Index

_

__getitem__() (paprica.parser.baseParser method) (paprica.parser.tileParser method) __init__() (paprica.atlaser.tileAtlaser method) (paprica.batcher.multiChannelAcquisition method) (paprica.converter.tileConverter method) (paprica.loader.tileLoader method) (paprica.parser.baseParser method) (paprica.parser.clearscopeParser method) (paprica.parser.colmParser method) (paprica.parser.tileParser method) (paprica.runner.clearscopeRunningPipeline method) (paprica.segmenter.multitileSegmenter method) (paprica.segmenter.tileSegmenter method) (paprica.stitcher.baseStitcher method) (paprica.stitcher.channelStitcher method) (paprica.stitcher.tileMerger method) (paprica.stitcher.tileStitcher method) (paprica.viewer.tileViewer method) __iter__() (paprica.parser.baseParser method) (paprica.parser.tileParser method) __len__() (paprica.parser.baseParser method) _are_labels_the_same() (paprica.segmenter.tileTrainer static method) _build_database() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) _build_sparse_graphs() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) _check_conversion() (paprica.runner.clearscopeRunningPipeline method) _check_for_apr_file() (paprica.runner.clearscopeRunningPipeline method) _compute_east_registration() (paprica.stitcher.tileStitcher method) _compute_registration_old() (paprica.stitcher.tileStitcher method) _compute_shift() (in module paprica.stitcher) _compute_south_registration() (paprica.stitcher.tileStitcher method) _convert_to_apr() (paprica.runner.clearscopeRunningPipeline method) _correct_offset() (paprica.parser.baseParser method) _erase_from_disk() (paprica.loader.tileLoader method) _filter_cells_flann() (paprica.segmenter.multitileSegmenter method) _find_if_lazy() (paprica.stitcher.tileMerger method) _find_particle() (paprica.segmenter.tileTrainer method) _get_acq_type() (paprica.batcher.multiChannelAcquisition method) _get_channel() (paprica.runner.clearscopeRunningPipeline method) _get_ind() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) _get_Ip_th() (paprica.batcher.multiChannelAcquisition method) _get_masked_proj_shifts() (in module paprica.stitcher) _get_max_proj_apr() (in module paprica.stitcher) _get_n_channels() (paprica.parser.clearscopeParser static method) (paprica.parser.colmParser static method) (paprica.parser.tileParser static method) _get_n_planes() (paprica.stitcher.tileMerger method) _get_ncol() (paprica.parser.tileParser method) _get_neighbors_map() (paprica.parser.baseParser method) _get_nrow() (paprica.parser.tileParser method) _get_nx() (paprica.stitcher.tileMerger method) _get_ny() (paprica.stitcher.tileMerger method) _get_nz() (paprica.stitcher.tileMerger method) _get_path_list() (paprica.parser.baseParser method) _get_proj_shifts() (in module paprica.stitcher) _get_row_col() (paprica.parser.clearscopeParser method) (paprica.runner.clearscopeRunningPipeline method)

_get_tile() (paprica.runner.clearscopeRunningPipeline method) _get_tile_list() (paprica.parser.baseParser method) _get_tile_position() (paprica.segmenter.multitileSegmenter method) (paprica.viewer.tileViewer method) _get_tiles_from_path() (paprica.parser.baseParser method) (paprica.parser.clearscopeParser method) (paprica.parser.colmParser method) (paprica.parser.tileParser method) _get_tiles_list() (paprica.batcher.multiChannelAcquisition method) _get_tiles_path() (paprica.parser.baseParser method) (paprica.parser.clearscopeParser method) (paprica.parser.colmParser method) _get_tiles_pattern() (paprica.parser.baseParser method) _get_total_neighbors_map() (paprica.parser.baseParser method) _get_type() (paprica.parser.tileParser method) _initialize_merged_array() (paprica.stitcher.tileMerger method) _initialize_merged_segmentation() (paprica.stitcher.tileMerger method) _is_new_tile_available() (paprica.runner.clearscopeRunningPipeline method) _is_number() (paprica.parser.colmParser static method) _is_tile_loaded() (paprica.viewer.tileViewer method) _is_valid_acquisition() (paprica.parser.clearscopeParser static method) (paprica.parser.colmParser static method) _load_clearscope() (paprica.loader.tileLoader method) _load_colm() (paprica.loader.tileLoader method) _load_data() (paprica.loader.tileLoader method) _load_max_projs() (paprica.stitcher.baseStitcher method) _load_raw() (paprica.loader.tileLoader method) _load_tile() (paprica.viewer.tileViewer method) _merge_cells() (paprica.segmenter.multitileSegmenter method) _optimize_sparse_graphs() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) _order_labels() (paprica.segmenter.tileTrainer method) _parse_acquisition_settings() (paprica.runner.clearscopeRunningPipeline method) _pre_stitch() (paprica.runner.clearscopeRunningPipeline method) _precompute_max_projs() (paprica.stitcher.baseStitcher method) _predict_on_APR_block() (in module paprica.segmenter) _print_info() (paprica.parser.baseParser method) (paprica.parser.tileParser method) (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) _process_GRAY_for_display() (paprica.stitcher.baseStitcher method) _process_RGB_for_display() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.baseStitcher method) _produce_registration_map() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) _project_tile() (paprica.runner.clearscopeRunningPipeline method) _reconstruct_x_slice() (paprica.stitcher.baseStitcher method) _reconstruct_y_slice() (paprica.stitcher.baseStitcher method) _reconstruct_z_slice() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.baseStitcher method) _register_tile() (paprica.runner.clearscopeRunningPipeline method) _regularize() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.baseStitcher method) _remove_ambiguities() (paprica.segmenter.tileTrainer method) _sample_pixel_list_on_APR() (paprica.segmenter.tileTrainer method) _save_max_projs() (paprica.stitcher.baseStitcher method) _segment_tile() (paprica.segmenter.multitileSegmenter method) _sort_tiles() (paprica.parser.baseParser method) _update_database() (paprica.stitcher.channelStitcher method) _update_next_tile() (paprica.runner.clearscopeRunningPipeline method)

