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Z
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__init__() (ark.phenotyping.cluster_helpers.CellSOMCluster method)
(ark.phenotyping.cluster_helpers.ConsensusCluster method)
(ark.phenotyping.cluster_helpers.PixelSOMCluster method)
(ark.phenotyping.cluster_helpers.PixieConsensusCluster method)
(ark.phenotyping.cluster_helpers.PixieSOMCluster method)
(ark.utils.data_utils.ClusterMaskData method)
(ark.utils.example_dataset.ExampleDataset method)
(ark.utils.metacluster_remap_gui.zscore_norm.ZScoreNormalize method)
A
add_consensus_labels_cell_table() (in module ark.phenotyping.cell_cluster_utils)
add_to_composite() (in module ark.segmentation.ez_seg.composites)
AnnCollectionKwargs (class in ark.utils.data_utils)
AnnDataIterDataPipe (class in ark.utils.data_utils)
append_distance_features_to_dataset() (in module ark.analysis.spatial_analysis_utils)
apply_cell_meta_cluster_remapping() (in module ark.phenotyping.cell_meta_clustering)
apply_pixel_meta_cluster_remapping() (in module ark.phenotyping.pixel_meta_clustering)
ark.analysis.cell_neighborhood_stats
module
ark.analysis.dimensionality_reduction
module
ark.analysis.neighborhood_analysis
module
ark.analysis.spatial_analysis_utils
module
ark.analysis.spatial_enrichment
module
ark.analysis.visualize
module
ark.phenotyping.cell_cluster_utils
module
ark.phenotyping.cell_meta_clustering
module
ark.phenotyping.cell_som_clustering
module
ark.phenotyping.cluster_helpers
module
ark.phenotyping.pixel_cluster_utils
module
ark.phenotyping.pixel_meta_clustering
module
ark.phenotyping.pixel_som_clustering
module
ark.phenotyping.pixie_preprocessing
module
ark.phenotyping.post_cluster_utils
module
ark.phenotyping.weighted_channel_comp
module
ark.segmentation.ez_seg.composites
module
ark.segmentation.ez_seg.ez_object_segmentation
module
ark.segmentation.ez_seg.ez_seg_display
module
ark.segmentation.ez_seg.ez_seg_utils
module
ark.segmentation.ez_seg.merge_masks
module
ark.segmentation.fiber_segmentation
module
ark.segmentation.marker_quantification
module
ark.segmentation.regionprops_extraction
module
ark.segmentation.segmentation_utils
module
ark.segmentation.signal_extraction
module
ark.spLDA.processing
module
ark.utils.data_utils
module
ark.utils.deepcell_service_utils
module
ark.utils.example_dataset
module
ark.utils.masking_utils
module
ark.utils.metacluster_remap_gui.colormap_helper
module
ark.utils.metacluster_remap_gui.file_reader
module
ark.utils.metacluster_remap_gui.metaclusterdata
module
ark.utils.metacluster_remap_gui.metaclustergui
module
ark.utils.metacluster_remap_gui.throttle
module
ark.utils.metacluster_remap_gui.zscore_norm
module
ark.utils.plot_utils
module
ark.utils.spatial_lda_utils
module
assign_consensus_labels() (ark.phenotyping.cluster_helpers.PixieConsensusCluster method)
assign_multi_compartment_features() (in module ark.segmentation.marker_quantification)
assign_single_compartment_features() (in module ark.segmentation.marker_quantification)
assign_som_clusters() (ark.phenotyping.cluster_helpers.CellSOMCluster method)
(ark.phenotyping.cluster_helpers.PixelSOMCluster method)
B
background_color (ark.utils.plot_utils.MetaclusterColormap attribute)
C
calc_dist_matrix() (in module ark.analysis.spatial_analysis_utils)
calculate_channel_percentiles() (in module ark.phenotyping.pixel_cluster_utils)
calculate_channel_spatial_enrichment() (in module ark.analysis.spatial_enrichment)
calculate_cluster_spatial_enrichment() (in module ark.analysis.spatial_enrichment)
calculate_density() (in module ark.segmentation.fiber_segmentation)
calculate_enrichment_stats() (in module ark.analysis.spatial_analysis_utils)
calculate_fiber_alignment() (in module ark.segmentation.fiber_segmentation)
calculate_mean_distance_to_all_cell_types() (in module ark.analysis.cell_neighborhood_stats)
calculate_mean_distance_to_cell_type() (in module ark.analysis.cell_neighborhood_stats)
