Index

A

aggregate_puncta_analysis() (in module exm.puncta.benchmark) algin_channels() (in module exm.beta.beta) algin_channels_function() (in module exm.beta.beta) algin_channels_function_new() (in module exm.beta.beta)

algin_channels_new() (in module exm.beta.beta) alignment_NCC() (in module exm.align.align_utils) apply_mask() (exm.stitching.tileset.Tile method) apply_new_ids() (in module exm.stitching.stitching) Args (class in exm.args)

B

blend() (in module exm.stitching.stitching)

blend2() (in module exm.stitching.stitching) blend_ind() (in module exm.beta.beta)

C

calculate_alignment_evaluation_ci() (in module exm.align.align_eval) calculate_coords_cpu() (in module exm.puncta.extract) calculate_coords_gpu() (in module exm.puncta.extract) chmod() (in module exm.utils.utils) configure_logger() (in module exm.utils.log) consolidate_channels() (in module exm.puncta.consolidate)

consolidate_channels_function() (in module exm.puncta.consolidate) consolidate_codes() (in module exm.puncta.consolidate) consolidate_codes_function() (in module exm.puncta.consolidate) create_blank_h5bdv() (exm.stitching.tileset.Tileset method) create_directroy_structure() (exm.args.Args method) create_folder_structure() (in module exm.io.io)

D

dedup_segmentation_ids() (exm.stitching.tileset.Tileset method) deduplicate_blob_ids() (in module exm.stitching.stitching) display_3d_masks() (in module exm.segmentation.segmentation)

display_img() (in module exm.utils.utils) downsample() (in module exm.io.io) downsample_volume() (in module exm.utils.utils)

E

enhance_and_filter_volume() (in module exm.utils.utils) execute_volumetric_alignment_bigstream() (in module exm.align.align) exm.align.align module exm.align.align_eval module exm.align.align_utils module exm.beta.beta module exm.io.io module exm.puncta.basecalling module exm.puncta.benchmark module

exm.puncta.consolidate module exm.puncta.extract module exm.puncta.improve module exm.puncta.inspect module exm.segmentation.segmentation module exm.stitching.stitching module exm.utils.log module exm.utils.utils module extract() (in module exm.puncta.extract)

F

fast_nd2_read_downscale() (exm.stitching.tileset.Tile method) find_intensity_scale() (exm.stitching.tileset.Tile method) (exm.stitching.tileset.Tileset method) find_nearest_points() (in module exm.puncta.improve) find_nearest_puncta() (in module exm.puncta.improve) find_overlapping_blobs() (in module exm.stitching.stitching)

foreground_segmentation() (in module exm.beta.beta) foreground_segmentation_new() (in module exm.beta.beta) from_array() (exm.stitching.tileset.Tile method) from_jp2() (exm.stitching.tileset.Tile method) from_nd2() (exm.stitching.tileset.Tile method) from_tiff() (exm.stitching.tileset.Tile method)

G

gene_barcode_mapping() (in module exm.utils.utils) generate_debug_candidate() (in module exm.utils.utils) get_all_blobs() (in module exm.stitching.stitching) get_bottom_surface() (in module exm.stitching.stitching) get_centroids() (exm.stitching.tileset.Tileset method) get_contact_surface() (in module exm.stitching.stitching) get_memory_config() (exm.args.Args method)

get_offsets() (in module exm.stitching.stitching) (in module exm.utils.utils) get_offsets_nd2() (in module exm.stitching.stitching) get_processing_recommendations() (exm.args.Args method) get_slice() (exm.stitching.tileset.Tileset method) get_tiles_overlaps() (in module exm.stitching.stitching) get_top_surface() (in module exm.stitching.stitching)

I

improve_nearest() (in module exm.puncta.improve) imsToVol() (in module exm.io.io) in_region() (in module exm.puncta.inspect) init_from_bdv() (exm.stitching.tileset.Tileset method) init_from_h5() (exm.stitching.tileset.Tileset method) init_from_jp2() (exm.stitching.tileset.Tileset method) init_from_nd2() (exm.stitching.tileset.Tileset method) init_from_tiff_files() (exm.stitching.tileset.Tileset method) inspect_across_rounds_plotly() (in module exm.puncta.inspect)

inspect_between_rounds_plotly() (in module exm.puncta.inspect) inspect_localmaximum_matplotlib() (in module exm.puncta.inspect) inspect_localmaximum_plotly() (in module exm.puncta.inspect) inspect_puncta_improvement_matplotlib() (in module exm.puncta.inspect) inspect_puncta_individual_matplotlib() (in module exm.puncta.inspect) inspect_puncta_individual_plotly() (in module exm.puncta.inspect) inspect_puncta_ROI_matplotlib() (in module exm.puncta.inspect) inspect_puncta_ROI_plotly() (in module exm.puncta.inspect) inspect_raw_matplotlib() (in module exm.puncta.inspect) inspect_raw_plotly() (in module exm.puncta.inspect)

