HistomicsTK
Installation
API Documentation
Examples
Contributing
Credits
HistomicsTK
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
V
|
W
|
Y
A
Annotation_iterator (class in histomicstk.workflows.workflow_runner)
annotations_to_contours_no_mask() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler)
apply_callback_to_all_annotations() (histomicstk.workflows.workflow_runner.Annotation_iterator method)
area_open() (in module histomicstk.segmentation.label)
assign_cellularity_scores() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
assign_colors_to_spixel_clusters() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
assign_components_by_thresholding() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
B
background_intensity() (in module histomicstk.preprocessing.color_normalization)
C
CD_single_tissue_piece (class in histomicstk.saliency.cellularity_detection_superpixels)
cdog() (in module histomicstk.filters.shape)
CDT_single_tissue_piece (class in histomicstk.saliency.cellularity_detection_thresholding)
cellularity_detection_workflow() (in module histomicstk.workflows.specific_workflows)
Cellularity_detector_superpixels (class in histomicstk.saliency.cellularity_detection_superpixels)
Cellularity_detector_thresholding (class in histomicstk.saliency.cellularity_detection_thresholding)
chan_vese() (in module histomicstk.segmentation.level_set)
clog() (in module histomicstk.filters.shape)
color_convolution() (in module histomicstk.preprocessing.color_deconvolution)
color_deconvolution() (in module histomicstk.preprocessing.color_deconvolution)
color_deconvolution_routine() (in module histomicstk.preprocessing.color_deconvolution)
color_normalize_unspecified_components() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
combs_with_unique_products() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler)
compact() (in module histomicstk.segmentation.label)
complement_stain_matrix() (in module histomicstk.preprocessing.color_deconvolution)
compute_fsd_features() (in module histomicstk.features)
compute_global_cell_graph_features() (in module histomicstk.features)
compute_gradient_features() (in module histomicstk.features)
compute_haralick_features() (in module histomicstk.features)
compute_intensity_features() (in module histomicstk.features)
compute_morphometry_features() (in module histomicstk.features)
compute_nuclei_features() (in module histomicstk.features)
compute_tile_foreground_fraction() (in module histomicstk.utils)
condense() (in module histomicstk.segmentation.label)
contours_to_labeled_object_mask() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler)
convert_image_to_matrix() (in module histomicstk.utils)
convert_matrix_to_image() (in module histomicstk.utils)
count_image() (in module histomicstk.segmentation.positive_pixel_count)
count_slide() (in module histomicstk.segmentation.positive_pixel_count)
create_mask_from_coords() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
create_review_galleries() (in module histomicstk.annotations_and_masks.review_gallery)
create_rtree() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)
D
deconvolution_based_normalization() (in module histomicstk.preprocessing.color_normalization)
del2() (in module histomicstk.utils)
delete() (in module histomicstk.segmentation.label)
delete_annotations_in_slide() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
delete_border() (in module histomicstk.segmentation.label)
delete_overlap() (in module histomicstk.segmentation.label)
detect_nuclei_kofahi() (in module histomicstk.segmentation.nuclear)
detect_tile_nuclei() (in module histomicstk.segmentation.nuclear)
dilate_xor() (in module histomicstk.segmentation.label)
dump_annotations_locally() (in module histomicstk.annotations_and_masks.annotation_database_parser)
dump_annotations_workflow() (in module histomicstk.annotations_and_masks.annotation_database_parser)
E
eigen() (in module histomicstk.utils)
embed_boundaries() (in module histomicstk.segmentation)
exclude_nonfinite() (in module histomicstk.utils)
F
find_potentially_cellular_regions() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
find_stain_index() (in module histomicstk.preprocessing.color_deconvolution)
find_top_cellular_regions() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
fit_poisson_mixture() (in module histomicstk.utils)
fix_GTcodes() (histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method)
G
gaussian_grad() (in module histomicstk.filters.edge)
gaussian_voting() (in module histomicstk.segmentation.nuclear)
get_all_rois_from_folder_v2() (in module histomicstk.annotations_and_masks.review_gallery)
get_all_rois_from_slide() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler)
get_all_rois_from_slide_v2() (in module histomicstk.annotations_and_masks.annotations_to_object_mask_handler)
get_annotation_documents_from_contours() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler)
get_bboxes_from_slide_annotations() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
get_concatenated_contours() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method)
get_contours_from_bin_mask() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler)
get_contours_from_mask() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler)
get_idxs_for_annots_overlapping_roi_by_bbox() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
get_image_and_mask_from_slide() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler)
get_image_from_htk_response() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
