Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Z A AcquisitionParams (class in core.parameters) add_to_processable_labels() (core.data_manager.DataManager method) align_2_images_cross_correlation() (in module imageProcessing.alignImages) align_by_masking() (matrixOperations.build_traces.BuildTraces method) align_fiducials_3d() (imageProcessing.alignImages3D.Drift3D method) align_fiducials_3d_file() (imageProcessing.alignImages3D.Drift3D method) align_fiducials_3d_in_folder() (imageProcessing.alignImages3D.Drift3D method) align_images_3d() (core.function_caller.Pipeline method) align_images_by_blocks() (in module imageProcessing.alignImages) alignByBlock (core.parameters.RegistrationParams attribute) AnalysisHiMMatrix (class in matrixOperations.HIMmatrixOperations) analyze_table() (in module postProcessing.analyze_localizations) analyze_trace() (in module postProcessing.trace_analyzer) annotate_heatmap() (in module core.saving) append() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) appends_traces() (in module postProcessing.trace_combinator) (in module postProcessing.trace_merge) apply_registrations() (core.function_caller.Pipeline method) apply_registrations_to_current_folder() (in module imageProcessing.alignImages) apply_registrations_to_filename() (in module imageProcessing.alignImages) apply_xy_shift_3d_images() (in module imageProcessing.alignImages) ApplyRegisterGlobal (class in imageProcessing.alignImages) area_max (core.parameters.SegmentationParams attribute) area_min (core.parameters.SegmentationParams attribute) args_to_str() (core.run_args.RunArgs method) assign_masks() (in module postProcessing.trace_assign_mask) (matrixOperations.build_traces.BuildTraces method) attributes_labels2cells() (in module matrixOperations.HIMmatrixOperations) B background_method (core.parameters.SegmentationParams attribute) background_sigma (core.parameters.RegistrationParams attribute) (core.parameters.SegmentationParams attribute) barcode_channel (core.parameters.AcquisitionParams attribute) barcode_statistics() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) binarize_coordinate() (in module matrixOperations.build_traces) block_size (core.parameters.ProjectionParams attribute) BlockAlignmentFile (class in core.data_file) blockSize (core.parameters.RegistrationParams attribute) blockSizeXY (core.parameters.RegistrationParams attribute) bootstrapping() (in module plots.plotting_functions) bootstraps_matrix() (in module plots.plotting_functions) BothImgRbgFile (class in core.data_file) brightest (core.parameters.SegmentationParams attribute) build_color_dict() (in module imageProcessing.localization_table) build_distance_matrix() (matrixOperations.build_matrix.BuildMatrix method) build_local_alignment_dict() (matrixOperations.register_localizations.RegisterLocalizations method) build_matrix() (in module core.function_caller) build_trace_by_clustering() (matrixOperations.build_traces.BuildTraces method) build_trace_by_masking() (matrixOperations.build_traces.BuildTraces method) build_traces() (in module core.function_caller) build_vector() (matrixOperations.build_traces.BuildTraces method) BuildMatrix (class in matrixOperations.build_matrix) BuildMatrixTempo (class in matrixOperations.build_matrix) builds_sc_distance_table() (matrixOperations.build_traces.BuildTraces method) BuildTraces (class in matrixOperations.build_traces) BuildTracesTempo (class in matrixOperations.build_traces) C calcul_error() (in module imageProcessing.alignImages) calculate_3_way_contact_matrix() (in module matrixOperations.HIMmatrixOperations) calculate_contact_probability_matrix() (in module matrixOperations.HIMmatrixOperations) calculate_ensemble_pwd_matrix() (in module matrixOperations.HIMmatrixOperations) calculate_n_matrix() (matrixOperations.build_matrix.BuildMatrix method) calculate_pwd_single_mask() (matrixOperations.build_matrix.BuildMatrix method) calculate_pwd_threshold() (postProcessing.trace_filter_advanced.FilterTraces method) centroidDifference_max (core.parameters.SegmentationParams attribute) check_blocksize() (in module toolbox.parameter_file.function_parameters) check_brightest() (in module toolbox.parameter_file.function_parameters) check_dict() (in module toolbox.parameter_file.function_parameters) check_roi_uniqueness() (core.data_manager.DataManager method) check_settings() (in