Index

_

__iter__() (spacr.io.CombineLoaders method)

__next__() (spacr.io.CombineLoaders method)

A

activate_knob() (spacr.gui_elements.spacrSlider method) activation_correlations_to_database() (in module spacr.utils) activation_maps_to_database() (in module spacr.utils) activations (spacr.utils.GradCAMGenerator attribute) active_color (spacr.gui_elements.AnnotateApp attribute) (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrEntry attribute) (spacr.gui_elements.spacrFrame attribute) (spacr.gui_elements.spacrProgressBar attribute) (spacr.gui_elements.spacrSlider attribute) add() (spacr.gui_elements.spacrContainer method) add_colored_border() (spacr.gui_elements.AnnotateApp method) add_column_to_database() (in module spacr.utils) add_images_to_tar() (in module spacr.utils) add_mapping_to_json() (in module generate_mapping) additional_buttons (spacr.gui.MainApp attribute) additional_gui_apps (spacr.gui.MainApp attribute) additional_info (spacr.gui_elements.spacrProgressBar attribute) adjust_cell_masks() (in module spacr.utils) adjusted_to_original_paths (spacr.gui_elements.AnnotateApp attribute) align (spacr.gui_elements.spacrLabel attribute) all_elements_match() (in module spacr.utils) all_to_all (spacr.plot.spacrGraph attribute) alpha (spacr.utils.FocalLossWithLogits attribute) amp (core.BaseTrainer.BaseTrainer attribute) analyze_calcium_oscillations() (in module spacr.timelapse) analyze_class_proportion() (in module spacr.submodules) analyze_endodyogeny() (in module spacr.submodules) analyze_percent_positive() (in module spacr.submodules) analyze_plaques() (in module spacr.submodules) analyze_recruitment() (in module spacr.submodules) animate_movement() (spacr.gui_elements.spacrSwitch method)

animate_switch() (spacr.gui_elements.spacrSwitch method) animate_zoom() (spacr.gui_elements.spacrButton method) animation (spacr.gui_elements.spacrButton attribute) annotate() (in module spacr.gui_utils) annotate_app() (in module spacr.gui_utils) annotate_conditions() (in module spacr.utils) annotate_filter_vision() (in module spacr.deep_spacr) annotate_predictions() (in module spacr.utils) annotate_with_image_refs() (in module spacr.gui_utils) AnnotateApp (class in spacr.gui_elements) annotation_column (spacr.gui_elements.AnnotateApp attribute) append_database() (in module spacr.sim) apply_augmentation() (in module spacr.io) (spacr.submodules.CellposeLazyDataset method) apply_brush() (spacr.gui_elements.ModifyMaskApp method) apply_brush_release() (spacr.gui_elements.ModifyMaskApp method) apply_cellpose_model() (in module spacr.submodules) apply_dividing_line() (spacr.gui_elements.ModifyMaskApp method) apply_dropout_rate() (spacr.utils.TorchModel method) apply_magic_wand() (spacr.gui_elements.ModifyMaskApp method) apply_mask() (in module spacr.utils) apply_model() (in module spacr.deep_spacr) apply_model_to_tar() (in module spacr.deep_spacr) apply_normalization() (spacr.gui_elements.ModifyMaskApp method) apply_transformation() (in module spacr.ml) apply_zoom_on_enter() (spacr.gui_elements.ModifyMaskApp method) args (in module main) (in module predict) assign_colors() (in module spacr.utils) attention (spacr.utils.SelfAttention attribute), [1] augment (spacr.submodules.CellposeLazyDataset attribute) augment_classes() (in module spacr.utils) augment_dataset() (in module spacr.utils) augment_image() (in module spacr.utils) augment_images() (in module spacr.utils) augment_single_image() (in module spacr.utils)

B

barecodes_reverse_complement() (in module spacr.sequencing) base_model (spacr.utils.TorchModel attribute) BasePredictor (class in core.BasePredictor) BaseTrainer (class in core.BaseTrainer) batch_queue (spacr.io.spacrDataLoader attribute) bce_loss (core.MEDIAR.Trainer.Trainer attribute) best_f1_score (core.BaseTrainer.BaseTrainer attribute) best_weights (core.BaseTrainer.BaseTrainer attribute) bg (spacr.gui_elements.spacrContainer attribute) bg_color (spacr.gui_elements.AnnotateApp attribute) (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrEntry attribute) (spacr.gui_elements.spacrProgressBar attribute) (spacr.gui_elements.spacrSlider attribute)

boundary_f1_score() (in module spacr.utils) BoundaryExclusion (class in train_tools.data_utils.custom.CellAware) button_bg (spacr.gui_elements.spacrDropdownMenu attribute) button_frame (spacr.gui_elements.AnnotateApp attribute) button_text (spacr.gui_elements.spacrDropdownMenu attribute) button_width (spacr.gui_elements.spacrDropdownMenu attribute)

C

Cache (class in spacr.utils) cache (spacr.utils.Cache attribute), [1] calculate_activation_correlations() (in module spacr.utils) calculate_grid_dimensions() (spacr.gui_elements.AnnotateApp method) calculate_iou() (in module spacr.utils) calculate_loss() (in module spacr.utils) calculate_p_values() (in module spacr.ml) calculate_permutation_importance() (in module spacr.sim) calculate_shortest_distance() (in module spacr.utils) cam_type (spacr.utils.GradCAMGenerator attribute) cancel_after_tasks() (in module spacr.gui_utils) canvas (in module spacr.gui_core) (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrEntry attribute) (spacr.gui_elements.spacrLabel attribute) (spacr.gui_elements.spacrSlider attribute) (spacr.gui_elements.spacrSwitch attribute) canvas_height (spacr.gui_elements.ModifyMaskApp attribute) (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrEntry attribute) canvas_to_image() (spacr.gui_elements.ModifyMaskApp method) canvas_widget (in module spacr.gui_core) canvas_width (spacr.gui_elements.ModifyMaskApp attribute) (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) categories (in module spacr.settings) category_keys (in module spacr.settings) cell_level_roc_auc() (in module spacr.sim) CellposeLazyDataset (class in spacr.submodules) cellprob_head (train_tools.models.MEDIARFormer.MEDIARFormer attribute) change_cell_ratio (train_tools.data_utils.custom.CellAware.IntensityDiversification attribute) channel_wise (train_tools.data_utils.custom.NormalizeImage.CustomNormalizeImage attribute) channels (spacr.gui_elements.AnnotateApp attribute) (spacr.utils.SelectChannels attribute) check_and_clean_data() (in module spacr.ml) check_cellpose_models() (in module spacr.spacr_cellpose) check_distribution() (in module spacr.ml), [1] check_index() (in module spacr.utils) check_mask_folder() (in module spacr.utils) check_multicollinearity() (in module spacr.utils) check_normality() (in module spacr.ml), [1] (in module spacr.utils) check_overlap() (in module spacr.utils) check_settings() (in module spacr.settings) check_src_folders_files() (in module spacr.gui_core) chi_pairwise() (in module spacr.sp_stats) choose_model() (in module spacr.utils) choose_p_adjust_method() (in module spacr.sp_stats) class_visualization() (in module spacr.utils) classes (spacr.io.spacrDataset attribute) classification_metrics() (in module spacr.utils) classifier() (in module spacr.sim) classifier_v2() (in module spacr.sim) clean_controls() (in module spacr.ml) cleanup() (spacr.io.spacrDataLoader method) cleanup_previous_instance() (in module spacr.gui_core) clear_description() (spacr.gui.MainApp method) (spacr.gui_elements.spacrButton method) clear_frame() (spacr.gui.MainApp method) clear_objects() (spacr.gui_elements.ModifyMaskApp method) clear_unused_figures() (in module spacr.gui_core) close_dropdown() (spacr.gui_elements.spacrCombo method) close_file_descriptors() (in module spacr.utils) close_multiprocessing_processes() (in module spacr.utils) cluster_feature_analysis() (in module spacr.utils) color_settings (spacr.gui.MainApp attribute) colors (spacr.plot.spacrGraph attribute) combine_results() (in module spacr.utils) CombinedDataset (class in spacr.io) CombineLoaders (class in spacr.io) command (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCheckbutton attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrSlider attribute) (spacr.gui_elements.spacrSwitch attribute) compare_cellpose_masks() (in module spacr.spacr_cellpose) compare_group (spacr.plot.spacrGraph attribute) compare_mask() (in module spacr.spacr_cellpose) compare_reads_to_scores() (in module spacr.submodules) compute_ap_over_iou_thresholds() (in module spacr.utils) compute_average_precision() (in module spacr.utils) compute_gradcam_and_predictions() (spacr.utils.GradCAMGenerator method)

