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Core Modules

  • Core Logic
    • Module Contents
      • preprocess_generate_masks()
      • generate_cellpose_masks()
      • generate_screen_graphs()
  • IO Utilities
    • Module Contents
      • process_non_tif_non_2D_images()
      • CombineLoaders
        • CombineLoaders.train_loaders
        • CombineLoaders.loader_iters
        • CombineLoaders.__iter__()
        • CombineLoaders.__next__()
      • CombinedDataset
        • CombinedDataset.datasets
        • CombinedDataset.lengths
        • CombinedDataset.total_length
        • CombinedDataset.shuffle
        • CombinedDataset.__getitem__()
        • CombinedDataset.__len__()
      • NoClassDataset
        • NoClassDataset.data_dir
        • NoClassDataset.transform
        • NoClassDataset.shuffle
        • NoClassDataset.load_to_memory
        • NoClassDataset.filenames
        • NoClassDataset.load_image()
        • NoClassDataset.__len__()
        • NoClassDataset.shuffle_dataset()
        • NoClassDataset.__getitem__()
      • spacrDataset
        • spacrDataset.data_dir
        • spacrDataset.classes
        • spacrDataset.transform
        • spacrDataset.shuffle
        • spacrDataset.pin_memory
        • spacrDataset.filenames
        • spacrDataset.labels
        • spacrDataset.load_image()
        • spacrDataset.__len__()
        • spacrDataset.shuffle_dataset()
        • spacrDataset.get_plate()
        • spacrDataset.__getitem__()
      • spacrDataLoader
        • spacrDataLoader.preload_batches
        • spacrDataLoader.batch_queue
        • spacrDataLoader.process
        • spacrDataLoader.current_batch_index
        • spacrDataLoader.pin_memory
        • spacrDataLoader.__iter__()
        • spacrDataLoader.__next__()
        • spacrDataLoader.cleanup()
        • spacrDataLoader.__del__()
      • TarImageDataset
        • TarImageDataset.members
        • TarImageDataset.tar_path
        • TarImageDataset.transform
        • TarImageDataset.__len__()
        • TarImageDataset.__getitem__()
      • load_images_from_paths()
      • concatenate_and_normalize()
      • delete_empty_subdirectories()
      • preprocess_img_data()
      • read_plot_model_stats()
      • convert_numpy_to_tiff()
      • generate_cellpose_train_test()
      • parse_gz_files()
      • generate_dataset()
      • generate_loaders()
      • generate_training_dataset()
      • training_dataset_from_annotation()
      • training_dataset_from_annotation_metadata()
      • generate_dataset_from_lists()
      • convert_separate_files_to_yokogawa()
      • convert_to_yokogawa()
      • apply_augmentation()
      • process_instruction()
      • prepare_cellpose_dataset()
  • General Utilities
    • Module Contents
      • spacr_path
      • filepaths_to_database()
      • activation_maps_to_database()
      • activation_correlations_to_database()
      • calculate_activation_correlations()
      • load_settings()
      • save_settings()
      • print_progress()
      • reset_mp()
      • is_multiprocessing_process()
      • close_file_descriptors()
      • close_multiprocessing_processes()
      • check_mask_folder()
      • smooth_hull_lines()
      • mask_object_count()
      • is_list_of_lists()
      • normalize_to_dtype()
      • annotate_conditions()
      • Cache
        • Cache.cache
        • Cache.max_size
        • Cache.get()
        • Cache.put()
      • ScaledDotProductAttention_v1
        • ScaledDotProductAttention_v1.d_k
        • ScaledDotProductAttention_v1.forward()
      • SelfAttention_v1
        • SelfAttention_v1.W_q
        • SelfAttention_v1.W_k
        • SelfAttention_v1.W_v
        • SelfAttention_v1.attention
        • SelfAttention_v1.forward()
      • ScaledDotProductAttention
        • ScaledDotProductAttention.d_k
        • ScaledDotProductAttention.forward()
      • SelfAttention
        • SelfAttention.W_q
        • SelfAttention.W_k
