Index

A

add_bases_legend() (in module iss_preprocess.vis.vis) add_mask_id() (in module iss_preprocess.pipeline.segment) adjacent_tiles_registration() (in module iss_preprocess.vis.diagnostics) align_channels_and_rounds() (in module iss_preprocess.reg.rounds_and_channels) align_within_channels() (in module iss_preprocess.reg.rounds_and_channels)

animate_sequencing_rounds() (in module iss_preprocess.vis.vis) annulus() (in module iss_preprocess.coppafish.utils) apply_corrections() (in module iss_preprocess.reg.rounds_and_channels) apply_illumination_correction() (in module iss_preprocess.image.correction) apply_symmetry() (in module iss_preprocess.call.spot_shape)

B

barcode_spots_dot_product() (in module iss_preprocess.call.omp)

basecall_rois() (in module iss_preprocess.call.call) basecall_tile() (in module iss_preprocess.pipeline.sequencing)

C

calculate_tile_positions() (in module iss_preprocess.pipeline.stitch) calculate_unmixing_coefficient() (in module iss_preprocess.image.correction) call_genes() (in module iss_preprocess.call.call) call_spots() (in module iss_preprocess.pipeline.pipeline) cellpose_segmentation() (in module iss_preprocess.segment.cells) check_affine_channel_registration() (in module iss_preprocess.diagnostics.diag_register) check_barcode_basecall() (in module iss_preprocess.diagnostics.diag_sequencing) check_barcode_calling() (in module iss_preprocess.diagnostics.diag_sequencing) check_barcode_mcherry_reg() (in module iss_preprocess.diagnostics.diag_stitching) check_hybridisation_setup() (in module iss_preprocess.diagnostics.diag_hybridisation), [1] check_omp_alpha_thresholds() (in module iss_preprocess.diagnostics.diag_sequencing) check_omp_setup() (in module iss_preprocess.diagnostics.diag_sequencing) check_omp_thresholds() (in module iss_preprocess.diagnostics.diag_sequencing) check_projection() (in module iss_preprocess.pipeline.project) check_ref_tile_registration() (in module iss_preprocess.diagnostics.diag_register) check_reg() (in module iss_preprocess.pipeline.ara_registration) check_reg2ref_using_stitched() (in module iss_preprocess.vis.diagnostics) check_reg_to_ref_correction() (in module iss_preprocess.diagnostics.diag_reg2ref) check_registration_to_reference() (in module iss_preprocess.diagnostics.diag_reg2ref) check_roi_dims() (in module iss_preprocess.pipeline.project) check_rolonies_registration() (in module iss_preprocess.diagnostics.diag_reg2ref)

check_segmentation() (in module iss_preprocess.diagnostics.diag_segmentation) check_sequencing_tile_registration() (in module iss_preprocess.diagnostics.diag_register) check_shift_correction() (in module iss_preprocess.diagnostics.diag_register) check_tile_reg2ref() (in module iss_preprocess.diagnostics.diag_reg2ref) check_tile_registration() (in module iss_preprocess.diagnostics.diag_register) check_tile_shifts() (in module iss_preprocess.diagnostics.diag_register) combine_overview_plots() (in module iss_preprocess.diagnostics.diag_stitching) compute_distribution() (in module iss_preprocess.image.correction) compute_spot_sign_image() (in module iss_preprocess.pipeline.sequencing) convolve_spots() (in module iss_preprocess.segment.spots) correct_by_block() (in module iss_preprocess.reg.rounds_and_channels) correct_hyb_shifts() (in module iss_preprocess.pipeline.register) correct_shifts() (in module iss_preprocess.pipeline.pipeline) correct_shifts_roi() (in module iss_preprocess.pipeline.register) correct_shifts_single_round_roi() (in module iss_preprocess.pipeline.register) correct_shifts_to_ref() (in module iss_preprocess.pipeline.register) count_spots() (in module iss_preprocess.segment.cells) create_all_single_averages() (in module iss_preprocess.pipeline.pipeline) create_grand_averages() (in module iss_preprocess.pipeline.pipeline) create_single_average() (in module iss_preprocess.pipeline.pipeline) crop_overview_registration() (in module iss_preprocess.pipeline.ara_registration)

D

debug_reg_to_ref() (in module iss_preprocess.diagnostics.diag_reg2ref) detect_genes_on_tile() (in module iss_preprocess.pipeline.sequencing)

detect_isolated_spots() (in module iss_preprocess.segment.spots) detect_spots() (in module iss_preprocess.segment.spots) detect_spots_by_shape() (in module iss_preprocess.call.spot_shape)

