Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | V | W | X | Z A add_feature_matrix() (in module harpy.tb) add_grid_labels() (in module harpy.im) add_image() (in module harpy.im) add_labels() (in module harpy.im) add_points() (in module harpy.pt) add_regionprops() (in module harpy.tb) add_shapes() (in module harpy.sh) add_table() (in module harpy.tb) aggregate_area() (harpy.utils.RasterAggregator method) aggregate_kurtosis() (harpy.utils.RasterAggregator method) aggregate_max() (harpy.utils.RasterAggregator method) aggregate_mean() (harpy.utils.RasterAggregator method) aggregate_min() (harpy.utils.RasterAggregator method) aggregate_skew() (harpy.utils.RasterAggregator method) aggregate_stats() (harpy.utils.RasterAggregator method) aggregate_sum() (harpy.utils.RasterAggregator method) aggregate_var() (harpy.utils.RasterAggregator method) align_labels() (in module harpy.im) allocate() (in module harpy.tb) allocate_intensity() (in module harpy.tb) analyse_genes_left_out() (in module harpy.qc) B batch_size (harpy.tb.ZarrDataLoader attribute) baysor_callable() (in module harpy.im) bin_counts() (in module harpy.tb) bounding_box_query() (in module harpy.utils) C calculate_instance_statistics() (harpy.utils.Featurizer method) cell_clustering_preprocess() (in module harpy.tb) cellpose_callable() (in module harpy.im) center_of_mass() (harpy.utils.RasterAggregator method) check_worker_number_rationality() (harpy.tb.ZarrDataLoader method) cluster_blobs() (in module harpy.datasets) cluster_cleanliness() (in module harpy.tb) cluster_intensity() (in module harpy.tb) cluster_intensity_heatmap() (in module harpy.pl) cluster_intensity_SOM() (in module harpy.tb) clustermap() (in module harpy.pl) codex_example() (in module harpy.datasets) combine() (in module harpy.im) convert_to_zarr_2() (in module harpy.io) correct_marker_genes() (in module harpy.tb) create_voronoi_boundaries() (in module harpy.sh) D dataset (harpy.tb.ZarrDataLoader attribute) drop_last (harpy.tb.ZarrDataLoader attribute) E enhance_contrast() (in module harpy.im) expand_labels() (in module harpy.im) extract_instances() (harpy.utils.Featurizer method) (in module harpy.tb) F featurize() (harpy.utils.Featurizer method) (in module harpy.tb) Featurizer (class in harpy.utils) filter_labels() (in module harpy.im) filter_on_size() (in module harpy.tb) filter_shapes() (in module harpy.sh) flowsom() (in module harpy.im) (in module harpy.tb) G gaussian_filtering() (in module harpy.im) get_dataarray() (in module harpy.im) get_registry() (in module harpy.datasets) get_spatialdata_registry() (in module harpy.datasets) group_snr_ratio() (in module harpy.pl) H harpy module harpy.datasets module harpy.externals module harpy.im module harpy.io module harpy.pl module harpy.pt module harpy.qc module harpy.sh module harpy.tb module harpy.utils module I image_histogram() (in module harpy.qc) instanseg_callable() (in module harpy.im) K kmeans() (in module harpy.tb) kronos_embedding() (in module harpy.utils) L leiden() (in module harpy.tb) M macsima() (in module harpy.io) macsima_colorectal_carcinoma() (in module harpy.datasets) macsima_colorectal_carcinoma_course() (in module harpy.datasets) macsima_example() (in module harpy.datasets) macsima_tonsil() (in module harpy.datasets) map_image() (in module harpy.im) map_labels() (in module harpy.im) match_labels_to_reference() (in module harpy.im) merge_labels() (in module harpy.im) merscope() (in module harpy.io) merscope_mouse_liver() (in module harpy.datasets) metric_histogram() (in module harpy.qc) metrics_histogram() (in module harpy.qc) mibi_example() (in module harpy.datasets) min_max_filtering() (in module harpy.im) module harpy harpy.datasets harpy.externals harpy.im harpy.io harpy.pl harpy.pt harpy.qc harpy.sh harpy.tb harpy.utils multiprocessing_context (harpy.tb.ZarrDataLoader attribute) multisample_blobs() (in module harpy.datasets) N nhood_enrichment() (in module harpy.tb) nhood_kmeans() (in module harpy.tb) normalize() (in module harpy.im) num_workers (harpy.tb.ZarrDataLoader attribute) O obs_scatter() (in module harpy.qc) P pin_memory (harpy.tb.ZarrDataLoader attribute) pin_memory_device (harpy.tb.ZarrDataLoader attribute) pixel_clustering_preprocess() (in module harpy.im) pixel_clusters() (in module harpy.pl) pixel_clusters_heatmap() (in module harpy.pl) pixie_example() (in module harpy.datasets) plot_instance_density() (in module harpy.pl) plot_sdata() (in module harpy.pl) plot_sdata_genes() (in module harpy.pl) plot_transcript_density() (in module harpy.pl) prefetch_factor (harpy.tb.ZarrDataLoader attribute) preprocess_proteomics() (in module harpy.tb) preprocess_transcriptomics() (in module harpy.tb) Q quantiles() (harpy.utils.Featurizer method) R radii_and_principal_axes() (harpy.utils.Featurizer method) RasterAggregator (class in harpy.utils) rasterize() (in module harpy.im) read_merscope_transcripts() (in module harpy.io) read_resolve_transcripts() (in module harpy.io) read_stereoseq_transcripts() (in module harpy.io) read_transcripts() (in module harpy.io) resolve_example() (in module harpy.datasets) run_object_classification() (in module harpy.externals.ilastik) S sampler (harpy.tb.ZarrDataLoader attribute) score_genes() (in module harpy.tb) score_genes_iter() (in module harpy.tb) segment() (in module harpy.im) segment_points() (in module harpy.im) segmentation_coverage() (in module harpy.qc) segmentation_histogram() (in module harpy.qc) set_epoch() (harpy.tb.ZarrIterableInstances method) signal_clustermap() (in module harpy.pl) snr_clustermap() (in module harpy.pl) snr_ratio() (in module harpy.pl) spatial_pixel_neighbors() (in module harpy.tb) T tiling_correction() (in module harpy.im) timeout (harpy.tb.ZarrDataLoader attribute) transcript_density() (in module harpy.im) V vectorize() (in module harpy.sh) vectra_example() (in module harpy.datasets) visium() (in module harpy.io) visium_hd() (in module harpy.io) visium_hd_example() (in module harpy.datasets) visium_hd_example_custom_binning() (in module harpy.datasets) W weighted_channel_expression() (in module harpy.tb) X xenium() (in module harpy.io) xenium_human_lung_cancer() (in module harpy.datasets) xenium_human_ovarian_cancer() (in module harpy.datasets) xenium_human_ovarian_cancer_course() (in module harpy.datasets) Z ZarrDataLoader (class in harpy.tb) ZarrIterableInstances (class in harpy.tb)