module toolbox.parameter_file.function_parameters) check_zmax() (imageProcessing.makeProjections.Project method) ChromatinTraceTable (class in matrixOperations.chromatin_trace_table) clustering() (postProcessing.trace_filter_advanced.FilterTraces static method) combine_blocks_image_by_reprojection() (in module imageProcessing.alignImages) comp_func() (in module matrixOperations.HIMmatrixOperations) compares_localizations() (imageProcessing.localization_table.LocalizationTable method) complete_with_default() (core.parameters.Parameters method) compute_global_shift() (in module imageProcessing.alignImages) compute_shift_by_block() (in module imageProcessing.alignImages) convert_dic_to_string() (in module toolbox.parameter_file.function_parameters) convert_list_to_string() (in module toolbox.parameter_file.function_parameters) convert_string_to_dictionnary() (in module toolbox.parameter_file.function_parameters) coord_2_distances() (in module matrixOperations.HIMmatrixOperations) core module core.dask_cluster module core.data_file module core.data_manager module core.function_caller module core.parameters module core.pyhim_logging module core.run_args module core.saving module create_dict_structure() (core.data_manager.DataManager method) create_distributed_client() (core.dask_cluster.DaskCluster method) create_folder() (in module core.data_manager) create_out_structure() (core.data_manager.DataManager method) create_output_table() (in module imageProcessing.alignImages3D) (in module imageProcessing.segmentSources3D) creates_user_mask() (in module postProcessing.mask_manual) D DAPI_channel (core.parameters.AcquisitionParams attribute) DaskCluster (class in core.dask_cluster) dataclass_json_config (core.parameters.AcquisitionParams attribute) (core.parameters.MatrixParams attribute) (core.parameters.ProjectionParams attribute) (core.parameters.RegistrationParams attribute) (core.parameters.SegmentationParams attribute) DataFile (class in core.data_file) DataManager (class in core.data_manager) debug_mask_filename() (in module matrixOperations.build_traces) decode_file_parts() (core.data_manager.DataManager method) (core.parameters.Parameters method) decode_rois() (in module imageProcessing.localization_table) decodes_trace() (in module matrixOperations.HIMmatrixOperations) deep_dict_update() (in module core.parameters) delete_data() (core.data_file.BlockAlignmentFile method) (core.data_file.BothImgRbgFile method) (core.data_file.DataFile method) (core.data_file.EqualizationHistogramsFile method) (core.data_file.RefDiffFile method) detect_overlapping_barcodes() (postProcessing.trace_filter_advanced.FilterTraces method) dispatch_files() (core.data_manager.DataManager method) display (core.parameters.ProjectionParams attribute) display_3d_assembled() (in module core.saving) distances_2_coordinates() (in module matrixOperations.HIMmatrixOperations) distribution_maximum_kernel_density_estimation() (in module matrixOperations.HIMmatrixOperations) Drift3D (class in imageProcessing.alignImages3D) E EcsvFile (class in core.data_file) EqualizationHistogramsFile (class in core.data_file) extract_files() (in module core.data_manager) F Feature (class in imageProcessing.makeProjections) fiducialBarcode_channel (core.parameters.AcquisitionParams attribute) fiducialDAPI_channel (core.parameters.AcquisitionParams attribute) fiducialMask_channel (core.parameters.AcquisitionParams attribute) fileNameRegExp (core.parameters.AcquisitionParams attribute) filter_barcode_table() (matrixOperations.filter_localizations.FilterLocalizations method) filter_folder() (matrixOperations.filter_localizations.FilterLocalizations method) filter_localizations() (in module core.function_caller) filter_localizations_quality() (matrixOperations.filter_localizations.FilterLocalizations method) filter_repeated_barcodes() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) filter_trace() (in module postProcessing.trace_combinator) filter_traces() (postProcessing.trace_filter_advanced.FilterTraces method) filter_traces_by_coordinate() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) filter_traces_by_n() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) FilterLocalizations (class in matrixOperations.filter_localizations) FilterLocalizationsTempo (class in matrixOperations.filter_localizations) FilterTraces (class in postProcessing.trace_filter_advanced) find_cycle() (in module imageProcessing.alignImages3D) find_files_to_process() (core.parameters.Parameters method) find_label() (core.data_manager.DataManager method) find_label_in_path() (in module postProcessing.mask_manual) find_optimal_kernel_width() (in module matrixOperations.HIMmatrixOperations) find_param_file() (core.data_manager.DataManager method) find_roi_name_in_path() (in module postProcessing.mask_manual) flux_min (core.parameters.MatrixParams attribute) flux_min_3D (core.parameters.MatrixParams attribute) FocalPlaneMatrixFile (class in core.data_file) folder (core.parameters.MatrixParams attribute) (core.parameters.ProjectionParams attribute) from_dict() (core.parameters.AcquisitionParams class method) (core.parameters.MatrixParams class method) (core.parameters.ProjectionParams class method) (core.parameters.RegistrationParams class method) (core.parameters.SegmentationParams class method) from_json() (core.parameters.AcquisitionParams class method) (core.parameters.MatrixParams class method) (core.parameters.ProjectionParams class method) (core.parameters.RegistrationParams class method) (core.parameters.SegmentationParams class method) fuses_sc_matrix_collated_from_datasets() (in module matrixOperations.HIMmatrixOperations) fwhm (core.parameters.SegmentationParams attribute) G get_2d_commands() (core.run_args.RunArgs static method) get_3d_commands() (core.run_args.RunArgs static method) get_a_dict_value() (in module core.function_caller) get_available_commands() (core.run_args.RunArgs static method) get_barcode_statistics() (in module postProcessing.analyze_localizations) (in module postProcessing.trace_analyzer) get_barcodes_per_cell() (in module matrixOperations.HIMmatrixOperations) get_coordinates_from_pwd_matrix() (in module matrixOperations.HIMmatrixOperations) get_detection_eff_barcodes() (in module matrixOperations.HIMmatrixOperations) get_dict_shifts() (in module postProcessing.mask_manual) get_dictionary_value() (in module core.parameters) get_file_table_new_name() (in module matrixOperations.filter_localizations) get_image_filename() (imageProcessing.imageProcessing.Image method) get_inputs() (core.data_manager.DataManager method) get_labeled_dict_value() (core.parameters.Parameters method) get_labelled_params() (core.parameters.Parameters method) get_mask_properties() (in module imageProcessing.segmentSources3D) get_multi_contact() (in module matrixOperations.HIMmatrixOperations) get_number_localization_per_barcode() (in module postProcessing.analyze_localizations) get_processable_labels() (core.data_manager.DataManager method) get_required_inputs() (imageProcessing.makeProjections.Feature method) get_rg_from_pwd() (in module matrixOperations.HIMmatrixOperations) get_root() (core.data_file.NpyFile method) (core.data_file.TifFile method) get_sectioned_params() (core.parameters.Parameters method) get_standard_parameters() (core.parameters.Parameters static method) get_tessellation() (in module imageProcessing.segmentMasks) get_xyz_statistics() (in module postProcessing.trace_analyzer) gets_matrix() (in module plots.plotting_functions) group_localizations_by_coordinate() (matrixOperations.build_traces.BuildTraces method) H hard_filtering() (postProcessing.trace_filter_advanced.FilterTraces method) heatmap() (in module core.saving) higher_threshold (core.parameters.RegistrationParams attribute) highlight_deprecated_params() (core.parameters.Params method) him_map_2d_to_1d() (postProcessing.trace_filter_advanced.FilterTraces static method) I Image (class in imageProcessing.imageProcessing) image_adjust() (in module imageProcessing.imageProcessing) image_block_alignment_3d() (in module imageProcessing.alignImages) image_show_with_values() (in module core.saving) image_show_with_values_single() (in module core.saving) imageProcessing module imageProcessing.alignImages module imageProcessing.alignImages3D module imageProcessing.imageProcessing module imageProcessing.localization_table module imageProcessing.makeProjections module imageProcessing.segmentMasks module imageProcessing.segmentMasks3D module imageProcessing.segmentSources3D module import_parameters() (in module toolbox.parameter_file.function_parameters) init_features() (core.function_caller.Pipeline