E

estimate_affine_for_tile() (in module iss_preprocess.reg.rounds_and_channels) estimate_channel_correction() (in module iss_preprocess.pipeline.sequencing) estimate_channel_correction_hybridisation() (in module iss_preprocess.pipeline.hybridisation) estimate_correction() (in module iss_preprocess.reg.rounds_and_channels) estimate_rotation_angle() (in module iss_preprocess.reg.rounds_and_channels) estimate_rotation_translation() (in module iss_preprocess.reg.rounds_and_channels) estimate_scale_rotation_translation() (in module iss_preprocess.reg.rounds_and_channels)

estimate_shifts_and_angles_for_tile() (in module iss_preprocess.reg.rounds_and_channels) estimate_shifts_by_coors() (in module iss_preprocess.pipeline.register) estimate_shifts_for_tile() (in module iss_preprocess.reg.rounds_and_channels) extract_hyb_spots_all() (in module iss_preprocess.pipeline.hybridisation) extract_hyb_spots_roi() (in module iss_preprocess.pipeline.hybridisation) extract_hyb_spots_tile() (in module iss_preprocess.pipeline.hybridisation) extract_spots() (in module iss_preprocess.call.call)

F

filter_mcherry_cells() (in module iss_preprocess.pipeline.segment) filter_ransac_shifts() (in module iss_preprocess.pipeline.register) filter_stack() (in module iss_preprocess.image.correction) find_edge_touching_masks() (in module iss_preprocess.pipeline.segment) find_gene_spots() (in module iss_preprocess.call.spot_shape) find_roi_position_on_cryostat() (in module iss_preprocess.io.load) (in module iss_preprocess.pipeline.ara_registration)

find_tile_order() (in module iss_preprocess.pipeline.stitch) find_tile_overlap() (in module iss_preprocess.pipeline.stitch) fstack() (in module iss_preprocess.image.fstack) fstack_channels() (in module iss_preprocess.image.fstack) ftrans2() (in module iss_preprocess.coppafish.utils)

G

gauss3P() (in module iss_preprocess.image.fstack) generate_channel_round_transforms() (in module iss_preprocess.reg.rounds_and_channels) get_big_masks() (in module iss_preprocess.pipeline.segment) get_cell_masks() (in module iss_preprocess.pipeline.segment) get_channel_reference_images() (in module iss_preprocess.reg.rounds_and_channels) get_channel_round_transforms() (in module iss_preprocess.io.load) get_cluster_means() (in module iss_preprocess.call.call) get_overlap_regions() (in module iss_preprocess.pipeline.segment) get_pixel_size() (in module iss_preprocess.io.load) get_processed_path() (in module iss_preprocess.io.load) get_raw_filename() (in module iss_preprocess.io.load)

get_raw_path() (in module iss_preprocess.io.load) get_reference_spots() (in module iss_preprocess.pipeline.sequencing) get_roi_dimensions() (in module iss_preprocess.io.load) get_spot_shape() (in module iss_preprocess.call.spot_shape) get_stack_for_cellpose() (in module iss_preprocess.pipeline.segment) get_tform_to_ref() (in module iss_preprocess.pipeline.stitch) get_tile_corners() (in module iss_preprocess.pipeline.stitch) get_tile_ome() (in module iss_preprocess.io.load) get_z_step() (in module iss_preprocess.io.load) get_zprofile() (in module iss_preprocess.io.load) gfocus() (in module iss_preprocess.image.fstack)

H

hanning_diff() (in module iss_preprocess.coppafish.utils)

hyb_spot_cluster_means() (in module iss_preprocess.pipeline.hybridisation)

I

iss_preprocess module iss_preprocess.call module iss_preprocess.call.call module iss_preprocess.call.omp module iss_preprocess.call.spot_shape module iss_preprocess.cli module iss_preprocess.config module iss_preprocess.coppafish module iss_preprocess.coppafish.utils module iss_preprocess.diagnostics.diag_ara module iss_preprocess.diagnostics.diag_hybridisation module, [1] iss_preprocess.diagnostics.diag_reg2ref module iss_preprocess.diagnostics.diag_register module iss_preprocess.diagnostics.diag_segmentation module iss_preprocess.diagnostics.diag_sequencing module iss_preprocess.diagnostics.diag_stitching module iss_preprocess.image module iss_preprocess.image.correction module iss_preprocess.image.fstack module iss_preprocess.io module iss_preprocess.io.load module

iss_preprocess.io.save module iss_preprocess.pipeline module iss_preprocess.pipeline.ara_registration module iss_preprocess.pipeline.hybridisation module iss_preprocess.pipeline.pipeline module iss_preprocess.pipeline.project module iss_preprocess.pipeline.register module iss_preprocess.pipeline.segment module iss_preprocess.pipeline.sequencing module iss_preprocess.pipeline.stitch module iss_preprocess.reg module iss_preprocess.reg.rounds_and_channels module iss_preprocess.segment module iss_preprocess.segment.barcodes module iss_preprocess.segment.cells module iss_preprocess.segment.roi module iss_preprocess.segment.spots module iss_preprocess.vis module iss_preprocess.vis.diagnostics module iss_preprocess.vis.vis module