calculate_pixel_intensity_percentile() (in module ark.phenotyping.pixel_cluster_utils)
calibrate() (ark.utils.metacluster_remap_gui.zscore_norm.ZScoreNormalize method)
cell_consensus_cluster() (in module ark.phenotyping.cell_meta_clustering)
CellSOMCluster (class in ark.phenotyping.cluster_helpers)
center_weighting_extraction() (in module ark.segmentation.signal_extraction)
centroid_dif() (in module ark.segmentation.regionprops_extraction)
change_displayname() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
check_empty_dst() (ark.utils.example_dataset.ExampleDataset method)
check_featurize_cell_table_args() (in module ark.utils.spatial_lda_utils)
check_for_modified_channels() (in module ark.phenotyping.pixel_cluster_utils)
check_format_cell_table_args() (in module ark.utils.spatial_lda_utils)
clear_selection() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
cluster_cells() (in module ark.phenotyping.cell_som_clustering)
cluster_column (ark.utils.data_utils.ClusterMaskData attribute)
cluster_count (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
cluster_id_column (ark.utils.data_utils.ClusterMaskData attribute)
cluster_id_to_name_path (ark.utils.plot_utils.MetaclusterColormap attribute)
cluster_in_metacluster() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
cluster_names (ark.utils.data_utils.ClusterMaskData property)
cluster_pixels() (in module ark.phenotyping.pixel_som_clustering)
cluster_type (ark.utils.plot_utils.MetaclusterColormap attribute)
ClusterClassTemplate (class in ark.phenotyping.cluster_helpers)
ClusterMaskData (class in ark.utils.data_utils)
clusters (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
clusters_with_metaclusters (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
cmap (ark.utils.plot_utils.MetaclusterColormap attribute)
cohort_cluster_plot() (in module ark.utils.plot_utils)
color_segmentation_by_stat() (in module ark.utils.plot_utils)
composite_builder() (in module ark.segmentation.ez_seg.composites)
compute_cell_cluster_weighted_channel_avg() (in module ark.phenotyping.weighted_channel_comp)
compute_cell_ratios() (in module ark.analysis.neighborhood_analysis)
compute_cell_som_cluster_cols_avg() (in module ark.phenotyping.cell_cluster_utils)
compute_close_cell_num() (in module ark.analysis.spatial_analysis_utils)
compute_close_cell_num_random() (in module ark.analysis.spatial_analysis_utils)
compute_cluster_metrics_inertia() (in module ark.analysis.neighborhood_analysis)
compute_cluster_metrics_silhouette() (in module ark.analysis.neighborhood_analysis)
compute_kmeans_inertia() (in module ark.analysis.spatial_analysis_utils)
compute_kmeans_silhouette() (in module ark.analysis.spatial_analysis_utils)
compute_marker_counts() (in module ark.segmentation.marker_quantification)
compute_mixing_score() (in module ark.analysis.neighborhood_analysis)
compute_neighbor_counts() (in module ark.analysis.spatial_analysis_utils)
compute_neighborhood_diversity() (in module ark.analysis.cell_neighborhood_stats)
compute_p2c_weighted_channel_avg() (in module ark.phenotyping.weighted_channel_comp)
compute_pixel_cluster_channel_avg() (in module ark.phenotyping.pixel_cluster_utils)
compute_topic_eda() (in module ark.spLDA.processing)
concatenate_csv() (in module ark.segmentation.segmentation_utils)
ConsensusCluster (class in ark.phenotyping.cluster_helpers)
convert (ark.utils.data_utils.AnnCollectionKwargs attribute)
convert_to_adata() (ark.utils.data_utils.ConvertToAnnData method)
ConvertToAnnData (class in ark.utils.data_utils)
convex_hull_resid() (in module ark.segmentation.regionprops_extraction)
create_c2pc_data() (in module ark.phenotyping.cell_cluster_utils)
create_cell_mask() (in module ark.utils.masking_utils)
create_cmap() (in module ark.utils.plot_utils)
create_deepcell_output() (in module ark.utils.deepcell_service_utils)
create_difference_matrices() (in module ark.spLDA.processing)
create_fov_pixel_data() (in module ark.phenotyping.pixie_preprocessing)
