iss_preprocess package

Subpackages

• iss_preprocess.call package
  • Submodules
  • iss_preprocess.call.call module
    • basecall_rois()
    • call_genes()
    • extract_spots()
    • get_cluster_means()
    • rois_to_array()
  • iss_preprocess.call.omp module
    • barcode_spots_dot_product()
    • make_background_vectors()
    • make_gene_templates()
    • omp()
    • omp_weighted()
    • refine_gene_templates()
    • run_omp()
  • iss_preprocess.call.spot_shape module
    • apply_symmetry()
    • detect_spots_by_shape()
    • find_gene_spots()
    • get_spot_shape()
  • Module contents
• iss_preprocess.config package
  • Module contents
• iss_preprocess.coppafish package
  • Submodules
  • iss_preprocess.coppafish.utils module
    • annulus()
    • ftrans2()
    • hanning_diff()
    • scaled_k_means()
  • Module contents
• iss_preprocess.diagnostics package
  • Submodules
  • iss_preprocess.diagnostics.diag_ara module
    • plot_ara_registration()
  • iss_preprocess.diagnostics.diag_hybridisation module
    • check_hybridisation_setup()
  • iss_preprocess.diagnostics.diag_hybridisation module
    • check_hybridisation_setup()
  • iss_preprocess.diagnostics.diag_reg2ref module
    • check_reg_to_ref_correction()
    • check_registration_to_reference()
    • check_rolonies_registration()
    • check_tile_reg2ref()
    • debug_reg_to_ref()
  • iss_preprocess.diagnostics.diag_register module
    • check_affine_channel_registration()
    • check_ref_tile_registration()
    • check_sequencing_tile_registration()
    • check_shift_correction()
    • check_tile_registration()
    • check_tile_shifts()
  • iss_preprocess.diagnostics.diag_segmentation module
    • check_segmentation()
    • plot_mcherry_gmm()
    • plot_unmixing_diagnostics()
  • iss_preprocess.diagnostics.diag_sequencing module
    • check_barcode_basecall()
    • check_barcode_calling()
    • check_omp_alpha_thresholds()
    • check_omp_setup()
    • check_omp_thresholds()
  • iss_preprocess.diagnostics.diag_stitching module
    • check_barcode_mcherry_reg()
    • combine_overview_plots()
    • plot_overview_images()
    • plot_single_overview()
• iss_preprocess.image package
  • Submodules
  • iss_preprocess.image.correction module
    • apply_illumination_correction()
    • calculate_unmixing_coefficient()
    • compute_distribution()
    • filter_stack()
    • tilestats_and_mean_image()
    • unmix_images()
  • iss_preprocess.image.fstack module
    • fstack()
    • fstack_channels()
    • gauss3P()
    • gfocus()
  • Module contents
• iss_preprocess.io package
  • Submodules
  • iss_preprocess.io.load module
    • find_roi_position_on_cryostat()
    • get_channel_round_transforms()
    • get_pixel_size()
    • get_processed_path()
    • get_raw_filename()
    • get_raw_path()
    • get_roi_dimensions()
    • get_tile_ome()
    • get_z_step()
    • get_zprofile()
    • load_correction_image()
    • load_hyb_probes_metadata()
    • load_mask_by_coors()
    • load_metadata()
    • load_micromanager_metadata()
    • load_ops()
    • load_section_position()
    • load_sequencing_rounds()
    • load_stack()
    • load_tile_by_coors()
  • iss_preprocess.io.save module
    • save_ome_tiff_pyramid()
    • write_stack()
  • Module contents
• iss_preprocess.pipeline package
  • Submodules
  • iss_preprocess.pipeline.ara_registration module
    • check_reg()
    • crop_overview_registration()
    • find_roi_position_on_cryostat()
    • load_coordinate_image()
    • load_registration_reference()
    • load_registration_reference_metadata()
    • make_area_image()
    • overview_single_roi()
    • register_overview_to_reference()
    • spots_ara_infos()
  • iss_preprocess.pipeline.hybridisation module
    • estimate_channel_correction_hybridisation()
    • extract_hyb_spots_all()
    • extract_hyb_spots_roi()
    • extract_hyb_spots_tile()
    • hyb_spot_cluster_means()
    • load_and_register_hyb_tile()
    • setup_hyb_spot_calling()
  • iss_preprocess.pipeline.pipeline module
    • call_spots()
    • correct_shifts()
    • create_all_single_averages()
    • create_grand_averages()
    • create_single_average()
    • overview_for_ara_registration()