compute_gradcam_maps() (spacr.utils.GradCAMGenerator method) compute_irm_penalty() (in module spacr.utils) compute_masks() (in module core.MEDIAR.utils) compute_precision_recall() (in module spacr.sim) compute_roc_auc() (in module spacr.sim) compute_saliency_and_predictions() (spacr.utils.SaliencyMapGenerator method) compute_saliency_maps() (spacr.utils.SaliencyMapGenerator method) compute_segmentation_ap() (in module spacr.utils) compute_smooth_grad() (spacr.deep_spacr.SmoothGrad method) concatenate_and_normalize() (in module spacr.io) conduct_prediction() (core.BasePredictor.BasePredictor method) conf_name (train_tools.utils.ConfLoader attribute) configure_logger() (in module spacr.logger) ConfLoader (class in train_tools.utils) ConfLoader.DictWithAttributeAccess (class in train_tools.utils) console_output (in module spacr.gui_core) control_filelist() (in module spacr.utils) conv1 (spacr.utils.EarlyFusion attribute) (spacr.utils.SpatialAttention attribute) convert_and_relabel_masks() (in module spacr.utils) convert_numpy_to_tiff() (in module spacr.io) convert_separate_files_to_yokogawa() (in module spacr.io) convert_settings_dict_for_gui() (in module spacr.gui_utils) convert_to_number() (in module spacr.app_annotate) (in module spacr.gui_utils) convert_to_yokogawa() (in module spacr.io) copy_images_to_consolidated() (in module spacr.utils) core module core.Baseline module core.Baseline.Predictor module core.Baseline.Trainer module core.Baseline.utils module core.BasePredictor module core.BaseTrainer module core.MEDIAR module core.MEDIAR.EnsemblePredictor module core.MEDIAR.Predictor module core.MEDIAR.Trainer module core.MEDIAR.utils module core.utils module correct_masks() (in module spacr.utils) correct_metadata() (in module spacr.utils) correct_metadata_column_names() (in module spacr.utils) correct_paths() (in module spacr.utils) count_phenotypes() (in module spacr.submodules) count_reads_in_fastq() (in module spacr.utils) create_circular_mask() (in module spacr.utils) create_consensus() (in module spacr.sequencing) create_database() (in module spacr.sim) create_grouped_plot() (in module spacr.plot) create_input_field() (in module spacr.gui_utils) create_interior_onehot() (in module core.Baseline.utils) create_menu_bar() (in module spacr.gui_elements) create_plot() (spacr.plot.spacrGraph method) create_rounded_rectangle() (spacr.gui_elements.spacrButton method) (spacr.gui_elements.spacrDropdownMenu method) (spacr.gui_elements.spacrSwitch method) create_sash() (spacr.gui_elements.spacrContainer method) create_startup_screen() (spacr.gui.MainApp method) create_venn_diagram() (in module spacr.plot) create_volcano_filename() (in module spacr.ml) create_widgets() (spacr.gui.MainApp method) criterion (core.Baseline.Trainer.Trainer attribute) (core.BaseTrainer.BaseTrainer attribute) cuda (spacr.utils.GradCAM attribute) current_batch_index (spacr.io.spacrDataLoader attribute) current_image_index (spacr.gui_elements.ModifyMaskApp attribute) custom_forward() (spacr.utils.CustomCellClassifier method) (spacr.utils.MultiScaleBlockWithAttention method) custom_volcano_plot() (in module spacr.toxo) CustomCellClassifier (class in spacr.utils) CustomLoadImage (class in train_tools.data_utils.custom.LoadImage) CustomLoadImaged (class in train_tools.data_utils.custom.LoadImage) CustomNormalizeImage (class in train_tools.data_utils.custom.NormalizeImage) CustomNormalizeImaged (class in train_tools.data_utils.custom.NormalizeImage)

D

d_k (spacr.utils.ScaledDotProductAttention attribute), [1], [2] data_column (spacr.plot.spacrGraph attribute) data_dir (spacr.io.NoClassDataset attribute), [1], [2] (spacr.io.spacrDataset attribute) dataloaders (core.BaseTrainer.BaseTrainer attribute) datasets (spacr.io.CombinedDataset attribute) db_path (spacr.gui_elements.AnnotateApp attribute) db_update_thread (spacr.gui_elements.AnnotateApp attribute) deep_spacr() (in module spacr.deep_spacr) deep_spacr_defaults() (in module spacr.settings) default_settings_analyze_percent_positive() (in module spacr.settings) delete_empty_subdirectories() (in module spacr.io) delete_folder() (in module spacr.utils) delete_intermedeate_files() (in module spacr.utils) descriptions (in module spacr.settings) device (core.BasePredictor.BasePredictor attribute) (core.BaseTrainer.BaseTrainer attribute) (spacr.mediar.MEDIARPredictor attribute) df (spacr.plot.spacrGraph attribute) diameters() (in module core.MEDIAR.utils) dice_coefficient() (in module spacr.utils)

dilated_conv1 (spacr.utils.MultiScaleBlockWithAttention attribute) directory_setter() (in module train_tools.utils) dispersion (spacr.ml.QuasiBinomial attribute) display_figure() (in module spacr.gui_core) display_gif_in_plot_frame() (in module spacr.gui_utils) display_image() (spacr.gui_elements.ModifyMaskApp method) display_image_and_mask() (spacr.mediar.MEDIARPredictor method) display_imgs_in_list() (in module spacr.mediar) display_media_in_plot_frame() (in module spacr.gui_utils) display_zoomed_image() (spacr.gui_elements.ModifyMaskApp method) dist_gen() (in module spacr.sim) download_dataset() (in module spacr.gui_utils) download_hug_dataset() (in module spacr.gui_utils) download_models() (in module spacr.utils) draw() (spacr.gui_elements.ModifyMaskApp method) draw_on_zoomed_mask() (spacr.gui_elements.ModifyMaskApp method) draw_rounded_rectangle() (spacr.gui_elements.spacrCombo method) (spacr.gui_elements.spacrEntry method) draw_rounded_square() (spacr.gui_elements.spacrCheck method) draw_slider() (spacr.gui_elements.spacrSlider method) dropdown_menu (spacr.gui_elements.spacrCombo attribute)