create_mantis_dir() (in module ark.utils.plot_utils)
create_mantis_project() (in module ark.phenotyping.post_cluster_utils)
(in module ark.segmentation.ez_seg.ez_seg_utils)
create_marker_count_matrices() (in module ark.segmentation.marker_quantification)
create_neighborhood_matrix() (in module ark.analysis.neighborhood_analysis)
create_object_masks() (in module ark.segmentation.ez_seg.ez_object_segmentation)
create_overlap_and_merge_visual() (in module ark.segmentation.ez_seg.ez_seg_display)
create_overlay() (in module ark.utils.plot_utils)
create_pixel_matrix() (in module ark.phenotyping.pixie_preprocessing)
D
display_channel_image() (in module ark.segmentation.ez_seg.ez_seg_display)
distinct_cmap() (in module ark.utils.metacluster_remap_gui.colormap_helper)
distinct_rgbs() (in module ark.utils.metacluster_remap_gui.colormap_helper)
download_example_dataset() (ark.utils.example_dataset.ExampleDataset method)
draw_boxplot() (in module ark.analysis.visualize)
draw_heatmap() (in module ark.analysis.visualize)
E
enable_debug_mode() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
erode_mask() (in module ark.utils.data_utils)
ExampleDataset (class in ark.utils.example_dataset)
extract_deepcell_response() (in module ark.utils.deepcell_service_utils)
F
featurize_cell_table() (in module ark.spLDA.processing)
filter_csvs_by_mask() (in module ark.segmentation.ez_seg.ez_seg_utils)
filter_labels_in_bbox() (in module ark.segmentation.ez_seg.merge_masks)
filter_with_nuclear_mask() (in module ark.phenotyping.pixel_cluster_utils)
find_and_copy_files() (in module ark.segmentation.ez_seg.ez_seg_utils)
find_fovs_missing_col() (in module ark.phenotyping.pixel_cluster_utils)
find_nuclear_label_id() (in module ark.segmentation.segmentation_utils)
fit() (ark.phenotyping.cluster_helpers.ConsensusCluster method)
fit_predict() (ark.phenotyping.cluster_helpers.ClusterClassTemplate method)
fixed_width_marker_names (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
format_cell_table() (in module ark.spLDA.processing)
fov_column (ark.utils.data_utils.ClusterMaskData attribute)
fov_density() (in module ark.spLDA.processing)
fov_mapping() (ark.utils.data_utils.ClusterMaskData method)
fovs (ark.utils.data_utils.AnnDataIterDataPipe property)
G
gap_stat() (in module ark.spLDA.processing)
generate_and_save_cell_cluster_masks() (in module ark.utils.data_utils)
generate_and_save_neighborhood_cluster_masks() (in module ark.utils.data_utils)
generate_and_save_pixel_cluster_masks() (in module ark.utils.data_utils)
generate_cell_distance_analysis() (in module ark.analysis.cell_neighborhood_stats)
generate_cell_masks() (in module ark.utils.masking_utils)
generate_cell_table() (in module ark.segmentation.marker_quantification)
generate_channel_spatial_enrichment_stats() (in module ark.analysis.spatial_enrichment)
generate_cluster_labels() (in module ark.analysis.spatial_analysis_utils)
generate_cluster_mask() (in module ark.utils.data_utils)
generate_cluster_matrix_results() (in module ark.analysis.neighborhood_analysis)
generate_cluster_spatial_enrichment_stats() (in module ark.analysis.spatial_enrichment)
generate_deepcell_input() (in module ark.utils.deepcell_service_utils)
generate_meta_avg_files() (in module ark.phenotyping.cell_meta_clustering)
(in module ark.phenotyping.pixel_meta_clustering)
generate_meta_cluster_colormap_dict() (in module ark.utils.metacluster_remap_gui.colormap_helper)
generate_neighborhood_diversity_analysis() (in module ark.analysis.cell_neighborhood_stats)
generate_new_cluster_resolution() (in module ark.phenotyping.post_cluster_utils)
generate_pixel_cluster_mask() (in module ark.utils.data_utils)
generate_remap_avg_count_files() (in module ark.phenotyping.cell_meta_clustering)
generate_remap_avg_files() (in module ark.phenotyping.pixel_meta_clustering)
generate_remap_avg_wc_files() (in module ark.phenotyping.weighted_channel_comp)
generate_signal_masks() (in module ark.utils.masking_utils)