method) initialize() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) initialize_cluster() (core.dask_cluster.DaskCluster method) initialize_lists() (matrixOperations.build_traces.BuildTraces method) initialize_parameters() (matrixOperations.build_matrix.BuildMatrix method) (matrixOperations.build_traces.BuildTraces method) initializes_masks() (matrixOperations.build_traces.BuildTraces method) intensity_max (core.parameters.SegmentationParams attribute) intensity_min (core.parameters.SegmentationParams attribute) interpret_cmd_list() (core.function_caller.Pipeline method) is_float() (in module toolbox.parameter_file.function_parameters) is_integer() (in module toolbox.parameter_file.function_parameters) is_notebook() (in module matrixOperations.HIMmatrixOperations) J joinsListArrays() (in module postProcessing.processHiMmatrix) JsonFile (class in core.data_file) K kde_fit() (in module matrixOperations.HIMmatrixOperations) KDtree_distance_threshold_mum (core.parameters.MatrixParams attribute) L lauch_dask_scheduler() (core.function_caller.Pipeline method) (in module toolbox.imagePreProcessing) launch_analysis() (matrixOperations.build_matrix.BuildMatrix method) (matrixOperations.build_traces.BuildTraces method) list_sc_to_keep() (in module matrixOperations.HIMmatrixOperations) load() (core.data_file.NpyFile method) (core.data_file.TifFile method) (imageProcessing.localization_table.LocalizationTable method) (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) load_alignment_dict() (in module core.parameters) load_data() (matrixOperations.HIMmatrixOperations.AnalysisHiMMatrix method) load_dict_shifts() (imageProcessing.alignImages3D.Drift3D method) load_image() (imageProcessing.imageProcessing.Image method) load_image_2d() (imageProcessing.imageProcessing.Image method) load_json() (in module core.parameters) (in module postProcessing.mask_manual) load_list() (in module matrixOperations.HIMmatrixOperations) load_local_alignment() (matrixOperations.register_localizations.RegisterLocalizations method) load_mask() (matrixOperations.build_traces.BuildTraces method) load_n_preprocess_image() (in module imageProcessing.alignImages3D) load_params() (in module postProcessing.mask_manual) load_reference() (core.data_manager.DataManager method) load_reference_fiducial() (imageProcessing.alignImages3D.Drift3D method) load_sc_data() (in module matrixOperations.HIMmatrixOperations) load_sc_data_matlab() (in module matrixOperations.HIMmatrixOperations) load_traces() (in module postProcessing.trace_combinator) (in module postProcessing.trace_merge) load_user_param() (core.data_manager.DataManager method) load_user_param_with_structure() (core.data_manager.DataManager method) loads_barcode_dict() (in module core.parameters) localAlignment (core.parameters.RegistrationParams attribute) LocalizationTable (class in imageProcessing.localization_table) Localize3D (class in imageProcessing.segmentSources3D) localize_2d_folder (core.parameters.SegmentationParams attribute) localize_3d_folder (core.parameters.SegmentationParams attribute) Logger (class in core.pyhim_logging) lower_threshold (core.parameters.RegistrationParams attribute) M main() (in module plots.figure3wayInteractions) (in module plots.figure4Mmatrix) (in module plots.figureN_HiMmatrices) (in module plots.figureSingleCell) (in module postProcessing.analyze_localizations) (in module postProcessing.mask_manual) (in module postProcessing.npy_to_tiff) (in module postProcessing.processHiMmatrix) (in module postProcessing.pwd_matrix_2_pdb) (in module postProcessing.trace_analyzer) (in module postProcessing.trace_assign_mask) (in module postProcessing.trace_combinator) (in module postProcessing.trace_filter) (in module postProcessing.trace_merge) (in module postProcessing.trace_plot) (in module postProcessing.trace_to_matrix) (in module pyHiM) (in module toolbox.file_handling.cleanHiM_run) (in module toolbox.file_handling.lndir) (in module toolbox.file_handling.unzipHiM_run) (in module toolbox.file_handling.zipHiM_run) (in module toolbox.imagePreProcessing) (in module toolbox.imageSegmentSpots) (in module toolbox.parameter_file.pyhim_parameters) (in module toolbox.runHiM_cluster) make_segmentations() (in module imageProcessing.segmentMasks) makesplotHiMLineProfile() (in module plots.figureN_HiMmatrices) makesPlotHistograms() (in module plots.figureSingleCell) manage_parallel_option() (core.function_caller.Pipeline