        • SelfAttention.W_v
        • SelfAttention.attention
        • SelfAttention.forward()
      • EarlyFusion
        • EarlyFusion.conv1
        • EarlyFusion.forward()
      • SpatialAttention
        • SpatialAttention.conv1
        • SpatialAttention.sigmoid
        • SpatialAttention.forward()
      • MultiScaleBlockWithAttention
        • MultiScaleBlockWithAttention.dilated_conv1
        • MultiScaleBlockWithAttention.spatial_attention
        • MultiScaleBlockWithAttention.custom_forward()
        • MultiScaleBlockWithAttention.forward()
      • CustomCellClassifier
        • CustomCellClassifier.early_fusion
        • CustomCellClassifier.multi_scale_block_1
        • CustomCellClassifier.fc1
        • CustomCellClassifier.use_checkpoint
        • CustomCellClassifier.custom_forward()
        • CustomCellClassifier.forward()
      • TorchModel
        • TorchModel.model_name
        • TorchModel.use_checkpoint
        • TorchModel.base_model
        • TorchModel.num_ftrs
        • TorchModel.apply_dropout_rate()
        • TorchModel.init_base_model()
        • TorchModel.get_weight_choice()
        • TorchModel.get_num_ftrs()
        • TorchModel.init_spacr_classifier()
        • TorchModel.forward()
      • FocalLossWithLogits
        • FocalLossWithLogits.alpha
        • FocalLossWithLogits.gamma
        • FocalLossWithLogits.forward()
      • ResNet
        • ResNet.initialize_base()
        • ResNet.forward()
      • split_my_dataset()
      • classification_metrics()
      • compute_irm_penalty()
      • choose_model()
      • calculate_loss()
      • pick_best_model()
      • get_paths_from_db()
      • save_file_lists()
      • augment_single_image()
      • augment_images()
      • augment_classes()
      • annotate_predictions()
      • initiate_counter()
      • add_images_to_tar()
      • generate_fraction_map()
      • fishers_odds()
      • model_metrics()
      • check_multicollinearity()
      • lasso_reg()
      • MLR()
      • get_files_from_dir()
      • create_circular_mask()
      • apply_mask()
      • invert_image()
      • resize_images_and_labels()
      • resize_labels_back()
      • calculate_iou()
      • match_masks()
      • compute_average_precision()
      • pad_to_same_shape()
      • compute_ap_over_iou_thresholds()
      • compute_segmentation_ap()
      • jaccard_index()
      • dice_coefficient()
      • extract_boundaries()
      • boundary_f1_score()
      • merge_touching_objects()
      • remove_intensity_objects()
      • SelectChannels
        • SelectChannels.channels
        • SelectChannels.__call__()
      • preprocess_image_v1()
      • SaliencyMapGenerator
        • SaliencyMapGenerator.model
        • SaliencyMapGenerator.compute_saliency_maps()
        • SaliencyMapGenerator.compute_saliency_and_predictions()
        • SaliencyMapGenerator.plot_activation_grid()
        • SaliencyMapGenerator.percentile_normalize()
      • GradCAMGenerator
        • GradCAMGenerator.model
        • GradCAMGenerator.target_layer
        • GradCAMGenerator.cam_type
        • GradCAMGenerator.gradients
        • GradCAMGenerator.activations
        • GradCAMGenerator.target_layer_module
        • GradCAMGenerator.hook_layers()
        • GradCAMGenerator.get_layer()
        • GradCAMGenerator.compute_gradcam_maps()
        • GradCAMGenerator.compute_gradcam_and_predictions()
        • GradCAMGenerator.plot_activation_grid()
        • GradCAMGenerator.percentile_normalize()
      • preprocess_image()
      • class_visualization()
      • get_submodules()
      • GradCAM
        • GradCAM.model
        • GradCAM.target_layers
        • GradCAM.cuda
        • GradCAM.forward()
        • GradCAM.__call__()
      • show_cam_on_image()
      • recommend_target_layers()
      • IntegratedGradients
        • IntegratedGradients.model
        • IntegratedGradients.generate_integrated_gradients()
      • get_db_paths()
      • get_sequencing_paths()