L

label_image() (in module iss_preprocess.segment.cells) load_and_register_hyb_tile() (in module iss_preprocess.pipeline.hybridisation) load_and_register_raw_stack() (in module iss_preprocess.pipeline.register) load_and_register_sequencing_tile() (in module iss_preprocess.pipeline.register) load_and_register_tile() (in module iss_preprocess.pipeline.register) load_coordinate_image() (in module iss_preprocess.pipeline.ara_registration) load_correction_image() (in module iss_preprocess.io.load) load_hyb_probes_metadata() (in module iss_preprocess.io.load) load_mask_by_coors() (in module iss_preprocess.io.load) load_metadata() (in module iss_preprocess.io.load)

load_micromanager_metadata() (in module iss_preprocess.io.load) load_ops() (in module iss_preprocess.io.load) load_registration_reference() (in module iss_preprocess.pipeline.ara_registration) load_registration_reference_metadata() (in module iss_preprocess.pipeline.ara_registration) load_section_position() (in module iss_preprocess.io.load) load_sequencing_rounds() (in module iss_preprocess.io.load) load_spot_sign_image() (in module iss_preprocess.pipeline.sequencing) load_stack() (in module iss_preprocess.io.load) load_tile_by_coors() (in module iss_preprocess.io.load) load_tile_ref_coors() (in module iss_preprocess.pipeline.stitch)

M

make_area_image() (in module iss_preprocess.pipeline.ara_registration) make_background_vectors() (in module iss_preprocess.call.omp) make_cell_dataframe() (in module iss_preprocess.pipeline.segment) make_gene_templates() (in module iss_preprocess.call.omp) make_lut() (in module iss_preprocess.vis.vis) make_spot_image() (in module iss_preprocess.segment.spots) mask (iss_preprocess.segment.roi.ROI property) merge_shifts() (in module iss_preprocess.pipeline.register) module iss_preprocess iss_preprocess.call iss_preprocess.call.call iss_preprocess.call.omp iss_preprocess.call.spot_shape iss_preprocess.cli iss_preprocess.config iss_preprocess.coppafish iss_preprocess.coppafish.utils iss_preprocess.diagnostics.diag_ara iss_preprocess.diagnostics.diag_hybridisation, [1] iss_preprocess.diagnostics.diag_reg2ref iss_preprocess.diagnostics.diag_register iss_preprocess.diagnostics.diag_segmentation iss_preprocess.diagnostics.diag_sequencing iss_preprocess.diagnostics.diag_stitching iss_preprocess.image iss_preprocess.image.correction iss_preprocess.image.fstack iss_preprocess.io iss_preprocess.io.load iss_preprocess.io.save iss_preprocess.pipeline iss_preprocess.pipeline.ara_registration iss_preprocess.pipeline.hybridisation iss_preprocess.pipeline.pipeline iss_preprocess.pipeline.project iss_preprocess.pipeline.register iss_preprocess.pipeline.segment iss_preprocess.pipeline.sequencing iss_preprocess.pipeline.stitch iss_preprocess.reg iss_preprocess.reg.rounds_and_channels iss_preprocess.segment iss_preprocess.segment.barcodes iss_preprocess.segment.cells iss_preprocess.segment.roi iss_preprocess.segment.spots iss_preprocess.vis iss_preprocess.vis.diagnostics iss_preprocess.vis.vis

N

npix (iss_preprocess.segment.roi.ROI property)

O

omp() (in module iss_preprocess.call.omp) omp_weighted() (in module iss_preprocess.call.omp)

overview_for_ara_registration() (in module iss_preprocess.pipeline.pipeline) overview_single_roi() (in module iss_preprocess.pipeline.ara_registration)