method) Mask3D (class in imageProcessing.segmentMasks3D) mask_2d_folder (core.parameters.SegmentationParams attribute) mask_3d_folder (core.parameters.SegmentationParams attribute) mask_channel (core.parameters.AcquisitionParams attribute) mask_expansion (core.parameters.MatrixParams attribute) masks2process (core.parameters.MatrixParams attribute) match_name() (in module toolbox.parameter_file.function_parameters) matrix_2_pdb() (in module postProcessing.pwd_matrix_2_pdb) matrixOperations module matrixOperations.build_matrix module matrixOperations.build_traces module matrixOperations.chromatin_trace_table module matrixOperations.filter_localizations module matrixOperations.HIMmatrixOperations module matrixOperations.register_localizations module MatrixParams (class in core.parameters) merge_results() (imageProcessing.alignImages.RegisterGlobal method) (imageProcessing.makeProjections.Feature method) mode (core.parameters.ProjectionParams attribute) module core core.dask_cluster core.data_file core.data_manager core.function_caller core.parameters core.pyhim_logging core.run_args core.saving imageProcessing imageProcessing.alignImages imageProcessing.alignImages3D imageProcessing.imageProcessing imageProcessing.localization_table imageProcessing.makeProjections imageProcessing.segmentMasks imageProcessing.segmentMasks3D imageProcessing.segmentSources3D matrixOperations matrixOperations.build_matrix matrixOperations.build_traces matrixOperations.chromatin_trace_table matrixOperations.filter_localizations matrixOperations.HIMmatrixOperations matrixOperations.register_localizations plots plots.figure3wayInteractions plots.figure4Mmatrix plots.figureN_HiMmatrices plots.figureSingleCell plots.plotting_functions postProcessing postProcessing.analyze_localizations postProcessing.mask_manual postProcessing.npy_to_tiff postProcessing.processHiMmatrix postProcessing.pwd_matrix_2_pdb postProcessing.trace_analyzer postProcessing.trace_assign_mask postProcessing.trace_combinator postProcessing.trace_filter postProcessing.trace_filter_advanced postProcessing.trace_merge postProcessing.trace_plot postProcessing.trace_to_matrix pyHiM toolbox toolbox.file_handling toolbox.file_handling.cleanHiM_run toolbox.file_handling.lndir toolbox.file_handling.unzipHiM_run toolbox.file_handling.zipHiM_run toolbox.imagePreProcessing toolbox.imageSegmentSpots toolbox.parameter_file toolbox.parameter_file.function_parameters toolbox.parameter_file.info_parameters toolbox.parameter_file.pyhim_parameters toolbox.runHiM_cluster N n_cells_loaded() (matrixOperations.HIMmatrixOperations.AnalysisHiMMatrix method) normalize_matrix() (in module matrixOperations.HIMmatrixOperations) (in module plots.plotting_functions) normalize_profile() (in module matrixOperations.HIMmatrixOperations) NpyFile (class in core.data_file) O open_him_traces() (postProcessing.trace_filter_advanced.FilterTraces method) operation (core.parameters.SegmentationParams attribute) outputFile (core.parameters.RegistrationParams attribute) (core.parameters.SegmentationParams attribute) P Parameters (class in core.parameters) Params (class in core.parameters) parse_arguments() (in module plots.figure3wayInteractions) (in module plots.figure4Mmatrix) (in module plots.figureN_HiMmatrices) (in module plots.figureSingleCell) (in module postProcessing.processHiMmatrix) (in module postProcessing.pwd_matrix_2_pdb) (in module postProcessing.trace_assign_mask) (in module postProcessing.trace_combinator) (in module postProcessing.trace_filter) (in module postProcessing.trace_filter_advanced) (in module postProcessing.trace_merge) (in module postProcessing.trace_plot) (in module postProcessing.trace_to_matrix) (in module toolbox.imagePreProcessing) (in module toolbox.imageSegmentSpots) parse_cmd() (core.run_args.RunArgs class method) parseArguments() (in module postProcessing.analyze_localizations) (in module postProcessing.trace_analyzer) Pipeline (class in core.function_caller) pixelSizeXY (core.parameters.AcquisitionParams attribute) pixelSizeZ (core.parameters.AcquisitionParams attribute) plot_1d_profile1dataset() (matrixOperations.HIMmatrixOperations.AnalysisHiMMatrix method) plot_1d_profile2datasets() (in module matrixOperations.HIMmatrixOperations) plot_2d_matrix_simple() (in module