get_mask_from_slide() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler)
get_merged_multipolygon() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)
get_roi_mask() (in module histomicstk.annotations_and_masks.annotations_to_masks_handler)
get_rotated_rectangular_coords() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
get_scale_factor_and_appendStr() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
get_single_annotation_document_from_contours() (in module histomicstk.annotations_and_masks.masks_to_annotations_handler)
get_slide_thumbnail() (in module histomicstk.saliency.tissue_detection)
get_tissue_boundary_annotation_documents() (in module histomicstk.saliency.tissue_detection)
get_tissue_mask() (in module histomicstk.saliency.tissue_detection)
glog() (in module histomicstk.filters.shape)
gradient_diffusion() (in module histomicstk.utils)
graycomatrixext() (in module histomicstk.features)
gvf_tracking() (in module histomicstk.segmentation.nuclear)
H
hessian() (in module histomicstk.utils)
histomicstk.annotations_and_masks
module
histomicstk.annotations_and_masks.annotation_and_mask_utils
module
histomicstk.annotations_and_masks.annotation_database_parser
module
histomicstk.annotations_and_masks.annotations_to_masks_handler
module
histomicstk.annotations_and_masks.annotations_to_object_mask_handler
module
histomicstk.annotations_and_masks.masks_to_annotations_handler
module
histomicstk.annotations_and_masks.polygon_merger
module
histomicstk.annotations_and_masks.polygon_merger_v2
module
histomicstk.annotations_and_masks.review_gallery
module
histomicstk.features
module
histomicstk.filters
module
histomicstk.filters.edge
module
histomicstk.filters.shape
module
histomicstk.preprocessing
module
histomicstk.preprocessing.augmentation
module
histomicstk.preprocessing.color_conversion
module
histomicstk.preprocessing.color_deconvolution
module
histomicstk.preprocessing.color_normalization
module
histomicstk.saliency
module
histomicstk.saliency.cellularity_detection_superpixels
module
histomicstk.saliency.cellularity_detection_thresholding
module
histomicstk.saliency.tissue_detection
module
histomicstk.segmentation
module
histomicstk.segmentation.label
module
histomicstk.segmentation.level_set
module
histomicstk.segmentation.nuclear
module
histomicstk.segmentation.positive_pixel_count
module
histomicstk.utils
module
histomicstk.workflows
module
histomicstk.workflows.specific_workflows
module
histomicstk.workflows.workflow_runner
module
hue_value (histomicstk.segmentation.positive_pixel_count.Parameters attribute)
hue_width (histomicstk.segmentation.positive_pixel_count.Parameters attribute)
I
initialize_labeled_mask() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
intensity_lower_limit (histomicstk.segmentation.positive_pixel_count.Parameters attribute)
intensity_strong_threshold (histomicstk.segmentation.positive_pixel_count.Parameters attribute)
intensity_upper_limit (histomicstk.segmentation.positive_pixel_count.Parameters attribute)
intensity_weak_threshold (histomicstk.segmentation.positive_pixel_count.Parameters attribute)
IntensityAverage (histomicstk.segmentation.positive_pixel_count.Output attribute)
IntensityAverageWeakAndPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)
IntensitySumPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)
IntensitySumStrongPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)
IntensitySumWeakPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)
L
lab_mean_std() (in module histomicstk.preprocessing.color_conversion)
lab_to_rgb() (in module histomicstk.preprocessing.color_conversion)
M
max_clustering() (in module histomicstk.segmentation.nuclear)
merge_colinear() (in module histomicstk.utils)
min_model() (in module histomicstk.segmentation.nuclear)
module
histomicstk.annotations_and_masks
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
histomicstk.filters
histomicstk.filters.edge
histomicstk.filters.shape
histomicstk.preprocessing
histomicstk.preprocessing.augmentation
histomicstk.preprocessing.color_conversion
histomicstk.preprocessing.color_deconvolution
histomicstk.preprocessing.color_normalization
histomicstk.saliency
histomicstk.saliency.cellularity_detection_superpixels
histomicstk.saliency.cellularity_detection_thresholding
histomicstk.saliency.tissue_detection
histomicstk.segmentation
histomicstk.segmentation.label
histomicstk.segmentation.level_set
histomicstk.segmentation.nuclear
histomicstk.segmentation.positive_pixel_count
histomicstk.utils
histomicstk.workflows
histomicstk.workflows.specific_workflows
histomicstk.workflows.workflow_runner
N
np_vec_no_jit_iou() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
NumberPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)
NumberStrongPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)
NumberTotalPixels (histomicstk.segmentation.positive_pixel_count.Output attribute)
NumberWeakPositive (histomicstk.segmentation.positive_pixel_count.Output attribute)
O
od_to_rgb() (in module histomicstk.preprocessing.color_conversion)
Output (class in histomicstk.segmentation.positive_pixel_count)
P
Parameters (class in histomicstk.segmentation.positive_pixel_count)
parse_annotations_to_local_tables() (in module histomicstk.annotations_and_masks.annotation_database_parser)
parse_slide_annotations_into_tables() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
perimeter() (in module histomicstk.segmentation.label)