E

early_fusion (spacr.utils.CustomCellClassifier attribute) EarlyFusion (class in spacr.utils) EnsemblePredictor (class in core.MEDIAR.EnsemblePredictor) ensure_after_tasks() (in module spacr.gui_utils) erase_brush() (spacr.gui_elements.ModifyMaskApp method) erase_brush_release() (spacr.gui_elements.ModifyMaskApp method) erase_object() (spacr.gui_elements.ModifyMaskApp method) error_bar_type (spacr.plot.spacrGraph attribute) evaluate module

evaluate_f1_score() (in module train_tools.measures) evaluate_f1_score_cellseg() (in module train_tools.measures) evaluate_model_performance() (in module spacr.deep_spacr) exit_button (spacr.gui_elements.AnnotateApp attribute) exp_name (core.BasePredictor.BasePredictor attribute) expected_types (in module spacr.settings) exponential_decay() (in module spacr.timelapse) extract_boundaries() (in module spacr.utils) extract_features() (in module spacr.utils) extract_sequence_and_quality() (in module spacr.sequencing) extract_tar_bz2_files() (in module spacr.utils)

F

f1_metric (core.BaseTrainer.BaseTrainer attribute) fc1 (spacr.utils.CustomCellClassifier attribute) fg_color (spacr.gui_elements.AnnotateApp attribute) (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrEntry attribute) (spacr.gui_elements.spacrFrame attribute) (spacr.gui_elements.spacrProgressBar attribute) (spacr.gui_elements.spacrSlider attribute) fig (in module spacr.gui_elements) (spacr.plot.spacrGraph attribute) fig_queue (in module spacr.gui_core) figure_index (in module spacr.gui_core) figures (in module spacr.gui_core) filenames (spacr.io.NoClassDataset attribute), [1], [2] (spacr.io.spacrDataset attribute) filepaths_to_database() (in module spacr.utils) fill_holes_in_mask() (in module spacr.utils) fill_objects() (spacr.gui_elements.ModifyMaskApp method) filter_and_save_csv() (in module spacr.utils) filter_channels() (spacr.gui_elements.AnnotateApp method) filter_columns() (in module spacr.utils) filter_dataframe_features() (in module spacr.utils) filtered_paths_annotations (spacr.gui_elements.AnnotateApp attribute) find_non_overlapping_position() (in module spacr.utils) find_optimal_threshold() (in module spacr.ml) finish_dividing_line() (spacr.gui_elements.ModifyMaskApp method) finish_drawing() (spacr.gui_elements.ModifyMaskApp method) finish_drawing_if_active() (spacr.gui_elements.ModifyMaskApp method) fishers_odds() (in module spacr.utils) fit_mixed_model() (in module spacr.ml) flow_error() (in module core.MEDIAR.utils) flush() (spacr.gui_utils.WriteToQueue method) FocalLossWithLogits (class in spacr.utils) folder_path (spacr.gui_elements.ModifyMaskApp attribute)

follow_flows() (in module core.MEDIAR.utils) font_family (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrEntry attribute) (spacr.gui_elements.spacrLabel attribute) font_loader (spacr.gui_elements.AnnotateApp attribute) (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrEntry attribute) (spacr.gui_elements.spacrLabel attribute) (spacr.gui_elements.spacrProgressBar attribute) font_name (spacr.gui_elements.spacrFont attribute) font_path (spacr.gui_elements.spacrFont attribute) font_size (spacr.gui_elements.AnnotateApp attribute) (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrEntry attribute) (spacr.gui_elements.spacrFont attribute) (spacr.gui_elements.spacrLabel attribute) (spacr.gui_elements.spacrProgressBar attribute) font_style (spacr.gui_elements.spacrFont attribute) (spacr.gui_elements.spacrLabel attribute) format_path_for_system() (in module spacr.utils) forward() (spacr.utils.CustomCellClassifier method) (spacr.utils.EarlyFusion method) (spacr.utils.FocalLossWithLogits method) (spacr.utils.GradCAM method) (spacr.utils.MultiScaleBlockWithAttention method) (spacr.utils.ResNet method) (spacr.utils.ScaledDotProductAttention method), [1], [2] (spacr.utils.SelfAttention method), [1] (spacr.utils.SpatialAttention method) (spacr.utils.TorchModel method) (train_tools.models.MEDIARFormer.MEDIARFormer method) from_ (spacr.gui_elements.spacrSlider attribute) function_gui_wrapper() (in module spacr.gui_utils)

G

gamma (spacr.utils.FocalLossWithLogits attribute) generate_activation_map() (in module spacr.deep_spacr) generate_annotate_fields() (in module spacr.gui_utils) generate_barecode_mapping() (in module spacr.sequencing) generate_cellpose_masks() (in module spacr.core) generate_cellpose_train_set() (in module spacr.measure) generate_cellpose_train_test() (in module spacr.io) generate_colors() (in module spacr.utils) generate_cytoplasm_mask() (in module spacr.utils) generate_dataset() (in module spacr.io) generate_dataset_from_lists() (in module spacr.io) generate_dna_matrix() (in module spacr.gui_elements) generate_fields() (in module spacr.settings) generate_floats() (in module spacr.sim) generate_fraction_map() (in module spacr.utils) generate_gene_list() (in module spacr.sim) generate_gene_weights() (in module spacr.sim) generate_image_path_map() (in module spacr.utils) generate_image_umap() (in module spacr.core) generate_integers() (in module spacr.sim) generate_integrated_gradients() (spacr.utils.IntegratedGradients method) generate_loaders() (in module spacr.io) generate_mapping module generate_mask_random_cmap() (in module spacr.plot) generate_masks_from_imgs() (in module spacr.spacr_cellpose) generate_mediar_masks() (in module spacr.core) generate_ml_scores() (in module spacr.ml) generate_paramiters() (in module spacr.sim) generate_path_list_from_db() (in module spacr.utils) generate_plate_heatmap() (in module spacr.plot) generate_plate_map() (in module spacr.sim) generate_power_law_distribution() (in module spacr.sim) generate_score_heatmap() (in module spacr.submodules) (in module spacr.toxo) generate_screen_graphs() (in module spacr.core) generate_shap_summary_plot() (in module spacr.sim) generate_training_dataset() (in module spacr.io) generate_well_score() (in module spacr.sim) get() (spacr.gui_elements.spacrSlider method) (spacr.gui_elements.spacrSwitch method) (spacr.utils.Cache method) get_analyze_plaque_settings() (in module spacr.settings) get_analyze_reads_default_settings() (in module spacr.settings) get_analyze_recruitment_default_settings() (in module spacr.settings) get_check_cellpose_models_default_settings() (in module spacr.settings) get_components() (in module spacr.measure) get_consensus_base() (in module spacr.sequencing) get_cuda_version() (in module spacr.utils) get_dataloaders_labeled() (in module train_tools.data_utils.datasetter)

