Index

_

__iter__() (spacr.io.CombineLoaders method)

__next__() (spacr.io.CombineLoaders method)

A

add() (spacr.gui_elements.spacrContainer method) add_colored_border() (spacr.gui_elements.AnnotateApp method) add_images_to_tar() (in module spacr.utils) adjust_cell_masks() (in module spacr.utils) all_elements_match() (in module spacr.core) analyze_associations() (in module spacr.graph_learning) analyze_calcium_oscillations() (in module spacr.timelapse) analyze_data_reg() (in module spacr.core) analyze_plaques() (in module spacr.core) analyze_recruitment() (in module spacr.core) animate_movement() (spacr.gui_elements.spacrSwitch method) animate_switch() (spacr.gui_elements.spacrSwitch method) animate_zoom() (spacr.gui_elements.spacrButton method) annotate() (in module spacr.gui_utils) annotate_app() (in module spacr.gui_utils) annotate_conditions() (in module spacr.utils) annotate_predictions() (in module spacr.utils) annotate_results() (in module spacr.core) annotate_with_image_refs() (in module spacr.gui_utils)

AnnotateApp (class in spacr.gui_elements) append_database() (in module spacr.sim) apply_brush() (spacr.gui_elements.ModifyMaskApp method) apply_brush_release() (spacr.gui_elements.ModifyMaskApp method) 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.core) (in module spacr.graph_learning) apply_model_to_tar() (in module spacr.core) apply_normalization() (spacr.gui_elements.ModifyMaskApp method) apply_transformation() (in module spacr.sequencing) apply_zoom_on_enter() (spacr.gui_elements.ModifyMaskApp method) assign_colors() (in module spacr.utils) 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

boundary_f1_score() (in module spacr.utils)

C

Cache (class in spacr.utils) cache (spacr.utils.Cache attribute) 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.sequencing) calculate_permutation_importance() (in module spacr.sim) cancel_after_tasks() (in module spacr.gui_utils) canvas_to_image() (spacr.gui_elements.ModifyMaskApp method) cell_level_roc_auc() (in module spacr.sim) check_cellpose_models() (in module spacr.core) check_index() (in module spacr.core) check_mask_folder() (in module spacr.utils) check_multicollinearity() (in module spacr.utils) check_normality() (in module spacr.sequencing) (in module spacr.utils) check_overlap() (in module spacr.utils) check_settings() (in module spacr.settings) choose_model() (in module spacr.utils) class_visualization() (in module spacr.utils) classification_metrics() (in module spacr.utils) classifier() (in module spacr.sim) classifier_v2() (in module spacr.sim) clean_controls() (in module spacr.sequencing) cleanup() (spacr.io.spacrDataLoader method) 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) combine_results() (in module spacr.utils) CombinedDataset (class in spacr.io)

CombineLoaders (class in spacr.io) compare_cellpose_masks() (in module spacr.core) compare_mask() (in module spacr.core) complement() (in module spacr.sequencing) compute_ap_over_iou_thresholds() (in module spacr.utils) compute_average_precision() (in module spacr.utils) compute_irm_penalty() (in module spacr.utils) compute_precision_recall() (in module spacr.sim) compute_roc_auc() (in module spacr.sim) 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) consensus_sequence() (in module spacr.sequencing) consensus_sequence_v1() (in module spacr.sequencing) construct_well_graph() (in module spacr.graph_learning) convert_and_relabel_masks() (in module spacr.utils) convert_numpy_to_tiff() (in module spacr.io) convert_settings_dict_for_gui() (in module spacr.gui_utils) correct_masks() (in module spacr.utils) correct_paths() (in module spacr.utils) count_mismatches() (in module spacr.sequencing) count_reads_in_fastq() (in module spacr.utils) create_circular_mask() (in module spacr.utils) create_database() (in module spacr.sim) create_graphs_for_wells() (in module spacr.graph_learning) create_input_field() (in module spacr.gui_utils) create_menu_bar() (in module spacr.gui_elements) 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_widgets() (spacr.gui.MainApp method) custom_forward() (spacr.utils.CustomCellClassifier method) (spacr.utils.MultiScaleBlockWithAttention method) CustomCellClassifier (class in spacr.utils)