L

load_all() (exm.stitching.tileset.Tileset method) load_config_yaml() (exm.args.Args method)

load_params() (exm.args.Args method) load_tile() (exm.stitching.tileset.Tileset method) local_to_global() (exm.stitching.tileset.Tileset method)

M

make_stitched_dedup_h5() (in module exm.stitching.stitching) make_stitched_h5() (in module exm.stitching.stitching) measure_round_alignment_NCC() (in module exm.align.align_eval) module exm.align.align exm.align.align_eval exm.align.align_utils exm.beta.beta exm.io.io exm.puncta.basecalling exm.puncta.benchmark exm.puncta.consolidate exm.puncta.extract exm.puncta.improve exm.puncta.inspect exm.segmentation.segmentation exm.stitching.stitching exm.utils.log exm.utils.utils

N

nd2ToChunk() (in module exm.io.io)

nd2ToSlice() (in module exm.io.io) nd2ToVol() (in module exm.io.io)

O

overlapping() (in module exm.stitching.stitching)

P

parse_sitk_log() (in module exm.io.io) plot_alignment_evaluation() (in module exm.align.align_eval) plot_benchmark_data() (in module exm.puncta.benchmark) plot_genes_global() (in module exm.puncta.inspect) plot_genes_global_zstep() (in module exm.puncta.inspect) preview_nd2() (exm.stitching.tileset.Tileset method) print() (exm.args.Args method)

produce_output_volume() (exm.stitching.tileset.Tileset method) puncta_all_nearest_points() (in module exm.puncta.improve) puncta_analysis() (in module exm.puncta.benchmark) puncta_assign_gene() (in module exm.puncta.basecalling) puncta_assign_nuclei() (in module exm.puncta.basecalling) puncta_extraction_cpu() (in module exm.puncta.extract) puncta_extraction_gpu() (in module exm.puncta.extract) puncta_nearest_points() (in module exm.puncta.improve)

Q

quantile_normalization() (in module exm.beta.beta)

R

readNd2() (in module exm.io.io) readXlsx() (in module exm.io.io) retrieve_all_puncta() (in module exm.utils.utils) retrieve_complete() (in module exm.utils.utils) retrieve_digit() (in module exm.utils.utils)

retrieve_gene() (in module exm.utils.utils) retrieve_img() (in module exm.utils.utils) retrieve_one_puncta() (in module exm.utils.utils) retrieve_summary() (in module exm.utils.utils) retrieve_vol() (in module exm.utils.utils)

S

save_as_jp2() (exm.stitching.tileset.Tile method) save_as_tiff() (exm.stitching.tileset.Tile method) save_config_yaml() (exm.args.Args method) save_gif() (in module exm.io.io) save_params() (exm.args.Args method) scale_intensity() (exm.stitching.tileset.Tile method) (exm.stitching.tileset.Tileset method)

scale_offset() (exm.stitching.tileset.Tileset method) segment_3d() (in module exm.segmentation.segmentation) set_params() (exm.args.Args method) set_permissions() (exm.args.Args method) show_slice() (exm.stitching.tileset.Tileset method) subtract_background_rolling_ball() (in module exm.utils.utils) subtract_background_top_hat() (in module exm.utils.utils)

T

template_matching() (in module exm.align.align_utils) tiff2H5() (in module exm.io.io)

Tile (class in exm.stitching.tileset) Tileset (class in exm.stitching.tileset) transform_ref_code() (in module exm.align.align)

U

update_offsets() (exm.stitching.tileset.Tileset method)

V

visualize_progress() (in module exm.utils.utils)

volumetric_alignment() (in module exm.align.align)

W

write_into_h5bdv() (exm.stitching.tileset.Tileset method)