P

phase_correlation_by_block() (in module iss_preprocess.reg.rounds_and_channels) plot_affine_debug_images() (in module iss_preprocess.vis.diagnostics) plot_all_rounds() (in module iss_preprocess.vis.diagnostics) plot_ara_registration() (in module iss_preprocess.diagnostics.diag_ara) plot_clusters() (in module iss_preprocess.vis.vis) plot_correction_images() (in module iss_preprocess.vis.diagnostics) plot_gene_matrix() (in module iss_preprocess.vis.vis) plot_gene_templates() (in module iss_preprocess.vis.vis) plot_mcherry_gmm() (in module iss_preprocess.diagnostics.diag_segmentation) plot_overview_images() (in module iss_preprocess.diagnostics.diag_stitching) plot_registration_correlograms() (in module iss_preprocess.vis.diagnostics) plot_round_registration_diagnostics() (in module iss_preprocess.vis.diagnostics)

plot_sequencing_rounds() (in module iss_preprocess.vis.vis) plot_single_overview() (in module iss_preprocess.diagnostics.diag_stitching) plot_spot_called_base() (in module iss_preprocess.vis.vis) plot_spot_sign_image() (in module iss_preprocess.vis.diagnostics) plot_spots() (in module iss_preprocess.vis.vis) plot_tilestats_distributions() (in module iss_preprocess.vis.diagnostics) plot_unmixing_diagnostics() (in module iss_preprocess.diagnostics.diag_segmentation) project_and_average() (in module iss_preprocess.pipeline.pipeline) project_mask() (in module iss_preprocess.segment.cells) project_round() (in module iss_preprocess.pipeline.project) project_tile() (in module iss_preprocess.pipeline.project) project_tile_by_coors() (in module iss_preprocess.pipeline.project) project_tile_row() (in module iss_preprocess.pipeline.project)

R

refine_gene_templates() (in module iss_preprocess.call.omp) register_acquisition() (in module iss_preprocess.pipeline.pipeline) register_adjacent_tiles() (in module iss_preprocess.pipeline.stitch) register_all_rois_within() (in module iss_preprocess.pipeline.stitch) register_channels_and_rounds() (in module iss_preprocess.reg.rounds_and_channels) register_channels_by_pairs() (in module iss_preprocess.pipeline.register) register_fluorescent_tile() (in module iss_preprocess.pipeline.register) register_image_channels() (in module iss_preprocess.reg.rounds_and_channels) register_overview_to_reference() (in module iss_preprocess.pipeline.ara_registration) register_reference_tile() (in module iss_preprocess.pipeline.pipeline) register_within_acquisition() (in module iss_preprocess.pipeline.stitch)

remove_all_duplicate_masks() (in module iss_preprocess.pipeline.segment) remove_overlapping_labels() (in module iss_preprocess.segment.cells) reproject_failed() (in module iss_preprocess.pipeline.project) ROI (class in iss_preprocess.segment.roi) rois_to_array() (in module iss_preprocess.call.call) round_to_rgb() (in module iss_preprocess.vis.vis) run_cellpose_segmentation() (in module iss_preprocess.pipeline.segment) run_correct_shifts() (in module iss_preprocess.pipeline.register) run_mask_projection() (in module iss_preprocess.pipeline.segment) run_omp() (in module iss_preprocess.call.omp) run_omp_on_tile() (in module iss_preprocess.pipeline.sequencing) run_register_reference_tile() (in module iss_preprocess.pipeline.register)

S

save_curated_dataframes() (in module iss_preprocess.pipeline.segment) save_mcherry_mask_df() (in module iss_preprocess.pipeline.segment) save_ome_tiff_pyramid() (in module iss_preprocess.io.save) save_unmixing_coefficients() (in module iss_preprocess.pipeline.segment) scaled_k_means() (in module iss_preprocess.coppafish.utils) segment_all_rois() (in module iss_preprocess.pipeline.segment) segment_all_tiles() (in module iss_preprocess.pipeline.segment) segment_and_stitch_mcherry_cells() (in module iss_preprocess.pipeline.pipeline) segment_mcherry_tile() (in module iss_preprocess.pipeline.segment) segment_roi() (in module iss_preprocess.pipeline.segment)

segment_spot_image() (in module iss_preprocess.segment.barcodes) segment_spots() (in module iss_preprocess.pipeline.segment) setup_barcode_calling() (in module iss_preprocess.pipeline.sequencing) setup_channel_correction() (in module iss_preprocess.pipeline.pipeline) setup_hyb_spot_calling() (in module iss_preprocess.pipeline.hybridisation) setup_omp() (in module iss_preprocess.pipeline.sequencing) spot_mask_value() (in module iss_preprocess.segment.cells) spots_ara_infos() (in module iss_preprocess.pipeline.ara_registration) stitch_and_register() (in module iss_preprocess.pipeline.stitch) stitch_registered() (in module iss_preprocess.pipeline.stitch) stitch_tiles() (in module iss_preprocess.pipeline.stitch)

T

tilestats_and_mean_image() (in module iss_preprocess.image.correction)

to_rgb() (in module iss_preprocess.vis.vis)

U

unmix_images() (in module iss_preprocess.image.correction)

unmix_tile() (in module iss_preprocess.pipeline.segment)

W

warp_stack_to_ref() (in module iss_preprocess.pipeline.stitch)

write_stack() (in module iss_preprocess.io.save)