      • load_image_paths()
      • merge_dataframes()
      • remove_highly_correlated_columns_v1()
      • filter_columns()
      • reduction_and_clustering()
      • remove_noise()
      • plot_embedding()
      • generate_colors()
      • assign_colors()
      • setup_plot()
      • plot_clusters()
      • plot_umap_images()
      • plot_images_by_cluster()
      • plot_image()
      • remove_canvas()
      • plot_clusters_grid()
      • plot_grid()
      • generate_path_list_from_db()
      • correct_paths()
      • delete_folder()
      • measure_test_mode()
      • preprocess_data()
      • remove_low_variance_columns()
      • remove_highly_correlated_columns()
      • filter_dataframe_features()
      • check_overlap()
      • find_non_overlapping_position()
      • search_reduction_and_clustering()
      • load_image()
      • extract_features()
      • check_normality()
      • random_forest_feature_importance()
      • perform_statistical_tests()
      • combine_results()
      • cluster_feature_analysis()
      • process_mask_file_adjust_cell()
      • adjust_cell_masks()
      • adjust_cell_masks_v1()
      • process_masks()
      • merge_regression_res_with_metadata()
      • process_vision_results()
      • get_ml_results_paths()
      • augment_image()
      • augment_dataset()
      • convert_and_relabel_masks()
      • correct_masks()
      • count_reads_in_fastq()
      • get_cuda_version()
      • all_elements_match()
      • prepare_batch_for_segmentation()
      • check_index()
      • map_condition()
      • download_models()
      • generate_cytoplasm_mask()
      • add_column_to_database()
      • fill_holes_in_mask()
      • correct_metadata_column_names()
      • control_filelist()
      • rename_columns_in_db()
      • group_feature_class()
      • delete_intermedeate_files()
      • filter_and_save_csv()
      • extract_tar_bz2_files()
      • calculate_shortest_distance()
      • format_path_for_system()
      • normalize_src_path()
      • generate_image_path_map()
      • copy_images_to_consolidated()
      • correct_metadata()
      • remove_outliers_by_group()
  • Settings
    • Module Contents
      • set_default_plot_merge_settings()
      • set_default_settings_preprocess_generate_masks()
      • set_default_plot_data_from_db()
      • set_default_settings_preprocess_img_data()
      • set_default_umap_image_settings()
      • get_measure_crop_settings()
      • set_default_analyze_screen()
      • set_default_train_test_model()
      • set_generate_training_dataset_defaults()
      • deep_spacr_defaults()
      • get_train_test_model_settings()
      • get_analyze_recruitment_default_settings()
      • get_default_test_cellpose_model_settings()
      • get_default_apply_cellpose_model_settings()
      • default_settings_analyze_percent_positive()
      • get_analyze_reads_default_settings()
      • get_map_barcodes_default_settings()
      • get_train_cellpose_default_settings()
      • set_generate_dataset_defaults()
      • get_perform_regression_default_settings()
      • get_check_cellpose_models_default_settings()
      • get_identify_masks_finetune_default_settings()
      • q
      • expected_types
      • categories
      • category_keys
      • check_settings()
      • generate_fields()
      • descriptions
      • set_annotate_default_settings()
      • set_default_generate_barecode_mapping()
      • get_default_generate_activation_map_settings()
      • get_analyze_plaque_settings()
      • set_graph_importance_defaults()
      • set_interperate_vision_model_defaults()
      • set_analyze_endodyogeny_defaults()
      • set_analyze_class_proportion_defaults()
      • get_plot_data_from_csv_default_settings()
  • Statistics
    • Module Contents
      • choose_p_adjust_method()
      • perform_normality_tests()
      • perform_levene_test()
      • perform_statistical_tests()
      • perform_posthoc_tests()