get_dataloaders_public() (in module train_tools.data_utils.datasetter) get_dataloaders_unlabeled() (in module train_tools.data_utils.datasetter) get_db_paths() (in module spacr.utils) get_default_apply_cellpose_model_settings() (in module spacr.settings) get_default_generate_activation_map_settings() (in module spacr.settings) get_default_test_cellpose_model_settings() (in module spacr.settings) get_figure() (spacr.plot.spacrGraph method) get_files_from_dir() (in module spacr.utils) get_font() (spacr.gui_elements.spacrFont method) get_font_path() (spacr.gui_elements.spacrFont method) get_icon_path() (spacr.gui_elements.spacrButton method) get_identify_masks_finetune_default_settings() (in module spacr.settings) get_layer() (spacr.utils.GradCAMGenerator method) get_map_barcodes_default_settings() (in module spacr.settings) get_masks() (in module core.MEDIAR.utils) get_measure_crop_settings() (in module spacr.settings) get_ml_results_paths() (in module spacr.utils) get_num_ftrs() (spacr.utils.TorchModel method) get_object_counts() (in module spacr.measure) get_on_image_click() (spacr.gui_elements.AnnotateApp method) get_optimum_threshold() (in module spacr.sim) get_paths_from_db() (in module spacr.utils) get_perform_regression_default_settings() (in module spacr.settings) get_plate() (spacr.io.spacrDataset method) get_results() (spacr.plot.spacrGraph method) get_scaling_factors() (spacr.gui_elements.ModifyMaskApp method) get_screen_dimensions() (in module spacr.gui_utils) get_sequencing_paths() (in module spacr.utils) get_submodules() (in module spacr.utils) get_train_cellpose_default_settings() (in module spacr.settings) get_train_test_model_settings() (in module spacr.settings) get_weight_choice() (spacr.utils.TorchModel method) get_weights() (in module spacr.mediar) gini() (in module spacr.sim), [1] gini_coefficient() (in module spacr.sim) gini_gene_well() (in module spacr.sim) global_image_refs (in module spacr.gui_utils) go_term_enrichment_by_column() (in module spacr.toxo) GradCAM (class in spacr.utils) GradCAMGenerator (class in spacr.utils) gradflow_head (train_tools.models.MEDIARFormer.MEDIARFormer attribute) gradients (spacr.utils.GradCAMGenerator attribute) graph_importance() (in module spacr.plot) graph_name (spacr.plot.spacrGraph attribute) graph_sequencing_stats() (in module spacr.sequencing) graph_type (spacr.plot.spacrGraph attribute) grid_frame (spacr.gui_elements.AnnotateApp attribute) group_feature_class() (in module spacr.utils) grouping_column (spacr.plot.spacrGraph attribute) gui_app() (in module spacr.gui)

H

hflip_tta (core.MEDIAR.Predictor.Predictor attribute) hide_all_settings() (in module spacr.gui_utils)

hide_tooltip() (spacr.gui_elements.spacrToolTip method) hook_layers() (spacr.utils.GradCAMGenerator method)

I

icon_name (spacr.gui_elements.spacrButton attribute) identify_instances_from_classmap() (in module core.Baseline.utils) identify_masks_finetune() (in module spacr.spacr_cellpose) image_filenames (spacr.gui_elements.ModifyMaskApp attribute) image_to_canvas() (spacr.gui_elements.ModifyMaskApp method) image_type (spacr.gui_elements.AnnotateApp attribute) images (spacr.gui_elements.AnnotateApp attribute) (spacr.io.NoClassDataset attribute) img_list_to_grid() (in module spacr.measure) import_settings() (in module spacr.gui_core) inactive_color (spacr.gui_elements.AnnotateApp attribute) (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCombo attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrFrame attribute) (spacr.gui_elements.spacrProgressBar attribute) (spacr.gui_elements.spacrSlider attribute) index (spacr.gui_elements.AnnotateApp attribute) index_control (in module spacr.gui_core) infected_vs_noninfected() (in module spacr.timelapse)

init_base_model() (spacr.utils.TorchModel method) init_file (in module spacr.mediar) init_spacr_classifier() (spacr.utils.TorchModel method) initialize_base() (spacr.utils.ResNet method) initialize_cuda() (in module spacr.gui_utils) initialize_flags() (spacr.gui_elements.ModifyMaskApp method) initiate_abort() (in module spacr.gui_core) initiate_annotation_app() (in module spacr.app_annotate) initiate_counter() (in module spacr.utils) initiate_make_mask_app() (in module spacr.app_make_masks) initiate_root() (in module spacr.gui_core) input_path (core.BasePredictor.BasePredictor attribute) IntegratedGradients (class in spacr.utils) IntensityDiversification (class in train_tools.data_utils.custom.CellAware) interperate_vision_model() (in module spacr.ml) (in module spacr.submodules) invert_image() (in module spacr.utils) invert_mask() (spacr.gui_elements.ModifyMaskApp method) is_list_of_lists() (in module spacr.utils) is_multiprocessing_process() (in module spacr.utils) is_zoomed_in (spacr.gui_elements.spacrButton attribute)

J

jaccard_index() (in module spacr.utils)

jitterplot_by_annotation() (in module spacr.plot) jump_to_click() (spacr.gui_elements.spacrSlider method)

K

knob (spacr.gui_elements.spacrSlider attribute)

knob_position (spacr.gui_elements.spacrSlider attribute) knob_radius (spacr.gui_elements.spacrSlider attribute)

L

label (spacr.gui_elements.spacrProgressBar attribute) (spacr.gui_elements.spacrSwitch attribute) labels (spacr.gui_elements.AnnotateApp attribute) (spacr.io.spacrDataset attribute) labels_to_flows() (in module core.MEDIAR.utils) language_chat() (in module spacr.chat_bot) lasso_reg() (in module spacr.utils) length (spacr.gui_elements.spacrSlider attribute) lengths (spacr.io.CombinedDataset attribute) link_by_iou() (in module spacr.timelapse) load_app() (in module spacr.gui_utils) (spacr.gui.MainApp method) load_first_image() (spacr.gui_elements.ModifyMaskApp method) load_font() (spacr.gui_elements.spacrFont method) load_icon() (spacr.gui_elements.spacrButton method) load_image() (in module spacr.utils) (spacr.io.NoClassDataset method), [1] (spacr.io.spacrDataset method)

load_image_and_mask() (spacr.gui_elements.ModifyMaskApp method) load_image_paths() (in module spacr.utils) load_images() (spacr.gui_elements.AnnotateApp method) load_images_from_paths() (in module spacr.io) load_model() (in module spacr.chat_bot) (spacr.mediar.MEDIARPredictor method) load_next_app() (in module spacr.gui_utils) load_settings() (in module spacr.utils) load_single_image() (spacr.gui_elements.AnnotateApp method) load_to_memory (spacr.io.NoClassDataset attribute), [1], [2] loader_iters (spacr.io.CombineLoaders attribute), [1] log_function_call() (in module spacr.logger) log_x (spacr.plot.spacrGraph attribute) log_y (spacr.plot.spacrGraph attribute) logger (in module spacr.logger) loss_metric (core.BaseTrainer.BaseTrainer attribute)