A

activate_conversion() (paprica.runner.clearscopeRunningPipeline method) activate_mask() (paprica.stitcher.baseStitcher method) activate_segmentation() (paprica.stitcher.baseStitcher method) activate_stitching() (paprica.runner.clearscopeRunningPipeline method)

add_annotations() (paprica.segmenter.tileTrainer method) apply_on_tile() (paprica.segmenter.tileTrainer method) apr_to_napari_Image() (in module paprica.viewer) apr_to_napari_Labels() (in module paprica.viewer) autoParser() (in module paprica.parser)

B

baseParser (class in paprica.parser) baseStitcher (class in paprica.stitcher)

batch_convert_to_apr() (paprica.converter.tileConverter method) batch_reconstruct_pixel() (paprica.converter.tileConverter method)

C

channelStitcher (class in paprica.stitcher) check_files_integrity() (paprica.parser.baseParser method) check_stitching() (paprica.viewer.tileViewer method) clearscopeParser (class in paprica.parser) clearscopeRunningPipeline (class in paprica.runner) colmParser (class in paprica.parser) compare_stitching() (in module paprica.viewer) compute_average_CR() (paprica.parser.baseParser method) compute_expected_registration() (paprica.stitcher.tileStitcher method)

compute_gradients() (in module paprica.segmenter) compute_gradmag() (in module paprica.segmenter) compute_laplacian() (in module paprica.segmenter) compute_multitile_segmentation() (paprica.segmenter.multitileSegmenter method) compute_registration() (paprica.stitcher.tileStitcher method) compute_registration_from_max_projs() (paprica.stitcher.tileStitcher method) compute_rigid_registration() (paprica.stitcher.channelStitcher method) compute_segmentation() (paprica.segmenter.tileSegmenter method) convert_all_channels() (paprica.batcher.multiChannelAcquisition method) crop() (paprica.stitcher.tileMerger method)

D

deactivate_compression() (paprica.converter.tileConverter method) (paprica.runner.clearscopeRunningPipeline method) deactivate_mask() (paprica.stitcher.baseStitcher method) deactivate_segmentation() (paprica.stitcher.baseStitcher method) display_all_tiles() (paprica.viewer.tileViewer method) display_apr() (in module paprica.viewer) display_apr_from_path() (in module paprica.viewer)

display_features() (paprica.segmenter.tileTrainer method) display_heatmap() (in module paprica.viewer) display_layers() (in module paprica.viewer) display_layers_pyramidal() (in module paprica.viewer) display_segmentation() (in module paprica.viewer) display_tiles() (paprica.viewer.tileViewer method) display_training_annotations() (paprica.segmenter.tileTrainer method) dump_stitcher() (paprica.stitcher.tileStitcher method)

E

equalize_hist() (paprica.stitcher.tileMerger method)

extract_and_merge_cells() (paprica.segmenter.multitileSegmenter method)

F

from_atlas() (paprica.atlaser.tileAtlaser class method) from_classifier() (paprica.segmenter.multitileSegmenter class method) (paprica.segmenter.tileSegmenter class method)

from_merger() (paprica.atlaser.tileAtlaser class method) from_trainer() (paprica.segmenter.multitileSegmenter class method) (paprica.segmenter.tileSegmenter class method)

