Index A | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | V A average_files() (in module utils) C ccf_v3_atlas_generation module change_cmap() (clustering.SingleVoxelClustering method) (clustering.SingleVoxelClusteringWrapper method) check_ids() (data_loading.DataLoaderAndPreproc method) check_transf() (data_loading.DataLoaderAndPreproc method) cluster_dataset() (clustering.SingleVoxelClustering method) clustering module compute_amplitude() (in module quantification) compute_amplitude_extrema() (clustering.SingleVoxelClusteringWrapper method) compute_amplitude_map() (clustering.SingleVoxelClustering method) compute_auc() (in module quantification) compute_corr_map() (correlation_analysis.CorrelationAnalysis method) compute_full_width_half_max() (in module quantification) compute_metrics() (quantification.TemporalQuantification method) compute_reliability_map() (quality_control.ReliabilityMaps method) compute_time_to_peak() (in module quantification) convert_projections_to_df() (in module utils) convert_to_zscore() (in module utils) correlation_analysis module CorrelationAnalysis (class in correlation_analysis) D data_iterator_excel_file() (data_loading.DataLoaderAndPreproc method) data_iterator_folder_tree() (data_loading.DataLoaderAndPreproc method) data_loading module DataLoaderAndPreproc (class in data_loading) display_atlas_mask_selected_regions() (clustering.SingleVoxelClusteringWrapper method) display_cluster_locations() (clustering.SingleVoxelClusteringWrapper method) E extract_features() (clustering.SingleVoxelClustering method) extract_info_excel_file() (data_loading.DataLoaderAndPreproc method) extract_info_from_region_file() (in module utils) F FeatureExtractor (class in features_extraction) features_extraction module flatten_volume() (clustering.SingleVoxelClustering method) flip_dims() (in module registration) Formatter (class in utils) FormatterBarcode (class in region_averaging_analysis) G generate_background_img() (clustering.SingleVoxelClustering method) generate_color_coded_atlas_flat() (in module utils) generate_regions_file() (in module ccf_v3_atlas_generation) generate_simplified_atlas() (in module ccf_v3_atlas_generation) get_all_id_acr() (in module ccf_v3_atlas_generation) get_atlas_and_info_paths() (in module utils) get_atlas_mask_from_regions() (in module utils) get_cluster_locations() (clustering.SingleVoxelClustering method) get_cluster_maps() (clustering.SingleVoxelClusteringWrapper method) get_cluster_transitions() (quantification.SpatialTransitionAnalysis method) get_names() (clustering.SingleVoxelClusteringWrapper method) get_outliers() (quality_control.OutlierFrameRemoval method) get_quantif_regions_from_transitions() (quantification.SpatialTransitionAnalysis method) get_regions_from_groups() (clustering.SingleVoxelClusteringWrapper method) (in module utils) get_regions_from_hemisphere() (in module utils) get_regions_in_atlas() (in module ccf_v3_atlas_generation) get_regions_traces() (region_averaging_analysis.RegionAveragingAnalysis method) get_signals() (clustering.SingleVoxelClusteringWrapper method) get_signals_or_coords() (clustering.SingleVoxelClustering method) I init_data_reduction_func() (data_loading.DataLoaderAndPreproc method) init_pattern() (correlation_analysis.CorrelationAnalysis method) interpolate3D() (in module registration) L list_selected_data() (data_loading.DataLoaderAndPreproc method) load_atlas() (in module ccf_v3_atlas_generation) (in module utils) load_data_and_tf() (in module registration) load_data_and_transf() (data_loading.DataLoaderAndPreproc method) load_object() (in module utils) M merge_clusters() (clustering.SingleVoxelClustering method) (clustering.SingleVoxelClusteringWrapper method) merge_transition_maps() (quantification.SpatialTransitionAnalysis method) module ccf_v3_atlas_generation clustering correlation_analysis data_loading features_extraction quality_control quantification region_averaging_analysis registration utils N name_from_path() (in module utils) normalize() (clustering.SingleVoxelClusteringWrapper method) normalize_data() (data_loading.DataLoaderAndPreproc method) O OutlierFrameRemoval (class in quality_control) P plot_barcode() (region_averaging_analysis.RegionAveragingAnalysis method) plot_metric() (quantification.TemporalQuantification method) plot_region() (region_averaging_analysis.RegionAveragingAnalysis method) plot_signals() (clustering.SingleVoxelClustering method) (clustering.SingleVoxelClusteringWrapper method) post_data_loading_average() (in module utils) post_data_loading_iterator() (in module utils) print_file_info() (clustering.SingleVoxelClustering method) print_metric() (quantification.TemporalQuantification method) print_quantification_per_hemisphere() (quantification.SpatialQuantification method) print_quantification_per_set() (quantification.SpatialQuantification method) print_quantification_region() (quantification.SpatialQuantification method) print_quantification_structure() (quantification.SpatialQuantification method) process() (clustering.SingleVoxelClusteringWrapper method) (correlation_analysis.CorrelationAnalysis method) (features_extraction.FeatureExtractor method) (quality_control.ReliabilityMaps method) process_data() (data_loading.DataLoaderAndPreproc method) projection() (in module utils) Q quality_control module quantification module quantification_per_region() (quantification.SpatialQuantification method) R region_averaging_analysis module region_loading() (in module clustering) RegionAveragingAnalysis (class in region_averaging_analysis) register_data() (in module registration) registration module ReliabilityMaps (class in quality_control) remove_unreliable() (quality_control.ReliabilityMaps method) replace_outliers() (quality_control.OutlierFrameRemoval method) replicate_folder_tree_structure() (data_loading.DataLoaderAndPreproc method) reset_cmap() (clustering.SingleVoxelClustering method) (clustering.SingleVoxelClusteringWrapper method) reshape_volume_for_display() (in module utils) S sankey_from_maps() (quantification.SpatialTransitionAnalysis method) save_object() (in module utils) scan_folder_tree() (data_loading.DataLoaderAndPreproc method) single_voxels_in_region() (in module utils) SingleVoxelClustering (class in clustering) SingleVoxelClusteringWrapper (class in clustering) SpatialQuantification (class in quantification) SpatialTransitionAnalysis (class in quantification) switch_colors_in_cmap() (clustering.SingleVoxelClustering method) (clustering.SingleVoxelClusteringWrapper method) T TemporalQuantification (class in quantification) U utils module V visualize() (features_extraction.FeatureExtractor method) visualize_volume() (in module registration) volume_loading() (in module clustering)