M

magic_wand_normal() (spacr.gui_elements.ModifyMaskApp method) magic_wand_zoomed() (spacr.gui_elements.ModifyMaskApp method) main module main() (in module evaluate) (in module main) (in module predict) main_buttons (spacr.gui.MainApp attribute) main_gui_apps (spacr.gui.MainApp attribute) main_thread_update_function() (in module spacr.gui_core) MainApp (class in spacr.gui) make_submission (core.BasePredictor.BasePredictor attribute) map_condition() (in module spacr.utils) map_sequences_to_names() (in module spacr.sequencing) mask_object_count() (in module spacr.utils) masks_folder (spacr.gui_elements.ModifyMaskApp attribute) masks_to_flows() (in module core.MEDIAR.utils) masks_to_flows_gpu() (in module core.MEDIAR.utils) match_masks() (in module spacr.utils) max_size (spacr.utils.Cache attribute), [1] measure_crop() (in module spacr.measure) measure_test_mode() (in module spacr.utils) measurement (spacr.gui_elements.AnnotateApp attribute) mediar_criterion() (core.MEDIAR.Trainer.Trainer method) mediar_path (in module spacr.mediar) MEDIARFormer (class in train_tools.models.MEDIARFormer) MEDIARPredictor (class in spacr.mediar) menu (spacr.gui_elements.spacrDropdownMenu attribute) merge_dataframes() (in module spacr.utils) merge_regression_res_with_metadata() (in module spacr.utils) merge_touching_objects() (in module spacr.utils) meta_key_postfix (train_tools.data_utils.custom.LoadImage.CustomLoadImaged attribute) meta_keys (train_tools.data_utils.custom.LoadImage.CustomLoadImaged attribute) minimum_cell_simulation() (in module spacr.ml) ml_analysis() (in module spacr.ml) MLR() (in module spacr.utils) model (core.BasePredictor.BasePredictor attribute) (core.BaseTrainer.BaseTrainer attribute) (spacr.deep_spacr.SmoothGrad attribute) (spacr.mediar.MEDIARPredictor attribute) (spacr.utils.GradCAM attribute) (spacr.utils.GradCAMGenerator attribute) (spacr.utils.IntegratedGradients attribute) (spacr.utils.SaliencyMapGenerator attribute) model1 (spacr.mediar.MEDIARPredictor attribute) model2 (spacr.mediar.MEDIARPredictor attribute) model_aux (core.MEDIAR.EnsemblePredictor.EnsemblePredictor attribute) model_fusion() (in module spacr.deep_spacr) model_knowledge_transfer() (in module spacr.deep_spacr) model_metrics() (in module spacr.utils) model_name (spacr.utils.TorchModel attribute) modify_figure() (in module spacr.gui_elements) modify_figure_properties() (in module spacr.gui_elements) ModifyMaskApp (class in spacr.gui_elements) module core core.Baseline core.Baseline.Predictor core.Baseline.Trainer core.Baseline.utils core.BasePredictor core.BaseTrainer core.MEDIAR core.MEDIAR.EnsemblePredictor core.MEDIAR.Predictor core.MEDIAR.Trainer core.MEDIAR.utils core.utils evaluate generate_mapping main predict SetupDict spacr spacr.app_annotate spacr.app_classify spacr.app_make_masks spacr.app_mask spacr.app_measure spacr.app_sequencing spacr.app_umap spacr.chat_bot spacr.core spacr.deep_spacr spacr.gui spacr.gui_core spacr.gui_elements spacr.gui_utils spacr.io spacr.logger spacr.measure spacr.mediar spacr.ml spacr.openai spacr.plot spacr.sequencing spacr.settings spacr.sim spacr.sp_stats spacr.spacr_cellpose spacr.submodules spacr.timelapse spacr.toxo spacr.utils spacr.version train_tools train_tools.data_utils train_tools.data_utils.custom train_tools.data_utils.custom.CellAware train_tools.data_utils.custom.LoadImage train_tools.data_utils.custom.NormalizeImage train_tools.data_utils.datasetter train_tools.data_utils.transforms train_tools.data_utils.utils train_tools.measures train_tools.models train_tools.models.MEDIARFormer train_tools.utils

move_knob() (spacr.gui_elements.spacrSlider method) mse_loss (core.MEDIAR.Trainer.Trainer attribute) multi_scale_block_1 (spacr.utils.CustomCellClassifier attribute) MultiScaleBlockWithAttention (class in spacr.utils)

N

n_samples (spacr.deep_spacr.SmoothGrad attribute) next_button (spacr.gui_elements.AnnotateApp attribute) next_image() (spacr.gui_elements.ModifyMaskApp method) next_page() (spacr.gui_elements.AnnotateApp method) no_valid (core.BaseTrainer.BaseTrainer attribute) NoClassDataset (class in spacr.io), [1] normalize (spacr.gui_elements.AnnotateApp attribute) (spacr.mediar.MEDIARPredictor attribute) (spacr.submodules.CellposeLazyDataset attribute) normalize_and_visualize() (in module spacr.plot)

normalize_array() (in module spacr.sim) normalize_channels (spacr.gui_elements.AnnotateApp attribute) normalize_image() (in module spacr.mediar) (spacr.gui_elements.AnnotateApp static method) (spacr.gui_elements.ModifyMaskApp method) normalize_src_path() (in module spacr.utils) normalize_to_dtype() (in module spacr.utils) normalizer (train_tools.data_utils.custom.NormalizeImage.CustomNormalizeImaged attribute) num_epochs (core.BaseTrainer.BaseTrainer attribute) num_ftrs (spacr.utils.TorchModel attribute)

O

official_paths_labeled() (in module generate_mapping) official_paths_tuning() (in module generate_mapping) offset (spacr.gui_elements.spacrSlider attribute) on_click() (spacr.gui_elements.spacrButton method) (spacr.gui_elements.spacrCombo method) (spacr.gui_elements.spacrDropdownMenu method) on_configure() (spacr.gui_elements.spacrContainer method) on_enter() (spacr.gui_elements.spacrButton method) (spacr.gui_elements.spacrDropdownMenu method) on_enter_sash() (spacr.gui_elements.spacrContainer method) on_focus_in() (spacr.gui_elements.spacrEntry method) on_focus_out() (spacr.gui_elements.spacrEntry method) on_leave() (spacr.gui_elements.spacrButton method) (spacr.gui_elements.spacrDropdownMenu method) on_leave_sash() (spacr.gui_elements.spacrContainer method) on_select() (spacr.gui_elements.spacrCombo method) (spacr.gui_elements.spacrDropdownMenu method) open_dropdown() (spacr.gui_elements.spacrCombo method)

open_settings_window() (spacr.gui_elements.AnnotateApp method) operation_type (spacr.gui_elements.spacrProgressBar attribute) opt (in module main) (in module predict) (train_tools.utils.ConfLoader attribute) optimizer (core.BaseTrainer.BaseTrainer attribute) OPTIMIZER (in module SetupDict) options (spacr.gui_elements.spacrDropdownMenu attribute) order (spacr.plot.spacrGraph attribute) orient (spacr.gui_elements.spacrContainer attribute) orig_annotation_columns (spacr.gui_elements.AnnotateApp attribute) outline (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrEntry attribute) output_dir (spacr.plot.spacrGraph attribute) output_path (core.BasePredictor.BasePredictor attribute) overlay_mask_on_image() (spacr.gui_elements.ModifyMaskApp method) overlay_masks_on_images() (in module spacr.plot) overwriting (train_tools.data_utils.custom.LoadImage.CustomLoadImaged attribute)

P

pad_to_same_shape() (in module spacr.utils) paired (spacr.plot.spacrGraph attribute) paired_read_chunked_processing() (in module spacr.sequencing) panes (spacr.gui_elements.spacrContainer attribute) parent_frame (in module spacr.gui_core) parse_gz_files() (in module spacr.io) parse_list() (in module spacr.gui_utils) parser (in module generate_mapping) (in module main) (in module predict) path_decoder() (in module train_tools.data_utils.utils) pending_updates (spacr.gui_elements.AnnotateApp attribute) percentile_normalize() (spacr.utils.GradCAMGenerator method) (spacr.utils.SaliencyMapGenerator method) percentiles (spacr.gui_elements.AnnotateApp attribute) (spacr.submodules.CellposeLazyDataset attribute) perform_levene_test() (in module spacr.sp_stats) (spacr.plot.spacrGraph method) perform_mixed_model() (in module spacr.ml) perform_normality_tests() (in module spacr.sp_stats) (spacr.plot.spacrGraph method) perform_posthoc_tests() (in module spacr.sp_stats) (spacr.plot.spacrGraph method) perform_regression() (in module spacr.ml) perform_resize() (spacr.gui_elements.spacrContainer method) perform_statistical_tests() (in module spacr.sp_stats) (in module spacr.utils) (spacr.plot.spacrGraph method) pick_best_model() (in module spacr.utils) pick_glm_family_and_link() (in module spacr.ml) pin_memory (spacr.io.spacrDataLoader attribute) (spacr.io.spacrDataset attribute) plot_activation_grid() (spacr.utils.GradCAMGenerator method) (spacr.utils.SaliencyMapGenerator method) plot_arrays() (in module spacr.plot) plot_cellpose_batch() (in module spacr.submodules) plot_clusters() (in module spacr.utils) plot_clusters_grid() (in module spacr.utils) plot_comparison_results() (in module spacr.plot) plot_confusion_matrix() (in module spacr.sim) plot_correlation_matrix() (in module spacr.sim) plot_data() (in module spacr.timelapse) plot_data_from_csv() (in module spacr.plot) plot_data_from_db() (in module spacr.plot) plot_embedding() (in module spacr.utils) plot_feature_importance() (in module spacr.plot) (in module spacr.sim) plot_gene_heatmaps() (in module spacr.toxo) plot_gene_phenotypes() (in module spacr.toxo) plot_grid() (in module spacr.utils) plot_histogram() (in module spacr.plot) (in module spacr.sim) plot_image() (in module spacr.utils) plot_image_grid() (in module spacr.plot) plot_image_mask_overlay() (in module spacr.plot) plot_images_and_arrays() (in module spacr.plot) plot_images_by_cluster() (in module spacr.utils) plot_lorenz_curves() (in module spacr.plot) plot_masks() (in module spacr.plot) plot_merged() (in module spacr.plot) plot_object_outlines() (in module spacr.plot) plot_partial_dependences() (in module spacr.sim)