D

Decoder (class in spacr.graph_learning) deep_spacr() (in module spacr.deep_spacr) deep_spacr_defaults() (in module spacr.settings) delete_empty_subdirectories() (in module spacr.io) delete_folder() (in module spacr.utils) dice_coefficient() (in module spacr.utils) display_figure() (in module spacr.gui_core) display_image() (spacr.gui_elements.ModifyMaskApp method)

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) 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)

E

EarlyFusion (class in spacr.utils) Encoder (class in spacr.graph_learning) ensure_after_tasks() (in module spacr.gui_utils) equalize_lengths() (in module spacr.sequencing) erase_brush() (spacr.gui_elements.ModifyMaskApp method) erase_brush_release() (spacr.gui_elements.ModifyMaskApp method) erase_object() (spacr.gui_elements.ModifyMaskApp method)

evaluate_model_performance() (in module spacr.deep_spacr) exponential_decay() (in module spacr.timelapse) extract_barcodes_from_fastq() (in module spacr.sequencing) extract_barcodes_from_fastq_v1() (in module spacr.sequencing) extract_barecodes() (in module spacr.sequencing) extract_boundaries() (in module spacr.utils) extract_features() (in module spacr.utils) extract_metadata_from_path() (in module spacr.graph_learning)

F

file_len() (in module spacr.sequencing) filepaths_to_database() (in module spacr.measure) fill_objects() (spacr.gui_elements.ModifyMaskApp method) filter_channels() (spacr.gui_elements.AnnotateApp method) filter_columns() (in module spacr.utils) filter_dataframe_features() (in module spacr.utils) find_grna() (in module spacr.sequencing) find_non_overlapping_position() (in module spacr.utils) find_optimal_threshold() (in module spacr.core) 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) flush() (spacr.gui_utils.WriteToQueue method)

FocalLossWithLogits (class in spacr.utils) forward() (spacr.graph_learning.Decoder method) (spacr.graph_learning.Encoder method) (spacr.graph_learning.GraphTransformer method) (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) (spacr.utils.SelfAttention method) (spacr.utils.SpatialAttention method) (spacr.utils.TorchModel method) function_gui_wrapper() (in module spacr.gui_utils)

G

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_dataset() (in module spacr.core) generate_dataset_from_lists() (in module spacr.core) generate_dependent_variable() (in module spacr.utils) generate_fields() (in module spacr.settings) generate_floats() (in module spacr.sim) generate_fraction_map() (in module spacr.sequencing) (in module spacr.utils) generate_gene_list() (in module spacr.sim) generate_gene_weights() (in module spacr.sim) 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.core) generate_mask_random_cmap() (in module spacr.plot) generate_masks_from_imgs() (in module spacr.core) generate_ml_scores() (in module spacr.core) generate_paramiters() (in module spacr.sim) generate_plate_heatmap() (in module spacr.plot) (in module spacr.sequencing) generate_plate_map() (in module spacr.sim) generate_power_law_distribution() (in module spacr.sim) generate_shap_summary_plot() (in module spacr.sim) generate_synthetic_grna_data() (in module spacr.graph_learning) generate_training_data_file_list() (in module spacr.core) generate_training_dataset() (in module spacr.core) generate_well_score() (in module spacr.sim) get() (spacr.gui_elements.spacrSwitch method) (spacr.utils.Cache method)