generate_som_avg_files() (in module ark.phenotyping.cell_som_clustering)
(in module ark.phenotyping.pixel_som_clustering)
generate_som_clusters() (ark.phenotyping.cluster_helpers.PixieSOMCluster method)
generate_som_to_meta_map() (ark.phenotyping.cluster_helpers.PixieConsensusCluster method)
generate_summary_stats() (in module ark.segmentation.fiber_segmentation)
generate_tile_stats() (in module ark.segmentation.fiber_segmentation)
generate_wc_avg_files() (in module ark.phenotyping.weighted_channel_comp)
generate_weighted_channel_avg_heatmap() (in module ark.phenotyping.weighted_channel_comp)
get_block_size() (in module ark.segmentation.ez_seg.ez_object_segmentation)
get_bounding_boxes() (in module ark.segmentation.ez_seg.merge_masks)
get_example_dataset() (in module ark.utils.example_dataset)
get_existing_mask_types() (in module ark.segmentation.marker_quantification)
get_metacluster_displayname() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
get_pos_cell_labels_channel() (in module ark.analysis.spatial_analysis_utils)
get_pos_cell_labels_cluster() (in module ark.analysis.spatial_analysis_utils)
get_single_compartment_props() (in module ark.segmentation.marker_quantification)
get_sorted_data() (in module ark.analysis.visualize)
H
harmonize_dtypes (ark.utils.data_utils.AnnCollectionKwargs attribute)
I
index_unique (ark.utils.data_utils.AnnCollectionKwargs attribute)
indices_strict (ark.utils.data_utils.AnnCollectionKwargs attribute)
inverse() (ark.utils.metacluster_remap_gui.zscore_norm.ZScoreNormalize method)
J
join_obs (ark.utils.data_utils.AnnCollectionKwargs attribute)
join_obsm (ark.utils.data_utils.AnnCollectionKwargs attribute)
join_vars (ark.utils.data_utils.AnnCollectionKwargs attribute)
L
label (ark.utils.data_utils.AnnCollectionKwargs attribute)
label_cells_by_cluster() (in module ark.utils.data_utils)
label_column (ark.utils.data_utils.ClusterMaskData attribute)
linkage_matrix (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
load_anndatas() (in module ark.utils.data_utils)
log_creator() (in module ark.segmentation.ez_seg.ez_seg_utils)
M
major_axis_equiv_diam_ratio() (in module ark.segmentation.regionprops_extraction)
major_minor_axis_ratio() (in module ark.segmentation.regionprops_extraction)
make_gui() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
make_plot_fn() (in module ark.utils.spatial_lda_utils)
make_widgets() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
map_segmentation_labels() (in module ark.utils.data_utils)
mapping (ark.utils.data_utils.ClusterMaskData attribute)
marker_count (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
marker_names (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
mc_colors (ark.utils.plot_utils.MetaclusterColormap attribute)
mcd (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui attribute)
merge_masks_seq() (in module ark.segmentation.ez_seg.merge_masks)
merge_masks_single() (in module ark.segmentation.ez_seg.merge_masks)
metacluster_colors (ark.utils.plot_utils.MetaclusterColormap attribute)
metacluster_count (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
metacluster_displaynames (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
metacluster_id_to_name (ark.utils.plot_utils.MetaclusterColormap attribute)
MetaclusterColormap (class in ark.utils.plot_utils)
MetaClusterData (class in ark.utils.metacluster_remap_gui.metaclusterdata)
metaclusterdata_from_files() (in module ark.utils.metacluster_remap_gui.file_reader)
MetaClusterGui (class in ark.utils.metacluster_remap_gui.metaclustergui)
metaclusters (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
module
ark.analysis.cell_neighborhood_stats
ark.analysis.dimensionality_reduction
ark.analysis.neighborhood_analysis
ark.analysis.spatial_analysis_utils
ark.analysis.spatial_enrichment
ark.analysis.visualize
ark.phenotyping.cell_cluster_utils
ark.phenotyping.cell_meta_clustering
ark.phenotyping.cell_som_clustering
ark.phenotyping.cluster_helpers