plots.plotting_functions) (matrixOperations.HIMmatrixOperations.AnalysisHiMMatrix method) plot_3d_shift_matrices() (in module core.saving) plot_4_images() (in module core.saving) plot_distance_histograms() (in module matrixOperations.HIMmatrixOperations) plot_distribution_fluxes() (imageProcessing.localization_table.LocalizationTable method) plot_ensemble_3_way_contact_matrix() (in module matrixOperations.HIMmatrixOperations) plot_ensemble_contact_probability_matrix() (in module matrixOperations.HIMmatrixOperations) plot_image_3d() (imageProcessing.segmentSources3D.Localize3D method) (in module imageProcessing.segmentMasks3D) plot_inverse_pwd_matrix() (in module matrixOperations.HIMmatrixOperations) plot_matrix() (in module matrixOperations.HIMmatrixOperations) plot_matrix_difference() (in module plots.plotting_functions) plot_mixed_matrix() (in module plots.plotting_functions) plot_raw_images_and_labels() (in module core.saving) plot_repeated_barcodes() (in module postProcessing.trace_filter_advanced) plot_sc_matrix() (in module plots.figureSingleCell) plot_single_contact_probability_matrix() (in module matrixOperations.HIMmatrixOperations) plot_single_pwd_matrice() (in module matrixOperations.HIMmatrixOperations) plot_Wilcoxon_matrix() (in module plots.plotting_functions) plotHiMLineProfile() (in module plots.figureN_HiMmatrices) plotMultipleHiMmatrices() (in module plots.figureN_HiMmatrices) plots module plots.figure3wayInteractions module plots.figure4Mmatrix module plots.figureN_HiMmatrices module plots.figureSingleCell module plots.plotting_functions module plots_all_matrices() (matrixOperations.build_matrix.BuildMatrix method) plots_barcode_statistics() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) plots_localization_projection() (in module imageProcessing.localization_table) plots_localizations() (imageProcessing.localization_table.LocalizationTable method) plots_traces() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) plotsBarcodesEfficiencies() (in module plots.figureSingleCell) plotsBarcodesPerCell() (in module plots.figureSingleCell) plotsRgvalues() (in module plots.figureSingleCell) plotsSubplot_sc_matrices() (in module plots.figureSingleCell) plotTADs() (in module plots.figureN_HiMmatrices) plotTrajectories() (in module plots.figureSingleCell) Png2DFile (class in core.data_file) postProcessing module postProcessing.analyze_localizations module postProcessing.mask_manual module postProcessing.npy_to_tiff module postProcessing.processHiMmatrix module postProcessing.pwd_matrix_2_pdb module postProcessing.trace_analyzer module postProcessing.trace_assign_mask module postProcessing.trace_combinator module postProcessing.trace_filter module postProcessing.trace_filter_advanced module postProcessing.trace_merge module postProcessing.trace_plot module postProcessing.trace_to_matrix module precise_z_planes() (imageProcessing.makeProjections.Project method) preprocess_2d_img() (in module imageProcessing.alignImages) preprocess_3d_image() (in module imageProcessing.imageProcessing) print_analyzing_label() (in module core.pyhim_logging) print_as_dict() (core.parameters.Params method) print_dashes() (in module core.pyhim_logging) print_dict() (in module core.parameters) print_framed_text() (in module core.pyhim_logging) print_log() (in module core.pyhim_logging) print_section() (in module core.pyhim_logging) print_session_name() (in module core.pyhim_logging) print_title() (in module core.pyhim_logging) print_unknown_params() (in module core.pyhim_logging) process_localizations() (in module postProcessing.analyze_localizations) process_traces() (in module postProcessing.trace_analyzer) (in module postProcessing.trace_assign_mask) Project (class in imageProcessing.makeProjections) projection_2d() (imageProcessing.makeProjections.Project method) ProjectionParams (class in core.parameters) pyHiM module R read_arguments() (in module toolbox.runHiM_cluster) reassemble_3d_image() (in module imageProcessing.imageProcessing) reducePlanes (core.parameters.SegmentationParams attribute) RefDiffFile (class in core.data_file) referenceFiducial (core.parameters.RegistrationParams attribute) reformat_dataframe() (postProcessing.trace_filter_advanced.FilterTraces static method) register() (matrixOperations.register_localizations.RegisterLocalizations method) register_barcode_map_file() (matrixOperations.register_localizations.RegisterLocalizations