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_db_paths() (in module spacr.utils) 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_map_barcodes_default_settings() (in module spacr.settings) 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_read_data() (in module spacr.sequencing) get_scaling_factors() (spacr.gui_elements.ModifyMaskApp method) get_sequence_data() (in module spacr.sequencing) get_sequencing_paths() (in module spacr.utils) get_submodules() (in module spacr.utils) get_top_two_matches() (in module spacr.sequencing) get_train_cellpose_default_settings() (in module spacr.settings) get_weight_choice() (spacr.utils.TorchModel method) gini() (in module spacr.sim) gini_coefficient() (in module spacr.sim) gini_gene_well() (in module spacr.sim) GradCAM (class in spacr.utils) GraphTransformer (class in spacr.graph_learning) grna_plate_heatmap() (in module spacr.sequencing) gui_app() (in module spacr.gui)

H

hide_all_settings() (in module spacr.gui_utils)

hide_tooltip() (spacr.gui_elements.spacrToolTip method)

I

identify_masks_finetune() (in module spacr.core) image_to_canvas() (spacr.gui_elements.ModifyMaskApp method) img_list_to_grid() (in module spacr.measure) import_settings() (in module spacr.gui_core) infected_vs_noninfected() (in module spacr.timelapse) init_base_model() (spacr.utils.TorchModel method) 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) IntegratedGradients (class in spacr.utils) 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)

J

jaccard_index() (in module spacr.utils)

jitterplot_by_annotation() (in module spacr.core) join_measurments_and_annotation() (in module spacr.core)

L

lasso_reg() (in module spacr.utils) 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) (spacr.io.spacrDataset method)

load_image_and_mask() (spacr.gui_elements.ModifyMaskApp method) load_image_paths() (in module spacr.utils) load_images() (in module spacr.graph_learning) (spacr.gui_elements.AnnotateApp method) load_mnist_data() (in module spacr.graph_learning) load_next_app() (in module spacr.gui_utils) load_single_image() (spacr.gui_elements.AnnotateApp method) loader_iters (spacr.io.CombineLoaders attribute) log_function_call() (in module spacr.logger)

M

magic_wand_normal() (spacr.gui_elements.ModifyMaskApp method) magic_wand_zoomed() (spacr.gui_elements.ModifyMaskApp method) main_thread_update_function() (in module spacr.gui_core) MainApp (class in spacr.gui) map_condition() (in module spacr.core) map_unmapped_grnas() (in module spacr.sequencing) mask_object_count() (in module spacr.utils) match_masks() (in module spacr.utils) max_size (spacr.utils.Cache attribute) measure_crop() (in module spacr.measure) measure_test_mode() (in module spacr.utils) merge_dataframes() (in module spacr.utils) merge_pred_mes() (in module spacr.core) merge_regression_res_with_metadata() (in module spacr.utils) merge_touching_objects() (in module spacr.utils) ml_analysis() (in module spacr.core) MLR() (in module spacr.utils) model_metrics() (in module spacr.utils) modify_figure() (in module spacr.gui_elements) modify_figure_properties() (in module spacr.gui_elements) ModifyMaskApp (class in spacr.gui_elements) module spacr spacr.app_annotate spacr.app_classify spacr.app_make_masks spacr.app_mask spacr.app_measure spacr.app_sequencing spacr.app_umap spacr.core spacr.deep_spacr spacr.graph_learning spacr.gui spacr.gui_core spacr.gui_elements spacr.gui_utils spacr.io spacr.logger spacr.measure spacr.plot spacr.sequencing spacr.settings spacr.sim spacr.sim_app spacr.timelapse spacr.utils spacr.version

MultiScaleBlockWithAttention (class in spacr.utils)

N

next_image() (spacr.gui_elements.ModifyMaskApp method) next_page() (spacr.gui_elements.AnnotateApp method) NoClassDataset (class in spacr.io) normalize_and_visualize() (in module spacr.plot)

normalize_array() (in module spacr.sim) normalize_image() (spacr.gui_elements.AnnotateApp static method) (spacr.gui_elements.ModifyMaskApp method) normalize_sequencing_data() (in module spacr.graph_learning) normalize_to_dtype() (in module spacr.utils)

O

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) overlay_mask_on_image() (spacr.gui_elements.ModifyMaskApp method)

