Index

_

__init__() (scallops.experiment.elements.Experiment method)

A

add_bases() (in module scallops.visualize.napari) agg_features() (in module scallops.features.agg) align_image() (in module scallops.registration.crosscorrelation) align_images() (in module scallops.registration.crosscorrelation)

apply_channel_crosstalk_matrix() (in module scallops.reads) apply_data_array() (in module scallops.xr) area_overlap() (in module scallops.segmentation.util) assign_barcodes_to_labels() (in module scallops.reads)

B

barcode_to_prefix() (in module scallops.reads)

base_call_mismatches_heatmap() (in module scallops.visualize.heatmap) base_counts() (in module scallops.reads)

C

cdf_plot() (in module scallops.visualize.distribution) channel_crosstalk_matrix() (in module scallops.reads) channel_hist_plot() (in module scallops.visualize.histogram) channel_thresholds() (in module scallops.visualize.utils) close_labels() (in module scallops.segmentation.util)

comparative_effect_scatter() (in module scallops.visualize.distribution) correct_mismatches() (in module scallops.reads) create_multiscene_hyperstack() (in module scallops.io) cyto_channel_summary() (in module scallops.segmentation) (in module scallops.segmentation.util)

D

decode_max() (in module scallops.reads)

decode_metric() (in module scallops.codebook) diagnose_registration() (in module scallops.visualize.registration)

E

estimate_scale_factors() (in module scallops.codebook) example_feature_summary_stats() (in module scallops.datasets)

Experiment (class in scallops.experiment.elements) experiment_composite() (in module scallops.visualize.composite) experiment_napari() (in module scallops.visualize.napari)

F

feldman_2019_small() (in module scallops.datasets) find_landmarks() (in module scallops.registration.landmarks)

find_objects() (in module scallops.features.find_objects) find_peaks() (in module scallops.spots)

G

get_image_spacing() (in module scallops.io)

get_pixel_positions() (in module scallops.io)

I

image2mask() (in module scallops.segmentation.util) image_to_codes() (in module scallops.codebook) images (scallops.experiment.elements.Experiment property) imcomposite() (in module scallops.visualize.composite) imnapari() (in module scallops.visualize.napari) imshow_plane() (in module scallops.visualize.imshow)

in_situ_barcode_hist_plot() (in module scallops.visualize.histogram) in_situ_identity_matrix_plot() (in module scallops.visualize.heatmap) iter_data_array() (in module scallops.xr) itk_align() (in module scallops.registration.itk) itk_align_to_reference_time() (in module scallops.registration.itk) itk_transform_image() (in module scallops.registration.itk) itk_transform_labels() (in module scallops.registration.itk)

L

label_features() (in module scallops.features.generate)

label_montage() (in module scallops.visualize.composite) labels (scallops.experiment.elements.Experiment property)

M

map_images() (in module scallops.experiment.util) match_template() (in module scallops.registration.landmarks) max_filter() (in module scallops.spots)

merge_sbs_phenotype() (in module scallops.reads) montage_plot() (in module scallops.visualize.composite) multicolor_labels() (in module scallops.visualize.utils)

N

normalize_base_intensities() (in module scallops.spots)

normalize_features() (in module scallops.features.normalize)

P

pairwise_channel_scatter_plot() (in module scallops.visualize.crosstalk) peak_thresholds_from_bases() (in module scallops.spots) peak_thresholds_from_reads() (in module scallops.spots) peaks_to_bases() (in module scallops.reads) physical_coords_to_px() (in module scallops.io)

plate_heatmap() (in module scallops.visualize.heatmap) plot_percentile_montage() (in module scallops.visualize.imshow) plot_plate() (in module scallops.visualize.imshow) plot_registration() (in module scallops.visualize.registration) plot_segmentation() (in module scallops.visualize.segmentation) plot_well_aggregated_heatmaps() (in module scallops.visualize.heatmap)

Q

quality_softmax() (in module scallops.reads)

R

radial_distortion_estimation() (in module scallops.visualize.napari) rank_features() (in module scallops.features.rank) read_barcodes() (in module scallops.io) read_experiment() (in module scallops.io) read_image() (in module scallops.io) read_in_situ_reads_and_barcodes() (in module scallops.io) read_ome_zarr_array() (in module scallops.zarr_io)

read_statistics() (in module scallops.reads) remove_boundary_labels() (in module scallops.segmentation.util) remove_labels_by_area() (in module scallops.segmentation.util) remove_labels_region_props() (in module scallops.segmentation.util) remove_masked_regions() (in module scallops.segmentation.util) remove_small_objects_std() (in module scallops.segmentation.util) ridge_plot() (in module scallops.visualize.distribution)

S

save() (scallops.experiment.elements.Experiment method) save_ome_tiff() (in module scallops.io) save_stack_imagej() (in module scallops.io) segment_cells_cellpose() (in module scallops.segmentation.cellpose) segment_cells_propagation() (in module scallops.segmentation.propagation)

segment_cells_watershed() (in module scallops.segmentation.watershed) segment_nuclei_cellpose() (in module scallops.segmentation.cellpose) segment_nuclei_stardist() (in module scallops.segmentation.stardist) segment_nuclei_watershed() (in module scallops.segmentation.watershed) std() (in module scallops.spots) summarize_base_call_mismatches() (in module scallops.reads)

T

threshold_quantile() (in module scallops.segmentation.util) tile_overlap_mask() (in module scallops.stitch.utils)

tiles_over_stitch() (in module scallops.visualize.imshow) to_label_crops() (in module scallops.io) transform_log() (in module scallops.spots)

U

unit_norm() (in module scallops.codebook)

V

volcano_plot() (in module scallops.visualize.distribution)

W

write_zarr() (in module scallops.zarr_io)