      • chi_pairwise()

Image Analysis

  • Measurement
    • Module Contents
      • get_components()
      • save_and_add_image_to_grid()
      • img_list_to_grid()
      • measure_crop()
      • process_meassure_crop_results()
      • generate_cellpose_train_set()
      • get_object_counts()
  • Plotting
    • Module Contents
      • plot_image_mask_overlay()
      • plot_cellpose4_output()
      • plot_masks()
      • generate_mask_random_cmap()
      • random_cmap()
      • plot_images_and_arrays()
      • plot_arrays()
      • plot_arrays_v1()
      • plot_merged()
      • generate_plate_heatmap()
      • plot_plates()
      • print_mask_and_flows()
      • plot_resize()
      • normalize_and_visualize()
      • visualize_masks()
      • visualize_cellpose_masks()
      • plot_comparison_results()
      • plot_object_outlines()
      • volcano_plot()
      • plot_histogram()
      • plot_lorenz_curves()
      • plot_permutation()
      • plot_feature_importance()
      • read_and_plot__vision_results()
      • jitterplot_by_annotation()
      • create_grouped_plot()
      • spacrGraph
        • spacrGraph.df
        • spacrGraph.grouping_column
        • spacrGraph.order
        • spacrGraph.data_column
        • spacrGraph.graph_type
        • spacrGraph.summary_func
        • spacrGraph.colors
        • spacrGraph.output_dir
        • spacrGraph.save
        • spacrGraph.error_bar_type
        • spacrGraph.remove_outliers
        • spacrGraph.theme
        • spacrGraph.representation
        • spacrGraph.paired
        • spacrGraph.all_to_all
        • spacrGraph.compare_group
        • spacrGraph.y_lim
        • spacrGraph.graph_name
        • spacrGraph.log_x
        • spacrGraph.log_y
        • spacrGraph.results_df
        • spacrGraph.sns_palette
        • spacrGraph.fig
        • spacrGraph.results_name
        • spacrGraph.raw_df
        • spacrGraph.preprocess_data()
        • spacrGraph.remove_outliers_from_plot()
        • spacrGraph.perform_normality_tests()
        • spacrGraph.perform_levene_test()
        • spacrGraph.perform_statistical_tests()
        • spacrGraph.perform_posthoc_tests()
        • spacrGraph.create_plot()
        • spacrGraph.get_results()
        • spacrGraph.get_figure()
      • plot_data_from_db()
      • plot_data_from_csv()
      • plot_region()
      • plot_image_grid()
      • overlay_masks_on_images()
      • graph_importance()
      • plot_proportion_stacked_bars()
      • create_venn_diagram()
  • Cellpose Integration
    • Module Contents
      • parse_cellpose4_output()
      • identify_masks_finetune()
      • generate_masks_from_imgs()
      • check_cellpose_models()
      • save_results_and_figure()
      • compare_mask()
      • compare_cellpose_masks()

Classification

  • Classical ML
    • Module Contents
      • QuasiBinomial
        • QuasiBinomial.dispersion
        • QuasiBinomial.variance()
      • calculate_p_values()
      • perform_mixed_model()
      • create_volcano_filename()
      • scale_variables()
      • select_glm_family()
      • prepare_formula()
      • fit_mixed_model()
      • check_and_clean_data()
      • minimum_cell_simulation()
      • process_model_coefficients()
      • check_distribution()
      • pick_glm_family_and_link()
      • regression_model()
      • regression()
      • save_summary_to_file()
      • perform_regression()
      • process_reads()
      • apply_transformation()
      • check_normality()
      • clean_controls()
      • process_scores()
      • generate_ml_scores()
      • ml_analysis()
      • shap_analysis()
      • find_optimal_threshold()
      • interperate_vision_model()
  • Deep Learning
    • Module Contents
      • apply_model()
      • apply_model_to_tar()
      • evaluate_model_performance()
      • test_model_core()
      • test_model_performance()
      • train_test_model()
      • train_model()
      • generate_activation_map()
      • visualize_classes()
