All modules for which code is available
- histomicstk.annotations_and_masks.annotation_and_mask_utils
- histomicstk.annotations_and_masks.annotation_database_parser
- histomicstk.annotations_and_masks.annotations_to_masks_handler
- histomicstk.annotations_and_masks.annotations_to_object_mask_handler
- histomicstk.annotations_and_masks.masks_to_annotations_handler
- histomicstk.annotations_and_masks.polygon_merger
- histomicstk.annotations_and_masks.polygon_merger_v2
- histomicstk.annotations_and_masks.review_gallery
- histomicstk.features.compute_fsd_features
- histomicstk.features.compute_global_cell_graph_features
- histomicstk.features.compute_gradient_features
- histomicstk.features.compute_haralick_features
- histomicstk.features.compute_intensity_features
- histomicstk.features.compute_morphometry_features
- histomicstk.features.compute_nuclei_features
- histomicstk.features.graycomatrixext
- histomicstk.filters.edge.gaussian_grad
- histomicstk.filters.shape.cdog
- histomicstk.filters.shape.clog
- histomicstk.filters.shape.glog
- histomicstk.filters.shape.vesselness
- histomicstk.preprocessing.augmentation.color_augmentation
- histomicstk.preprocessing.color_conversion.lab_mean_std
- histomicstk.preprocessing.color_conversion.lab_to_rgb
- histomicstk.preprocessing.color_conversion.od_to_rgb
- histomicstk.preprocessing.color_conversion.rgb_to_hsi
- histomicstk.preprocessing.color_conversion.rgb_to_lab
- histomicstk.preprocessing.color_conversion.rgb_to_od
- histomicstk.preprocessing.color_conversion.rgb_to_sda
- histomicstk.preprocessing.color_conversion.sda_to_rgb
- histomicstk.preprocessing.color_deconvolution.color_convolution
- histomicstk.preprocessing.color_deconvolution.color_deconvolution
- histomicstk.preprocessing.color_deconvolution.complement_stain_matrix
- histomicstk.preprocessing.color_deconvolution.find_stain_index
- histomicstk.preprocessing.color_deconvolution.rgb_separate_stains_macenko_pca
- histomicstk.preprocessing.color_deconvolution.rgb_separate_stains_xu_snmf
- histomicstk.preprocessing.color_deconvolution.separate_stains_macenko_pca
- histomicstk.preprocessing.color_deconvolution.separate_stains_xu_snmf
- histomicstk.preprocessing.color_normalization.background_intensity
- histomicstk.preprocessing.color_normalization.deconvolution_based_normalization
- histomicstk.preprocessing.color_normalization.reinhard
- histomicstk.preprocessing.color_normalization.reinhard_stats
- histomicstk.saliency.cellularity_detection_superpixels
- histomicstk.saliency.cellularity_detection_thresholding
- histomicstk.saliency.tissue_detection
- histomicstk.segmentation.embed_boundaries
- histomicstk.segmentation.label.area_open
- histomicstk.segmentation.label.compact
- histomicstk.segmentation.label.condense
- histomicstk.segmentation.label.delete
- histomicstk.segmentation.label.delete_border
- histomicstk.segmentation.label.delete_overlap
- histomicstk.segmentation.label.dilate_xor
- histomicstk.segmentation.label.perimeter
- histomicstk.segmentation.label.remove_overlap_nuclei
- histomicstk.segmentation.label.shuffle
- histomicstk.segmentation.label.split
- histomicstk.segmentation.label.trace_object_boundaries
- histomicstk.segmentation.label.width_open
- histomicstk.segmentation.level_set.chan_vese
- histomicstk.segmentation.level_set.reg_edge
- histomicstk.segmentation.nuclear.detect_nuclei_kofahi
- histomicstk.segmentation.nuclear.detect_tile_nuclei
- histomicstk.segmentation.nuclear.gaussian_voting
- histomicstk.segmentation.nuclear.gvf_tracking
- histomicstk.segmentation.nuclear.max_clustering
- histomicstk.segmentation.nuclear.min_model
- histomicstk.segmentation.positive_pixel_count
- histomicstk.segmentation.rag
- histomicstk.segmentation.rag_add_layer
- histomicstk.segmentation.rag_color
- histomicstk.utils.compute_tile_foreground_fraction
- histomicstk.utils.convert_image_to_matrix
- histomicstk.utils.convert_matrix_to_image
- histomicstk.utils.del2
- histomicstk.utils.eigen
- histomicstk.utils.exclude_nonfinite
- histomicstk.utils.fit_poisson_mixture
- histomicstk.utils.gradient_diffusion
- histomicstk.utils.hessian
- histomicstk.utils.merge_colinear
- histomicstk.utils.sample_pixels
- histomicstk.utils.simple_mask
- histomicstk.workflows.specific_workflows
- histomicstk.workflows.workflow_runner