G

gaussian_blur() (in module paprica.segmenter) get_area_mask_by_acronym() (paprica.atlaser.tileAtlaser method) get_cell_number_by_acronym() (paprica.atlaser.tileAtlaser method) get_cells_density() (paprica.atlaser.tileAtlaser method) get_cells_density_per_region() (paprica.atlaser.tileAtlaser method) get_cells_id() (paprica.atlaser.tileAtlaser method)

get_cells_number_per_region() (paprica.atlaser.tileAtlaser method) get_layers_all_tiles() (paprica.viewer.tileViewer method) get_loc_id() (paprica.atlaser.tileAtlaser method) get_microscope_list() (in module paprica.parser) get_number_of_channels() (in module paprica.parser) get_ontology_mapping() (paprica.atlaser.tileAtlaser method) get_overlap() (paprica.parser.colmParser method)

I

interpolate_missing_frames() (paprica.parser.clearscopeParser method)

L

lazy_load_segmentation() (paprica.loader.tileLoader method) lazy_load_tile() (paprica.loader.tileLoader method) load_atlas() (paprica.atlaser.tileAtlaser method) load_classifier() (paprica.segmenter.tileTrainer method) load_database() (paprica.stitcher.baseStitcher method)

load_labels() (paprica.segmenter.tileTrainer method) load_neighbors() (paprica.loader.tileLoader method) load_neighbors_segmentation() (paprica.loader.tileLoader method) load_segmentation() (paprica.loader.tileLoader method) load_tile() (paprica.loader.tileLoader method)

M

make_lazy_loadable() (paprica.parser.baseParser method) manually_annotate() (paprica.segmenter.tileTrainer method) map_feature() (in module paprica.segmenter) max_sum_over_single_max() (in module paprica.stitcher) merge_additive() (paprica.stitcher.tileMerger method) merge_max() (paprica.stitcher.tileMerger method) merge_segmentation() (paprica.stitcher.tileMerger method) module paprica.atlaser paprica.batcher paprica.converter paprica.loader paprica.parser paprica.runner paprica.segmenter paprica.stitcher paprica.viewer

mse() (in module paprica.stitcher) multiChannelAcquisition (class in paprica.batcher) multitileSegmenter (class in paprica.segmenter)

P

paprica.atlaser module paprica.batcher module paprica.converter module paprica.loader module paprica.parser module paprica.runner module paprica.segmenter module

paprica.stitcher module paprica.viewer module particle_levels() (in module paprica.segmenter) phase_cross_correlation() (in module paprica.stitcher) phase_cross_correlation_cv() (in module paprica.stitcher) plot_graph() (paprica.stitcher.tileStitcher method) plot_min_trees() (paprica.stitcher.tileStitcher method) plot_particles_size_distribution() (paprica.loader.tileLoader method) plot_registration_map() (paprica.stitcher.tileStitcher method) plot_stitching_info() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method)

R

reconstruct_3D_all_channels() (paprica.batcher.multiChannelAcquisition method) reconstruct_colored_projection() (in module paprica.viewer) reconstruct_slice() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.baseStitcher method)

reconstruct_z_color() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.baseStitcher method) register_to_atlas() (paprica.atlaser.tileAtlaser method) resolution_callback() (in module paprica.viewer) run() (paprica.runner.clearscopeRunningPipeline method)

S

save_cells() (paprica.segmenter.multitileSegmenter method) save_classifier() (paprica.segmenter.tileTrainer method) save_database() (paprica.stitcher.baseStitcher method) save_labels() (paprica.segmenter.tileTrainer method) segment_training_tile() (paprica.segmenter.tileTrainer method) set_compression() (paprica.converter.tileConverter method) (paprica.runner.clearscopeRunningPipeline method) set_downsample() (paprica.stitcher.tileMerger method)

set_lim() (paprica.stitcher.channelStitcher method) set_overlap_margin() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) set_regularization() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.baseStitcher method) set_z_range() (paprica.runner.clearscopeRunningPipeline method) (paprica.stitcher.tileStitcher method) stitch_acq() (paprica.batcher.multiChannelAcquisition method)

T

tile_from_apr() (in module paprica.loader) tile_from_path() (in module paprica.loader) tileAtlaser (class in paprica.atlaser) tileConverter (class in paprica.converter) tileLoader (class in paprica.loader) tileMerger (class in paprica.stitcher)

tileParser (class in paprica.parser) tileSegmenter (class in paprica.segmenter) tileStitcher (class in paprica.stitcher) tileTrainer (class in paprica.segmenter) tileViewer (class in paprica.viewer) train_classifier() (paprica.segmenter.tileTrainer method)

V

view_tile() (paprica.loader.tileLoader method)