.py
histomicstk/features/compute_haralick_features.py
histomicstk/features/compute_intensity_features.py
histomicstk/features/compute_morphometry_features.py
histomicstk/features/compute_nuclei_features.py
histomicstk/features/graycomatrixext.py
histomicstk/filters/__init__.py
histomicstk/filters/edge/__init__.py
histomicstk/filters/edge/gaussian_grad.py
histomicstk/filters/shape/__init__.py
histomicstk/filters/shape/cdog.py
histomicstk/filters/shape/clog.py
histomicstk/filters/shape/glog.py
histomicstk/filters/shape/vesselness.py
histomicstk/preprocessing/__init__.py
histomicstk/preprocessing/augmentation/__init__.py
histomicstk/preprocessing/augmentation/color_augmentation.py
histomicstk/preprocessing/color_conversion/__init__.py
histomicstk/preprocessing/color_conversion/lab_mean_std.py
histomicstk/preprocessing/color_conversion/lab_to_rgb.py
histomicstk/preprocessing/color_conversion/od_to_rgb.py
histomicstk/preprocessing/color_conversion/rgb_to_hsi.py
histomicstk/preprocessing/color_conversion/rgb_to_lab.py
histomicstk/preprocessing/color_conversion/rgb_to_od.py
histomicstk/preprocessing/color_conversion/rgb_to_sda.py
histomicstk/preprocessing/color_conversion/sda_to_rgb.py
histomicstk/preprocessing/color_deconvolution/__init__.py
histomicstk/preprocessing/color_deconvolution/_linalg.py
histomicstk/preprocessing/color_deconvolution/color_convolution.py
histomicstk/preprocessing/color_deconvolution/color_deconvolution.py
histomicstk/preprocessing/color_deconvolution/complement_stain_matrix.py
histomicstk/preprocessing/color_deconvolution/find_stain_index.py
histomicstk/preprocessing/color_deconvolution/rgb_separate_stains_macenko_pca.py
histomicstk/preprocessing/color_deconvolution/rgb_separate_stains_xu_snmf.py
histomicstk/preprocessing/color_deconvolution/separate_stains_macenko_pca.py
histomicstk/preprocessing/color_deconvolution/separate_stains_xu_snmf.py
histomicstk/preprocessing/color_deconvolution/stain_color_map.py
histomicstk/preprocessing/color_normalization/__init__.py
histomicstk/preprocessing/color_normalization/background_intensity.py
histomicstk/preprocessing/color_normalization/deconvolution_based_normalization.py
histomicstk/preprocessing/color_normalization/reinhard.py
histomicstk/preprocessing/color_normalization/reinhard_stats.py
histomicstk/preprocessing/tests/test_normalization_and_augmentation.py
histomicstk/saliency/__init__.py
histomicstk/saliency/cellularity_detection_superpixels.py
histomicstk/saliency/cellularity_detection_thresholding.py
histomicstk/saliency/tissue_detection.py
histomicstk/saliency/tests/test_saliency.py
histomicstk/segmentation/__init__.py
histomicstk/segmentation/embed_boundaries.py
histomicstk/segmentation/positive_pixel_count.py
histomicstk/segmentation/rag.py
histomicstk/segmentation/rag_add_layer.py
histomicstk/segmentation/rag_color.py
histomicstk/segmentation/label/CMakeLists.txt
histomicstk/segmentation/label/__init__.py
histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx
histomicstk/segmentation/label/area_open.py
histomicstk/segmentation/label/compact.py
histomicstk/segmentation/label/condense.py
histomicstk/segmentation/label/delete.py
histomicstk/segmentation/label/delete_border.py
histomicstk/segmentation/label/delete_overlap.py
histomicstk/segmentation/label/dilate_xor.py
histomicstk/segmentation/label/perimeter.py
histomicstk/segmentation/label/remove_overlap_nuclei.py
histomicstk/segmentation/label/shuffle.py
histomicstk/segmentation/label/split.py
histomicstk/segmentation/label/trace_object_boundaries.py
histomicstk/segmentation/label/width_open.py
histomicstk/segmentation/level_set/__init__.py
histomicstk/segmentation/level_set/chan_vese.py
histomicstk/segmentation/level_set/reg_edge.py
histomicstk/segmentation/nuclear/CMakeLists.txt
histomicstk/segmentation/nuclear/__init__.py
histomicstk/segmentation/nuclear/_max_clustering_cython.pyx
histomicstk/segmentation/nuclear/detect_nuclei_kofahi.py
histomicstk/segmentation/nuclear/detect_tile_nuclei.py
histomicstk/segmentation/nuclear/gaussian_voting.py
histomicstk/segmentation/nuclear/gvf_tracking.py
histomicstk/segmentation/nuclear/max_clustering.py
histomicstk/segmentation/nuclear/min_model.py
histomicstk/utils/__init__.py
histomicstk/utils/compute_tile_foreground_fraction.py
histomicstk/utils/convert_image_to_matrix.py
histomicstk/utils/convert_matrix_to_image.py
histomicstk/utils/del2.py
histomicstk/utils/eigen.py
histomicstk/utils/exclude_nonfinite.py
histomicstk/utils/fit_poisson_mixture.py
histomicstk/utils/general_utils.py
histomicstk/utils/girder_convenience_utils.py
histomicstk/utils/gradient_diffusion.py
histomicstk/utils/hessian.py
histomicstk/utils/merge_colinear.py
histomicstk/utils/sample_pixels.py
histomicstk/utils/simple_mask.py
histomicstk/utils/tests/test_girder_convenience_utils.py
histomicstk/workflows/__init__.py
histomicstk/workflows/specific_workflows.py
histomicstk/workflows/workflow_runner.py
histomicstk/workflows/tests/test_workflow_runner.py