ark.phenotyping.pixel_cluster_utils
ark.phenotyping.pixel_meta_clustering
ark.phenotyping.pixel_som_clustering
ark.phenotyping.pixie_preprocessing
ark.phenotyping.post_cluster_utils
ark.phenotyping.weighted_channel_comp
ark.segmentation.ez_seg.composites
ark.segmentation.ez_seg.ez_object_segmentation
ark.segmentation.ez_seg.ez_seg_display
ark.segmentation.ez_seg.ez_seg_utils
ark.segmentation.ez_seg.merge_masks
ark.segmentation.fiber_segmentation
ark.segmentation.marker_quantification
ark.segmentation.regionprops_extraction
ark.segmentation.segmentation_utils
ark.segmentation.signal_extraction
ark.spLDA.processing
ark.utils.data_utils
ark.utils.deepcell_service_utils
ark.utils.example_dataset
ark.utils.masking_utils
ark.utils.metacluster_remap_gui.colormap_helper
ark.utils.metacluster_remap_gui.file_reader
ark.utils.metacluster_remap_gui.metaclusterdata
ark.utils.metacluster_remap_gui.metaclustergui
ark.utils.metacluster_remap_gui.throttle
ark.utils.metacluster_remap_gui.zscore_norm
ark.utils.plot_utils
ark.utils.spatial_lda_utils
move_dendro_labels() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
move_example_dataset() (ark.utils.example_dataset.ExampleDataset method)
multiple_mask_display() (in module ark.segmentation.ez_seg.ez_seg_display)
N
n_clusters (ark.phenotyping.cluster_helpers.ClusterClassTemplate property)
(ark.utils.data_utils.ClusterMaskData attribute)
nc_ratio() (in module ark.segmentation.regionprops_extraction)
new_metacluster() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
(ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
norm (ark.utils.plot_utils.MetaclusterColormap attribute)
normalize_data() (ark.phenotyping.cluster_helpers.CellSOMCluster method)
(ark.phenotyping.cluster_helpers.PixelSOMCluster method)
(ark.phenotyping.cluster_helpers.PixieSOMCluster method)
normalize_rows() (in module ark.phenotyping.pixel_cluster_utils)
num_concavities() (in module ark.segmentation.regionprops_extraction)
O
onpick() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
onpick_remap() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
onpick_select() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
output_mapping_filename (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData property)
overlay_mask_outlines() (in module ark.segmentation.ez_seg.ez_seg_display)
P
path_suffixes (ark.utils.example_dataset.ExampleDataset attribute)
perim_square_over_area() (in module ark.segmentation.regionprops_extraction)
pixel_consensus_cluster() (in module ark.phenotyping.pixel_meta_clustering)
PixelSOMCluster (class in ark.phenotyping.cluster_helpers)
PixieConsensusCluster (class in ark.phenotyping.cluster_helpers)
PixieSOMCluster (class in ark.phenotyping.cluster_helpers)
plot_barchart() (in module ark.analysis.visualize)
plot_cluster() (in module ark.utils.plot_utils)
plot_continuous_variable() (in module ark.utils.plot_utils)
plot_dim_reduced_data() (in module ark.analysis.dimensionality_reduction)
plot_fiber_segmentation_steps() (in module ark.segmentation.fiber_segmentation)
plot_fovs_with_topics() (in module ark.utils.spatial_lda_utils)
plot_hist_thresholds() (in module ark.phenotyping.post_cluster_utils)
plot_neighborhood_cluster_result() (in module ark.utils.plot_utils)
plot_pixel_cell_cluster() (in module ark.utils.plot_utils)
plot_topics_heatmap() (in module ark.utils.spatial_lda_utils)
positive_pixels_extraction() (in module ark.segmentation.signal_extraction)
predict() (ark.phenotyping.cluster_helpers.ConsensusCluster method)
predict_data() (ark.phenotyping.cluster_helpers.ConsensusCluster method)
preprocess_fov() (in module ark.phenotyping.pixie_preprocessing)
R
read_spatial_lda_file() (in module ark.utils.spatial_lda_utils)
relabel_segmentation() (in module ark.utils.data_utils)
remap() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
remap_current_selection() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