plot_permutation() (in module spacr.plot) plot_plates() (in module spacr.plot) plot_proportion_stacked_bars() (in module spacr.plot) plot_region() (in module spacr.plot) plot_resize() (in module spacr.plot) plot_resize_v1() (in module spacr.plot) plot_roc_pr() (in module spacr.sim) plot_simulations() (in module spacr.sim) plot_umap_images() (in module spacr.utils) position (spacr.gui_elements.spacrSlider attribute) position_to_value() (spacr.gui_elements.spacrSlider method) post_gt (core.BaseTrainer.BaseTrainer attribute) post_menu() (spacr.gui_elements.spacrDropdownMenu method) post_pred (core.BaseTrainer.BaseTrainer attribute) post_regression_analysis() (in module spacr.submodules) power_law_dist_gen() (in module spacr.sim) pprint_config() (in module train_tools.utils) predict module predict_batch() (spacr.mediar.MEDIARPredictor method) Predictor (class in core.Baseline.Predictor) (class in core.MEDIAR.Predictor) prefilter_paths_annotations() (spacr.gui_elements.AnnotateApp method) preload_batches (spacr.io.spacrDataLoader attribute) prepare_batch_for_segmentation() (in module spacr.utils) prepare_cellpose_dataset() (in module spacr.io) prepare_formula() (in module spacr.ml) preprocess_data() (in module spacr.utils) (spacr.plot.spacrGraph method) preprocess_generate_masks() (in module spacr.core) preprocess_image() (in module spacr.utils), [1] (spacr.mediar.MEDIARPredictor method) preprocess_img_data() (in module spacr.io) preprocess_pathogen_data() (in module spacr.timelapse) previous_button (spacr.gui_elements.AnnotateApp attribute) previous_image() (spacr.gui_elements.ModifyMaskApp method) previous_page() (spacr.gui_elements.AnnotateApp method) print_learning_device() (in module core.utils) print_mask_and_flows() (in module spacr.plot) print_progress() (in module spacr.utils) print_widget_structure() (in module spacr.gui_utils) print_with_logging() (in module core.utils) proceed_with_app() (in module spacr.gui_utils) process (spacr.io.spacrDataLoader attribute) process_chunk() (in module spacr.sequencing) process_console_queue() (in module spacr.gui_core) process_console_queue_v2() (in module spacr.gui_core) process_fig_queue() (in module spacr.gui_core) process_instruction() (in module spacr.io) process_masks() (in module spacr.utils) process_meassure_crop_results() (in module spacr.measure) process_model_coefficients() (in module spacr.ml), [1] process_non_tif_non_2D_images() (in module spacr.io) process_reads() (in module spacr.ml) process_scores() (in module spacr.ml) process_stdout_stderr() (in module spacr.gui_utils) process_vision_results() (in module spacr.utils) progress_bar (in module spacr.gui_core) progress_label (in module spacr.gui_core) public_paths_labeled() (in module generate_mapping) public_transforms (in module train_tools.data_utils.transforms) put() (spacr.utils.Cache method)

Q

q (in module spacr.gui_core) (in module spacr.settings) (spacr.gui_utils.WriteToQueue attribute)

quantiles (spacr.mediar.MEDIARPredictor attribute) QuasiBinomial (class in spacr.ml)

R

random_cmap() (in module spacr.plot) random_forest_feature_importance() (in module spacr.utils) random_seeder() (in module train_tools.utils) randscale_intensity (train_tools.data_utils.custom.CellAware.IntensityDiversification attribute) raw_df (spacr.plot.spacrGraph attribute) read_and_plot__vision_results() (in module spacr.plot) read_plot_model_stats() (in module spacr.io) read_simulations_table() (in module spacr.sim) readers (train_tools.data_utils.custom.LoadImage.CustomLoadImage attribute) recommend_target_layers() (in module spacr.utils) recreate_image_grid() (spacr.gui_elements.AnnotateApp method) reducer_hyperparameter_search() (in module spacr.core) reduction_and_clustering() (in module spacr.utils) regression() (in module spacr.ml) regression_model() (in module spacr.ml) regression_roc_auc() (in module spacr.sim) relabel_objects() (spacr.gui_elements.ModifyMaskApp method) release_knob() (spacr.gui_elements.spacrSlider method) remove_bad_flow_masks() (in module core.MEDIAR.utils) remove_canvas() (in module spacr.utils) remove_columns_with_single_value() (in module spacr.sim) remove_constant_columns() (in module spacr.sim) remove_highly_correlated_columns() (in module spacr.utils), [1] remove_intensity_objects() (in module spacr.utils) remove_low_variance_columns() (in module spacr.utils) remove_noise() (in module spacr.utils)

remove_outliers (spacr.plot.spacrGraph attribute) remove_outliers_from_plot() (spacr.plot.spacrGraph method) remove_small_objects() (spacr.gui_elements.ModifyMaskApp method) rename_columns_in_db() (in module spacr.utils) reposition_panes() (spacr.gui_elements.spacrContainer method) representation (spacr.plot.spacrGraph attribute) reset_mp() (in module spacr.utils) resize_arrays() (spacr.gui_elements.ModifyMaskApp method) resize_images_and_labels() (in module spacr.utils) resize_labels_back() (in module spacr.utils) resize_slider() (spacr.gui_elements.spacrSlider method) ResNet (class in spacr.utils) restart_gui_app() (in module spacr.gui_elements) results_df (spacr.plot.spacrGraph attribute) results_name (spacr.plot.spacrGraph attribute) reverse_complement() (in module spacr.sequencing) root (spacr.gui_elements.AnnotateApp attribute) (spacr.gui_elements.ModifyMaskApp attribute) rounded_rectangle() (spacr.gui_elements.spacrFrame method) run_and_save() (in module spacr.sim) run_annotate_app() (in module spacr.gui_utils) run_experiment() (in module spacr.sim) run_function_gui() (in module spacr.gui_utils) run_multiple_simulations() (in module spacr.sim) run_simulation() (in module spacr.sim) run_test() (spacr.mediar.MEDIARPredictor method)