method) register_barcodes() (matrixOperations.register_localizations.RegisterLocalizations method) register_global_folder (core.parameters.RegistrationParams attribute) register_local_folder (core.parameters.RegistrationParams attribute) register_localizations() (in module core.function_caller) RegisterGlobal (class in imageProcessing.alignImages) RegisterLocalizations (class in matrixOperations.register_localizations) RegisterLocalizationsTempo (class in matrixOperations.register_localizations) RegistrationParams (class in core.parameters) reinterpolate_z() (in module imageProcessing.makeProjections) remove_barcode() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) remove_duplicates() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) (postProcessing.trace_filter_advanced.FilterTraces static method) remove_extension() (in module core.data_manager) remove_inhomogeneous_background() (in module imageProcessing.alignImages) remove_nans() (in module postProcessing.pwd_matrix_2_pdb) remove_none_from_list() (in module core.function_caller) remove_uncorrected_localizations (core.parameters.MatrixParams attribute) residual_max (core.parameters.SegmentationParams attribute) retrieve_kernel_density_estimator() (in module matrixOperations.HIMmatrixOperations) retrieve_sc_matrix() (matrixOperations.HIMmatrixOperations.AnalysisHiMMatrix method) returnCellsHighestNumberPWD() (in module plots.figureSingleCell) RNA_channel (core.parameters.AcquisitionParams attribute) run() (core.function_caller.Pipeline method) (imageProcessing.alignImages.RegisterGlobal method) (imageProcessing.makeProjections.Feature method) (imageProcessing.makeProjections.Project method) (in module postProcessing.trace_combinator) (in module postProcessing.trace_merge) (matrixOperations.build_matrix.BuildMatrix method) (matrixOperations.build_traces.BuildTraces method) run_pattern() (in module core.function_caller) RunArgs (class in core.run_args) runtime() (in module postProcessing.pwd_matrix_2_pdb) (in module postProcessing.trace_filter) (in module postProcessing.trace_plot) (in module postProcessing.trace_to_matrix) S save() (core.data_file.BlockAlignmentFile method) (core.data_file.BothImgRbgFile method) (core.data_file.DataFile method) (core.data_file.EcsvFile method) (core.data_file.EqualizationHistogramsFile method) (core.data_file.FocalPlaneMatrixFile method) (core.data_file.JsonFile method) (core.data_file.NpyFile method) (core.data_file.Png2DFile method) (core.data_file.RefDiffFile method) (imageProcessing.localization_table.LocalizationTable method) (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) save_data() (core.data_manager.DataManager method) save_image_2d() (imageProcessing.imageProcessing.Image method) save_image_2d_cmd() (in module core.saving) save_image_as_blocks() (in module core.saving) save_individual_labels() (postProcessing.trace_filter_advanced.FilterTraces method) save_json() (in module core.data_file) save_matrices() (matrixOperations.build_matrix.BuildMatrix method) save_parameters_loaded() (core.data_manager.DataManager method) save_to_astropy() (postProcessing.trace_filter_advanced.FilterTraces method) scatter_3d_image() (in module imageProcessing.imageProcessing) schema() (core.parameters.AcquisitionParams class method) (core.parameters.MatrixParams class method) (core.parameters.ProjectionParams class method) (core.parameters.RegistrationParams class method) (core.parameters.SegmentationParams class method) search_local_shift() (matrixOperations.register_localizations.RegisterLocalizations method) search_local_shift_block_3d() (matrixOperations.register_localizations.RegisterLocalizations method) segment_mask_inhomog_background() (in module imageProcessing.segmentMasks) segment_mask_stardist() (in module imageProcessing.segmentMasks) segment_masks() (core.function_caller.Pipeline method) (in module imageProcessing.segmentMasks) segment_masks_3d() (core.function_caller.Pipeline method) (imageProcessing.segmentMasks3D.Mask3D method) segment_masks_3d_file() (imageProcessing.segmentMasks3D.Mask3D method) segment_masks_3d_in_folder() (imageProcessing.segmentMasks3D.Mask3D method) segment_source_flat_background() (in module imageProcessing.segmentMasks) segment_source_inhomog_background() (in module imageProcessing.segmentMasks) segment_sources_3d() (core.function_caller.Pipeline