renumber_masks() (in module ark.segmentation.ez_seg.ez_seg_utils)
run_consensus_clustering() (ark.phenotyping.cluster_helpers.PixieConsensusCluster method)
run_deepcell_direct() (in module ark.utils.deepcell_service_utils)
run_fiber_segmentation() (in module ark.segmentation.fiber_segmentation)
run_pixel_consensus_assignment() (in module ark.phenotyping.pixel_meta_clustering)
run_pixel_som_assignment() (in module ark.phenotyping.pixel_som_clustering)
S
save_colored_mask() (in module ark.utils.plot_utils)
save_colored_masks() (in module ark.utils.plot_utils)
save_fov_mask() (in module ark.utils.data_utils)
save_output_mapping() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
save_segmentation_labels() (in module ark.segmentation.segmentation_utils)
save_som_to_meta_map() (ark.phenotyping.cluster_helpers.PixieConsensusCluster method)
save_spatial_lda_file() (in module ark.utils.spatial_lda_utils)
scale_data() (ark.phenotyping.cluster_helpers.PixieConsensusCluster method)
segment_fibers() (in module ark.segmentation.fiber_segmentation)
select_metacluster() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
selected_clusters (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui attribute)
selection_mask (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui property)
set_marker_order() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
set_minimum_color_for_colormap() (in module ark.utils.plot_utils)
shannon_diversity() (in module ark.analysis.cell_neighborhood_stats)
smooth_channels() (in module ark.phenotyping.pixel_cluster_utils)
split_img_stack() (in module ark.utils.data_utils)
split_large_nuclei() (in module ark.segmentation.segmentation_utils)
stitch_images_by_shape() (in module ark.utils.data_utils)
subtract_from_composite() (in module ark.segmentation.ez_seg.composites)
T
throttle() (in module ark.utils.metacluster_remap_gui.throttle)
tif_overlay_preprocess() (in module ark.utils.plot_utils)
total_intensity_extraction() (in module ark.segmentation.signal_extraction)
train_cell_som() (in module ark.phenotyping.cell_som_clustering)
train_pixel_som() (in module ark.phenotyping.pixel_som_clustering)
train_som() (ark.phenotyping.cluster_helpers.CellSOMCluster method)
(ark.phenotyping.cluster_helpers.PixelSOMCluster method)
(ark.phenotyping.cluster_helpers.PixieSOMCluster method)
transform_expression_matrix() (in module ark.segmentation.segmentation_utils)
U
unassigned_color (ark.utils.plot_utils.MetaclusterColormap attribute)
unassigned_id (ark.utils.data_utils.ClusterMaskData attribute)
(ark.utils.plot_utils.MetaclusterColormap attribute)
unique_fovs (ark.utils.data_utils.ClusterMaskData attribute)
update_current_metacluster() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
update_current_metacluster_displayname() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
update_current_metacluster_handler() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
update_gui() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
update_pixel_meta_labels() (in module ark.phenotyping.pixel_meta_clustering)
update_zscore() (ark.utils.metacluster_remap_gui.metaclustergui.MetaClusterGui method)
V
verify_unique_meta_clusters() (in module ark.phenotyping.cluster_helpers)
visualize_dimensionality_reduction() (in module ark.analysis.dimensionality_reduction)
visualize_fov_graphs() (in module ark.analysis.visualize)
visualize_fov_stats() (in module ark.analysis.visualize)
visualize_neighbor_cluster_metrics() (in module ark.analysis.visualize)
visualize_patient_population_distribution() (in module ark.analysis.visualize)
visualize_topic_eda() (in module ark.analysis.visualize)
W
which_metacluster() (ark.utils.metacluster_remap_gui.metaclusterdata.MetaClusterData method)
within_cluster_sums() (in module ark.utils.spatial_lda_utils)
Z
zip_input_files() (in module ark.utils.deepcell_service_utils)
ZScoreNormalize (class in ark.utils.metacluster_remap_gui.zscore_norm)
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