S

SaliencyMapGenerator (class in spacr.utils) sash_thickness (spacr.gui_elements.spacrContainer attribute) sashes (spacr.gui_elements.spacrContainer attribute) save (spacr.plot.spacrGraph attribute) save_and_add_image_to_grid() (in module spacr.measure) save_data() (in module spacr.sim) save_df_to_hdf5() (in module spacr.sequencing) save_figure() (in module spacr.timelapse) save_figure_as_format() (in module spacr.gui_elements) save_file_lists() (in module spacr.utils) save_mask() (spacr.gui_elements.ModifyMaskApp method) save_plot() (in module spacr.sim) save_qc_df_to_csv() (in module spacr.sequencing) save_results_and_figure() (in module spacr.spacr_cellpose) save_results_dataframe() (in module spacr.timelapse) save_settings() (in module spacr.utils) save_shap_plot() (in module spacr.sim) save_summary_to_file() (in module spacr.ml) save_unique_combinations_to_csv() (in module spacr.sequencing) saver_process() (in module spacr.sequencing) scale_factor (spacr.gui_elements.ModifyMaskApp attribute) scale_variables() (in module spacr.ml) ScaledDotProductAttention (class in spacr.utils), [1] scaler (core.BaseTrainer.BaseTrainer attribute) scheduler (core.BaseTrainer.BaseTrainer attribute) SCHEDULER (in module SetupDict) scrollable_frame (in module spacr.gui_core) search_reduction_and_clustering() (in module spacr.utils) segmentation_head (train_tools.models.MEDIARFormer.MEDIARFormer attribute) select_glm_family() (in module spacr.ml) SelectChannels (class in spacr.utils) selected_app (spacr.gui.MainApp attribute) selected_value (spacr.gui_elements.spacrCombo attribute) SelfAttention (class in spacr.utils), [1] sequence_plates() (in module spacr.sim) set() (spacr.gui_elements.spacrCombo method) (spacr.gui_elements.spacrSlider method) (spacr.gui_elements.spacrSwitch method) set_analyze_class_proportion_defaults() (in module spacr.settings) set_analyze_endodyogeny_defaults() (in module spacr.settings) set_annotate_default_settings() (in module spacr.settings) set_cpu_affinity() (in module spacr.gui_utils) set_dark_style() (in module spacr.gui_elements) set_default_analyze_screen() (in module spacr.settings) set_default_generate_barecode_mapping() (in module spacr.settings) set_default_plot_merge_settings() (in module spacr.settings) set_default_settings_preprocess_generate_masks() (in module spacr.settings) set_default_settings_preprocess_img_data() (in module spacr.settings) set_default_settings_preprocess_img_data_v1() (in module spacr.settings) set_default_train_test_model() (in module spacr.settings) set_default_umap_image_settings() (in module spacr.settings) set_element_size() (in module spacr.gui_elements) set_generate_dataset_defaults() (in module spacr.settings) set_generate_training_dataset_defaults() (in module spacr.settings) set_globals() (in module spacr.gui_core) set_graph_importance_defaults() (in module spacr.settings) set_high_priority() (in module spacr.gui_utils) set_interperate_vision_model_defaults() (in module spacr.settings) set_label_position() (spacr.gui_elements.spacrProgressBar method) set_text() (spacr.gui_elements.spacrLabel method) set_to() (spacr.gui_elements.spacrSlider method) set_zoom_rectangle_end() (spacr.gui_elements.ModifyMaskApp method) set_zoom_rectangle_start() (spacr.gui_elements.ModifyMaskApp method) settings_button (spacr.gui_elements.AnnotateApp attribute) setup_button_section() (in module spacr.gui_core) setup_canvas() (spacr.gui_elements.ModifyMaskApp method) setup_console() (in module spacr.gui_core) setup_frame() (in module spacr.gui_utils) setup_function_toolbar() (spacr.gui_elements.ModifyMaskApp method) setup_mode_toolbar() (spacr.gui_elements.ModifyMaskApp method) setup_navigation_toolbar() (spacr.gui_elements.ModifyMaskApp method) setup_plot() (in module spacr.utils) setup_plot_section() (in module spacr.gui_core) setup_settings_panel() (in module spacr.gui_core) setup_usage_panel() (in module spacr.gui_core) setup_zoom_toolbar() (spacr.gui_elements.ModifyMaskApp method) SetupDict module shap_analysis() (in module spacr.ml) show_cam_on_image() (in module spacr.utils) show_description() (spacr.gui.MainApp method) show_index (spacr.gui_elements.spacrSlider attribute) show_next_figure() (in module spacr.gui_core) show_previous_figure() (in module spacr.gui_core) show_text (spacr.gui_elements.spacrButton attribute) show_tooltip() (spacr.gui_elements.spacrToolTip method) shuffle (spacr.io.CombinedDataset attribute) (spacr.io.NoClassDataset attribute), [1], [2] (spacr.io.spacrDataset attribute) shuffle_dataset() (spacr.io.NoClassDataset method), [1] (spacr.io.spacrDataset method) shutdown() (spacr.gui_elements.AnnotateApp method) sigmoid (spacr.utils.SpatialAttention attribute) single_read_chunked_processing() (in module spacr.sequencing) size (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrDropdownMenu attribute) slider_line (spacr.gui_elements.spacrSlider attribute) smooth_hull_lines() (in module spacr.utils) SmoothGrad (class in spacr.deep_spacr) sns_palette (spacr.plot.spacrGraph attribute) spacr module spacr.app_annotate module spacr.app_classify module

spacr.app_make_masks module spacr.app_mask module spacr.app_measure module spacr.app_sequencing module spacr.app_umap module spacr.chat_bot module spacr.core module spacr.deep_spacr module spacr.gui module spacr.gui_core module spacr.gui_elements module spacr.gui_utils module spacr.io module spacr.logger module spacr.measure module spacr.mediar module spacr.ml module spacr.openai module spacr.plot module spacr.sequencing module spacr.settings module spacr.sim module spacr.sp_stats module spacr.spacr_cellpose module spacr.submodules module spacr.timelapse module spacr.toxo module spacr.utils module spacr.version module spacrButton (class in spacr.gui_elements) spacrCheck (class in spacr.gui_elements) spacrCheckbutton (class in spacr.gui_elements) spacrCombo (class in spacr.gui_elements) spacrContainer (class in spacr.gui_elements) spacrDataLoader (class in spacr.io) spacrDataset (class in spacr.io) spacrDropdownMenu (class in spacr.gui_elements) spacrEntry (class in spacr.gui_elements) spacrFigShow() (in module spacr.gui_utils) spacrFont (class in spacr.gui_elements) spacrFrame (class in spacr.gui_elements) spacrGraph (class in spacr.plot) spacrLabel (class in spacr.gui_elements) spacrProgressBar (class in spacr.gui_elements) spacrScrollbarStyle() (in module spacr.gui_elements) spacrSlider (class in spacr.gui_elements) spacrSwitch (class in spacr.gui_elements) spacrToolTip (class in spacr.gui_elements) spatial_attention (spacr.utils.MultiScaleBlockWithAttention attribute) SpatialAttention (class in spacr.utils) specified_length (spacr.gui_elements.spacrSlider attribute) split_my_dataset() (in module spacr.utils) split_train_valid() (in module train_tools.data_utils.utils) src (spacr.gui_elements.AnnotateApp attribute) standardize_figure() (in module spacr.gui_elements) start_annotate_app() (in module spacr.app_annotate) start_classify_app() (in module spacr.app_classify) start_dividing_line() (spacr.gui_elements.ModifyMaskApp method) start_make_mask_app() (in module spacr.app_make_masks) start_mask_app() (in module spacr.app_mask) start_measure_app() (in module spacr.app_measure) start_process() (in module spacr.gui_core) start_resize() (spacr.gui_elements.spacrContainer method) start_seq_app() (in module spacr.app_sequencing) start_umap_app() (in module spacr.app_umap) status_label (spacr.gui_elements.AnnotateApp attribute) stdev_spread (spacr.deep_spacr.SmoothGrad attribute) steps2D_interp() (in module core.MEDIAR.utils) style (spacr.gui_elements.spacrLabel attribute) (spacr.gui_elements.spacrProgressBar attribute) style_out (spacr.gui_elements.spacrLabel attribute) summarize_per_well() (in module spacr.timelapse) summarize_per_well_inf_non_inf() (in module spacr.timelapse) summary_func (spacr.plot.spacrGraph attribute) swich_back_annotation_column() (spacr.gui_elements.AnnotateApp method) switch (spacr.gui_elements.spacrSwitch attribute) switch_bg (spacr.gui_elements.spacrSwitch attribute)