perturb_stain_concentration() (in module histomicstk.preprocessing.augmentation)
Polygon_merger (class in histomicstk.annotations_and_masks.polygon_merger)
Polygon_merger_v2 (class in histomicstk.annotations_and_masks.polygon_merger_v2)
R
rag() (in module histomicstk.segmentation)
rag_add_layer() (in module histomicstk.segmentation)
rag_color() (in module histomicstk.segmentation)
RatioStrongToPixels (histomicstk.segmentation.positive_pixel_count.Output attribute)
RatioStrongToTotal (histomicstk.segmentation.positive_pixel_count.Output attribute)
RatioTotalToPixels (histomicstk.segmentation.positive_pixel_count.Output attribute)
RatioWeakToPixels (histomicstk.segmentation.positive_pixel_count.Output attribute)
reg_edge() (in module histomicstk.segmentation.level_set)
reinhard() (in module histomicstk.preprocessing.color_normalization)
reinhard_stats() (in module histomicstk.preprocessing.color_normalization)
reinhard_stats_rgb() (in module histomicstk.preprocessing.color_normalization)
remove_overlap_nuclei() (in module histomicstk.segmentation.label)
restrict_mask_to_single_tissue_piece() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
(histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
rgb_perturb_stain_concentration() (in module histomicstk.preprocessing.augmentation)
rgb_separate_stains_macenko_pca() (in module histomicstk.preprocessing.color_deconvolution)
rgb_separate_stains_xu_snmf() (in module histomicstk.preprocessing.color_deconvolution)
rgb_to_hsi() (in module histomicstk.preprocessing.color_conversion)
rgb_to_lab() (in module histomicstk.preprocessing.color_conversion)
rgb_to_od() (in module histomicstk.preprocessing.color_conversion)
rgb_to_sda() (in module histomicstk.preprocessing.color_conversion)
rotate_point_list() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
run() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method)
(histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)
(histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
(histomicstk.saliency.cellularity_detection_superpixels.Cellularity_detector_superpixels method)
(histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
(histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method)
(histomicstk.workflows.workflow_runner.Slide_iterator method)
(histomicstk.workflows.workflow_runner.Workflow_runner method)
run_for_single_group() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)
S
sample_pixels() (in module histomicstk.utils)
saturation_minimum (histomicstk.segmentation.positive_pixel_count.Parameters attribute)
scale_slide_annotations() (in module histomicstk.annotations_and_masks.annotation_and_mask_utils)
sda_to_rgb() (in module histomicstk.preprocessing.color_conversion)
separate_stains_macenko_pca() (in module histomicstk.preprocessing.color_deconvolution)
separate_stains_xu_snmf() (in module histomicstk.preprocessing.color_deconvolution)
set_color_normalization_target() (histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method)
set_color_normalization_values() (histomicstk.saliency.cellularity_detection_superpixels.Cellularity_detector_superpixels method)
set_contours_from_all_masks() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method)
set_contours_slice() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)
set_hierarchy() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)
set_merged_contours() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method)
set_roi_bboxes() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method)
set_shared_roi_edges() (histomicstk.annotations_and_masks.polygon_merger.Polygon_merger method)
set_slide_ids() (histomicstk.workflows.workflow_runner.Slide_iterator method)
set_slide_info_and_get_tissue_mask() (histomicstk.saliency.cellularity_detection_superpixels.Cellularity_detector_superpixels method)
(histomicstk.saliency.cellularity_detection_thresholding.Cellularity_detector_thresholding method)
set_superpixel_assignment() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
set_superpixel_features() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
set_superpixel_mask() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
set_tissue_rgb() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
(histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
set_tree_dict() (histomicstk.annotations_and_masks.polygon_merger_v2.Polygon_merger_v2 method)
shuffle() (in module histomicstk.segmentation.label)
simple_mask() (in module histomicstk.segmentation)
(in module histomicstk.utils)
Slide_iterator (class in histomicstk.workflows.workflow_runner)
split() (in module histomicstk.segmentation.label)
stain_color_map (in module histomicstk.preprocessing.color_deconvolution)
stain_unmixing_routine() (in module histomicstk.preprocessing.color_deconvolution)
T
threshold_multichannel() (in module histomicstk.saliency.tissue_detection)
trace_object_boundaries() (in module histomicstk.segmentation.label)
V
vesselness() (in module histomicstk.filters.shape)
visualize_contiguous_superpixels() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
visualize_individual_superpixels() (histomicstk.saliency.cellularity_detection_superpixels.CD_single_tissue_piece method)
visualize_results() (histomicstk.saliency.cellularity_detection_thresholding.CDT_single_tissue_piece method)
W
width_open() (in module histomicstk.segmentation.label)
Workflow_runner (class in histomicstk.workflows.workflow_runner)
Y
yield_callback_output_for_annotation() (histomicstk.workflows.workflow_runner.Annotation_iterator method)