P

pad_to_same_shape() (in module spacr.utils) parse_gz_files() (in module spacr.sequencing) parse_list() (in module spacr.gui_utils) perform_mixed_model() (in module spacr.sequencing) perform_regression() (in module spacr.sequencing) perform_resize() (spacr.gui_elements.spacrContainer method) perform_statistical_tests() (in module spacr.utils) pick_best_model() (in module spacr.utils) plot_arrays() (in module spacr.plot) 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.sequencing) (in module spacr.timelapse) plot_embedding() (in module spacr.utils) plot_feature_importance() (in module spacr.plot) (in module spacr.sim) plot_grid() (in module spacr.utils) plot_histogram() (in module spacr.plot) (in module spacr.sim) plot_image() (in module spacr.utils) 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) (in module spacr.sequencing)

plot_resize() (in module spacr.plot) plot_roc_pr() (in module spacr.sim) plot_saliency_maps() (spacr.utils.SaliencyMapGenerator method) plot_simulations() (in module spacr.sim) plot_umap_images() (in module spacr.utils) pos_dict() (in module spacr.sequencing) post_menu() (spacr.gui_elements.spacrDropdownMenu method) power_law_dist_gen() (in module spacr.sim) precess_reads() (in module spacr.sequencing) prefilter_paths_annotations() (spacr.gui_elements.AnnotateApp method) prepare_batch_for_cellpose() (in module spacr.core) preprocess_data() (in module spacr.utils) preprocess_generate_masks() (in module spacr.core) preprocess_image() (in module spacr.graph_learning) (in module spacr.utils) preprocess_img_data() (in module spacr.io) preprocess_pathogen_data() (in module spacr.timelapse) previous_image() (spacr.gui_elements.ModifyMaskApp method) previous_page() (spacr.gui_elements.AnnotateApp method) print_mask_and_flows() (in module spacr.plot) print_progress() (in module spacr.utils) proceed_with_app() (in module spacr.gui_utils) process_barecodes() (in module spacr.sequencing) process_chunk_for_consensus() (in module spacr.sequencing) process_chunk_for_mapping() (in module spacr.sequencing) process_console_queue() (in module spacr.gui_core) process_fig_queue() (in module spacr.gui_core) process_masks() (in module spacr.utils) process_meassure_crop_results() (in module spacr.measure) process_reads() (in module spacr.core) process_scores() (in module spacr.sequencing) process_sequencing_df() (in module spacr.graph_learning) process_stdout_stderr() (in module spacr.gui_utils) process_vision_results() (in module spacr.utils) put() (spacr.utils.Cache method)

R

random_cmap() (in module spacr.plot) random_forest_feature_importance() (in module spacr.utils) read_and_plot__vision_results() (in module spacr.plot) read_plot_model_stats() (in module spacr.io) read_simulations_table() (in module spacr.sim) recommend_target_layers() (in module spacr.utils) reducer_hyperparameter_search() (in module spacr.core) reduction_and_clustering() (in module spacr.utils) regression() (in module spacr.sequencing) regression_analasys() (in module spacr.core) regression_model() (in module spacr.sequencing) regression_roc_auc() (in module spacr.sim) relabel_objects() (spacr.gui_elements.ModifyMaskApp method) 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) remove_intensity_objects() (in module spacr.utils)

remove_low_variance_columns() (in module spacr.utils) remove_noise() (in module spacr.utils) remove_outliers() (in module spacr.sequencing) remove_small_objects() (spacr.gui_elements.ModifyMaskApp method) reposition_panes() (spacr.gui_elements.spacrContainer method) 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) ResNet (class in spacr.utils) reverse_complement() (in module spacr.sequencing) 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)