T

tar_path (spacr.io.TarImageDataset attribute) target_layer (spacr.utils.GradCAMGenerator attribute) target_layer_module (spacr.utils.GradCAMGenerator attribute) target_layers (spacr.utils.GradCAM attribute) target_size (spacr.submodules.CellposeLazyDataset attribute) TarImageDataset (class in spacr.io) terminate (spacr.gui_elements.AnnotateApp attribute) test (spacr.mediar.MEDIARPredictor attribute) test_cellpose_model() (in module spacr.submodules) test_model_core() (in module spacr.deep_spacr) test_model_performance() (in module spacr.deep_spacr) text (spacr.gui_elements.spacrButton attribute) (spacr.gui_elements.spacrCheckbutton attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrLabel attribute) (spacr.gui_elements.spacrSwitch attribute) (spacr.gui_elements.spacrToolTip attribute) theme (spacr.plot.spacrGraph attribute) thickness (spacr.gui_elements.spacrSlider attribute) thread_control (in module spacr.gui_core) threshold (spacr.gui_elements.AnnotateApp attribute) to (spacr.gui_elements.spacrSlider attribute) toggle() (spacr.gui_elements.spacrSwitch method) toggle_brush_mode() (spacr.gui_elements.ModifyMaskApp method) toggle_dividing_line_mode() (spacr.gui_elements.ModifyMaskApp method) toggle_draw_mode() (spacr.gui_elements.ModifyMaskApp method) toggle_erase_mode() (spacr.gui_elements.ModifyMaskApp method) toggle_magic_wand_mode() (spacr.gui_elements.ModifyMaskApp method) toggle_settings() (in module spacr.gui_core) toggle_variable() (spacr.gui_elements.spacrCheck method) toggle_zoom_mode() (spacr.gui_elements.ModifyMaskApp method) tooltip_window (spacr.gui_elements.spacrToolTip attribute) torch_CPU (in module core.MEDIAR.utils) torch_GPU (in module core.MEDIAR.utils) TorchModel (class in spacr.utils) total_length (spacr.io.CombinedDataset attribute) train() (core.BaseTrainer.BaseTrainer method) train_and_classify() (spacr.gui_elements.AnnotateApp method) train_button (spacr.gui_elements.AnnotateApp attribute)

train_cellpose() (in module spacr.submodules) train_loaders (spacr.io.CombineLoaders attribute), [1] train_model() (in module spacr.deep_spacr) train_test_model() (in module spacr.deep_spacr) train_tools module train_tools.data_utils module train_tools.data_utils.custom module train_tools.data_utils.custom.CellAware module train_tools.data_utils.custom.LoadImage module train_tools.data_utils.custom.NormalizeImage module train_tools.data_utils.datasetter module train_tools.data_utils.transforms module train_tools.data_utils.utils module train_tools.measures module train_tools.models module train_tools.models.MEDIARFormer module train_tools.utils module train_transforms (in module train_tools.data_utils.transforms) Trainer (class in core.Baseline.Trainer) (class in core.MEDIAR.Trainer) TRAINER (in module SetupDict) training_dataset_from_annotation() (in module spacr.io) training_dataset_from_annotation_metadata() (in module spacr.io) transform (spacr.io.NoClassDataset attribute), [1], [2] (spacr.io.spacrDataset attribute) (spacr.io.TarImageDataset attribute) tuning_transforms (in module train_tools.data_utils.transforms)

U

unlabeled_transforms (in module train_tools.data_utils.transforms) update_check() (spacr.gui_elements.spacrCheck method) update_database_worker() (spacr.gui_elements.AnnotateApp method) update_description() (spacr.gui.MainApp method) (spacr.gui_elements.spacrButton method) update_display() (spacr.gui_elements.ModifyMaskApp method) update_dividing_line_preview() (spacr.gui_elements.ModifyMaskApp method) update_figure() (in module spacr.gui_core) update_gui_text() (spacr.gui_elements.AnnotateApp method) update_html() (spacr.gui_elements.AnnotateApp static method) update_label() (spacr.gui_elements.spacrProgressBar method) update_mouse_info() (spacr.gui_elements.ModifyMaskApp method)

update_original_mask() (spacr.gui_elements.ModifyMaskApp method) update_original_mask_from_zoom() (spacr.gui_elements.ModifyMaskApp method) update_queue (spacr.gui_elements.AnnotateApp attribute) update_scores_and_get_cm() (in module spacr.sim) update_settings() (spacr.gui_elements.AnnotateApp method) update_slider_from_entry() (spacr.gui_elements.spacrSlider method) update_styles() (spacr.gui_elements.spacrDropdownMenu method) update_switch() (spacr.gui_elements.spacrSwitch method) update_zoom_box() (spacr.gui_elements.ModifyMaskApp method) usage_bars (in module spacr.gui_core) use_checkpoint (spacr.utils.CustomCellClassifier attribute) (spacr.utils.TorchModel attribute) use_magic_wand() (spacr.gui_elements.ModifyMaskApp method)

V

valid_frequency (core.BaseTrainer.BaseTrainer attribute) valid_transforms (in module train_tools.data_utils.transforms) validate_and_adjust_beta_params() (in module spacr.sim) value (spacr.gui_elements.spacrSlider attribute) value_to_position() (spacr.gui_elements.spacrSlider method) values (spacr.gui_elements.spacrCombo attribute) var (spacr.gui_elements.spacrCombo attribute) variable (spacr.gui_elements.spacrCheck attribute) (spacr.gui_elements.spacrCheckbutton attribute) (spacr.gui_elements.spacrDropdownMenu attribute) (spacr.gui_elements.spacrSwitch attribute) variance() (spacr.ml.QuasiBinomial method)

vars_dict (in module spacr.gui_core) version (in module spacr.version) version_str (in module spacr.version) vflip_tta (core.MEDIAR.Predictor.Predictor attribute) vis_dists() (in module spacr.sim) visualize_all() (in module spacr.sim) visualize_cellpose_masks() (in module spacr.plot) visualize_classes() (in module spacr.deep_spacr) visualize_integrated_gradients() (in module spacr.deep_spacr) visualize_masks() (in module spacr.plot) visualize_smooth_grad() (in module spacr.deep_spacr) volcano_plot() (in module spacr.plot)

W

W_k (spacr.utils.SelfAttention attribute), [1] W_q (spacr.utils.SelfAttention attribute), [1] W_v (spacr.utils.SelfAttention attribute), [1]

widget (spacr.gui_elements.spacrToolTip attribute) write() (spacr.gui_utils.WriteToQueue method) write_pred_mask() (core.BasePredictor.BasePredictor method) WriteToQueue (class in spacr.gui_utils)

Y

y_lim (spacr.plot.spacrGraph attribute)

Z

zoom_icon() (spacr.gui_elements.spacrButton method)