method) (imageProcessing.segmentSources3D.Localize3D method) segment_sources_3d_file() (imageProcessing.segmentSources3D.Localize3D method) segment_sources_3d_in_folder() (imageProcessing.segmentSources3D.Localize3D method) SegmentationParams (class in core.parameters) select_traces_wo_duplicates() (postProcessing.trace_filter_advanced.FilterTraces static method) set_channel() (core.parameters.Parameters method) set_default() (in module core.parameters) set_label_decoder() (core.data_manager.DataManager method) set_labelled_params() (core.data_manager.DataManager method) set_params_from_cmds() (core.function_caller.Pipeline method) set_up() (core.data_manager.DataManager method) setup_filter_values() (matrixOperations.filter_localizations.FilterLocalizations method) setup_logger() (core.pyhim_logging.Logger method) setup_md_file() (core.pyhim_logging.Logger method) shift_3d_mask() (in module postProcessing.mask_manual) show_image() (imageProcessing.imageProcessing.Image method) (in module postProcessing.mask_manual) show_image_masks() (in module imageProcessing.segmentMasks) show_image_sources() (in module imageProcessing.segmentMasks) shuffle_matrix() (in module matrixOperations.HIMmatrixOperations) sigma_max (core.parameters.SegmentationParams attribute) sort_cells_by_number_pwd() (in module matrixOperations.HIMmatrixOperations) stardist_basename (core.parameters.SegmentationParams attribute) stardist_network (core.parameters.SegmentationParams attribute) stardist_network3D (core.parameters.SegmentationParams attribute) T tesselation (core.parameters.SegmentationParams attribute) tessellate_masks() (in module imageProcessing.segmentMasks) threshold_over_std (core.parameters.SegmentationParams attribute) TifFile (class in core.data_file) to_dict() (core.parameters.AcquisitionParams method) (core.parameters.MatrixParams method) (core.parameters.ProjectionParams method) (core.parameters.RegistrationParams method) (core.parameters.SegmentationParams method) to_json() (core.parameters.AcquisitionParams method) (core.parameters.MatrixParams method) (core.parameters.ProjectionParams method) (core.parameters.RegistrationParams method) (core.parameters.SegmentationParams method) tolerance (core.parameters.RegistrationParams attribute) toleranceDrift (core.parameters.MatrixParams attribute) toolbox module toolbox.file_handling module toolbox.file_handling.cleanHiM_run module toolbox.file_handling.lndir module toolbox.file_handling.unzipHiM_run module toolbox.file_handling.zipHiM_run module toolbox.imagePreProcessing module toolbox.imageSegmentSpots module toolbox.parameter_file module toolbox.parameter_file.function_parameters module toolbox.parameter_file.info_parameters module toolbox.parameter_file.pyhim_parameters module toolbox.runHiM_cluster module trace_keep_label() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) trace_remove_label() (matrixOperations.chromatin_trace_table.ChromatinTraceTable method) trace_statistics() (postProcessing.trace_filter_advanced.FilterTraces method) tracing_method (core.parameters.MatrixParams attribute) try_get_client() (in module core.dask_cluster) U unknown_params (core.parameters.AcquisitionParams attribute) (core.parameters.MatrixParams attribute) (core.parameters.ProjectionParams attribute) (core.parameters.RegistrationParams attribute) (core.parameters.SegmentationParams attribute) update_parameters() (in module toolbox.parameter_file.function_parameters) upsample_factor (core.parameters.RegistrationParams attribute) V visualize2D() (in module plots.figureSingleCell) visualize3D() (in module plots.figureSingleCell) W warn_default() (in module core.parameters) warn_pop() (in module core.parameters) Wilcoxon_matrix() (in module plots.plotting_functions) window_security (core.parameters.ProjectionParams attribute) write_string_to_file() (in module core.pyhim_logging) write_xyz_2_pdb() (in module matrixOperations.HIMmatrixOperations) X xyz_2_pdb() (in module postProcessing.pwd_matrix_2_pdb) Z z_offset (core.parameters.MatrixParams attribute) z_project_option (core.parameters.ProjectionParams attribute) zBinning (core.parameters.AcquisitionParams attribute) zmax (core.parameters.ProjectionParams attribute) zmin (core.parameters.ProjectionParams attribute) zwindows (core.parameters.ProjectionParams attribute)