S

SaliencyMapGenerator (class in spacr.utils) save_and_add_image_to_grid() (in module spacr.measure) save_data() (in module spacr.sim) 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_results_and_figure() (in module spacr.core) save_results_dataframe() (in module spacr.timelapse) save_settings() (in module spacr.utils) save_shap_plot() (in module spacr.sim) save_to_hdf() (in module spacr.sequencing) ScaledDotProductAttention (class in spacr.utils) search_reduction_and_clustering() (in module spacr.utils) SelectChannels (class in spacr.utils) SelfAttention (class in spacr.utils) sequence_plates() (in module spacr.sim) set() (spacr.gui_elements.spacrCombo method) (spacr.gui_elements.spacrSwitch method) 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_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_training_dataset_defaults() (in module spacr.settings) set_globals() (in module spacr.gui_core) set_high_priority() (in module spacr.gui_utils) set_label_position() (spacr.gui_elements.spacrProgressBar method) set_text() (spacr.gui_elements.spacrLabel method) set_zoom_rectangle_end() (spacr.gui_elements.ModifyMaskApp method) set_zoom_rectangle_start() (spacr.gui_elements.ModifyMaskApp method) 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_progress_frame() (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) shap_analysis() (in module spacr.core) show_cam_on_image() (in module spacr.utils) show_description() (spacr.gui.MainApp method) show_next_figure() (in module spacr.gui_core) show_previous_figure() (in module spacr.gui_core) show_tooltip() (spacr.gui_elements.spacrToolTip method) shuffle_dataset() (spacr.io.NoClassDataset method) (spacr.io.spacrDataset method) shutdown() (spacr.gui_elements.AnnotateApp method) smooth_hull_lines() (in module spacr.utils) SmoothGrad (class in spacr.deep_spacr) 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.core module spacr.deep_spacr module spacr.graph_learning 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.plot module spacr.sequencing module spacr.settings module spacr.sim module spacr.sim_app module spacr.timelapse 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) spacrLabel (class in spacr.gui_elements) spacrProgressBar (class in spacr.gui_elements) spacrScrollbarStyle() (in module spacr.gui_elements) spacrSwitch (class in spacr.gui_elements) spacrToolTip (class in spacr.gui_elements) SpatialAttention (class in spacr.utils) split_fastq() (in module spacr.sequencing) split_my_dataset() (in module spacr.utils) 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) summarize_per_well() (in module spacr.timelapse) summarize_per_well_inf_non_inf() (in module spacr.timelapse)

T

TarImageDataset (class in spacr.io) test_error() (in module spacr.sequencing) test_model_core() (in module spacr.deep_spacr) test_model_performance() (in module spacr.deep_spacr) 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) TorchModel (class in spacr.utils) train() (in module spacr.graph_learning) train_cellpose() (in module spacr.core) train_graph_transformer() (in module spacr.graph_learning) train_loaders (spacr.io.CombineLoaders attribute) train_model() (in module spacr.deep_spacr) train_test_model() (in module spacr.deep_spacr) training_dataset_from_annotation() (in module spacr.core) translate_barecodes() (in module spacr.sequencing) truncate_read() (in module spacr.sequencing)

U

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_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_scores_and_get_cm() (in module spacr.sim) update_styles() (spacr.gui_elements.spacrDropdownMenu method) update_switch() (spacr.gui_elements.spacrSwitch method) update_zoom_box() (spacr.gui_elements.ModifyMaskApp method) use_magic_wand() (spacr.gui_elements.ModifyMaskApp method)

V

validate_and_adjust_beta_params() (in module spacr.sim) vert_horiz() (in module spacr.sequencing) 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_grad_cam() (in module spacr.deep_spacr) visualize_integrated_gradients() (in module spacr.deep_spacr) visualize_masks() (in module spacr.plot) visualize_saliency_map() (in module spacr.deep_spacr) visualize_smooth_grad() (in module spacr.deep_spacr) volcano_plot() (in module spacr.plot)

W

write() (spacr.gui_utils.WriteToQueue method)

WriteToQueue (class in spacr.gui_utils)

Z

zoom_icon() (spacr.gui_elements.spacrButton method)