    • project_and_average()
    • register_acquisition()
    • register_reference_tile()
    • segment_and_stitch_mcherry_cells()
    • setup_channel_correction()
  • iss_preprocess.pipeline.project module
    • check_projection()
    • check_roi_dims()
    • project_round()
    • project_tile()
    • project_tile_by_coors()
    • project_tile_row()
    • reproject_failed()
  • iss_preprocess.pipeline.register module
    • correct_hyb_shifts()
    • correct_shifts_roi()
    • correct_shifts_single_round_roi()
    • correct_shifts_to_ref()
    • estimate_shifts_by_coors()
    • filter_ransac_shifts()
    • load_and_register_raw_stack()
    • load_and_register_sequencing_tile()
    • load_and_register_tile()
    • merge_shifts()
    • register_channels_by_pairs()
    • register_fluorescent_tile()
    • run_correct_shifts()
    • run_register_reference_tile()
  • iss_preprocess.pipeline.segment module
    • add_mask_id()
    • filter_mcherry_cells()
    • find_edge_touching_masks()
    • get_big_masks()
    • get_cell_masks()
    • get_overlap_regions()
    • get_stack_for_cellpose()
    • make_cell_dataframe()
    • remove_all_duplicate_masks()
    • run_cellpose_segmentation()
    • run_mask_projection()
    • save_curated_dataframes()
    • save_mcherry_mask_df()
    • save_unmixing_coefficients()
    • segment_all_rois()
    • segment_all_tiles()
    • segment_mcherry_tile()
    • segment_roi()
    • segment_spots()
    • unmix_tile()
  • iss_preprocess.pipeline.sequencing module
    • basecall_tile()
    • compute_spot_sign_image()
    • detect_genes_on_tile()
    • estimate_channel_correction()
    • get_reference_spots()
    • load_spot_sign_image()
    • run_omp_on_tile()
    • setup_barcode_calling()
    • setup_omp()
  • iss_preprocess.pipeline.stitch module
    • calculate_tile_positions()
    • find_tile_order()
    • find_tile_overlap()
    • get_tform_to_ref()
    • get_tile_corners()
    • load_tile_ref_coors()
    • register_adjacent_tiles()
    • register_all_rois_within()
    • register_within_acquisition()
    • stitch_and_register()
    • stitch_registered()
    • stitch_tiles()
    • warp_stack_to_ref()
  • Module contents
• iss_preprocess.reg package
  • Submodules
  • iss_preprocess.reg.rounds_and_channels module
    • align_channels_and_rounds()
    • align_within_channels()
    • apply_corrections()
    • correct_by_block()
    • estimate_affine_for_tile()
    • estimate_correction()
    • estimate_rotation_angle()
    • estimate_rotation_translation()
    • estimate_scale_rotation_translation()
    • estimate_shifts_and_angles_for_tile()
    • estimate_shifts_for_tile()
    • generate_channel_round_transforms()
    • get_channel_reference_images()
    • phase_correlation_by_block()
    • register_channels_and_rounds()
    • register_image_channels()
  • Module contents
• iss_preprocess.segment package
  • Submodules
  • iss_preprocess.segment.barcodes module
    • segment_spot_image()
  • iss_preprocess.segment.cells module
    • cellpose_segmentation()
    • count_spots()
    • label_image()
    • project_mask()
    • remove_overlapping_labels()
    • spot_mask_value()
  • iss_preprocess.segment.roi module
    • ROI
      • ROI.mask
      • ROI.npix
  • iss_preprocess.segment.spots module
    • convolve_spots()
    • detect_isolated_spots()
    • detect_spots()
    • make_spot_image()
  • Module contents
• iss_preprocess.vis package
  • Submodules
  • iss_preprocess.vis.diagnostics module
    • adjacent_tiles_registration()
    • check_reg2ref_using_stitched()
    • plot_affine_debug_images()
    • plot_all_rounds()
    • plot_correction_images()
    • plot_registration_correlograms()
    • plot_round_registration_diagnostics()
    • plot_spot_sign_image()
    • plot_tilestats_distributions()
  • iss_preprocess.vis.vis module
    • add_bases_legend()
    • animate_sequencing_rounds()
    • make_lut()
    • plot_clusters()
    • plot_gene_matrix()
    • plot_gene_templates()
    • plot_sequencing_rounds()
    • plot_spot_called_base()
    • plot_spots()
    • round_to_rgb()
    • to_rgb()
  • Module contents

Submodules

iss_preprocess.cli module

Module contents