      • visualize_integrated_gradients()
      • SmoothGrad
        • SmoothGrad.model
        • SmoothGrad.n_samples
        • SmoothGrad.stdev_spread
        • SmoothGrad.compute_smooth_grad()
      • visualize_smooth_grad()
      • deep_spacr()
      • model_knowledge_transfer()
      • model_fusion()
      • annotate_filter_vision()

GUI Components

  • GUI Main App
    • Module Contents
      • MainApp
        • MainApp.color_settings
        • MainApp.main_buttons
        • MainApp.additional_buttons
        • MainApp.main_gui_apps
        • MainApp.additional_gui_apps
        • MainApp.selected_app
        • MainApp.create_widgets()
        • MainApp.create_startup_screen()
        • MainApp.update_description()
        • MainApp.show_description()
        • MainApp.clear_description()
        • MainApp.load_app()
        • MainApp.clear_frame()
      • gui_app()
  • GUI Core
    • Module Contents
      • q
      • console_output
      • parent_frame
      • vars_dict
      • canvas
      • canvas_widget
      • scrollable_frame
      • progress_label
      • fig_queue
      • figures
      • figure_index
      • progress_bar
      • usage_bars
      • index_control
      • thread_control
      • toggle_settings()
      • display_figure()
      • clear_unused_figures()
      • show_previous_figure()
      • show_next_figure()
      • process_fig_queue()
      • update_figure()
      • setup_plot_section()
      • set_globals()
      • import_settings()
      • setup_settings_panel()
      • setup_console()
      • setup_button_section()
      • setup_usage_panel()
      • initiate_abort()
      • check_src_folders_files()
      • start_process()
      • process_console_queue()
      • main_thread_update_function()
      • cleanup_previous_instance()
      • initiate_root()
  • GUI Elements
    • Module Contents
      • fig
      • restart_gui_app()
      • create_menu_bar()
      • set_element_size()
      • set_dark_style()
      • spacrFont
        • spacrFont.font_name
        • spacrFont.font_style
        • spacrFont.font_size
        • spacrFont.font_path
        • spacrFont.get_font_path()
        • spacrFont.load_font()
        • spacrFont.get_font()
      • spacrContainer
        • spacrContainer.orient
        • spacrContainer.bg
        • spacrContainer.sash_thickness
        • spacrContainer.panes
        • spacrContainer.sashes
        • spacrContainer.add()
        • spacrContainer.create_sash()
        • spacrContainer.reposition_panes()
        • spacrContainer.on_configure()
        • spacrContainer.on_enter_sash()
        • spacrContainer.on_leave_sash()
        • spacrContainer.start_resize()
        • spacrContainer.perform_resize()
      • spacrEntry
        • spacrEntry.bg_color
        • spacrEntry.active_color
        • spacrEntry.fg_color
        • spacrEntry.outline
        • spacrEntry.font_family
        • spacrEntry.font_size
        • spacrEntry.font_loader
        • spacrEntry.canvas_height
        • spacrEntry.canvas
        • spacrEntry.draw_rounded_rectangle()
        • spacrEntry.on_focus_in()
        • spacrEntry.on_focus_out()
      • spacrCheck
        • spacrCheck.bg_color
        • spacrCheck.active_color
        • spacrCheck.fg_color
        • spacrCheck.inactive_color
        • spacrCheck.variable
        • spacrCheck.canvas_width
        • spacrCheck.canvas_height
        • spacrCheck.canvas
        • spacrCheck.draw_rounded_square()
        • spacrCheck.update_check()
        • spacrCheck.toggle_variable()
      • spacrCombo
        • spacrCombo.bg_color
        • spacrCombo.active_color
        • spacrCombo.fg_color
        • spacrCombo.inactive_color
        • spacrCombo.font_family
        • spacrCombo.font_size
        • spacrCombo.font_loader
        • spacrCombo.values
        • spacrCombo.canvas_width
        • spacrCombo.canvas_height
        • spacrCombo.canvas
        • spacrCombo.var
        • spacrCombo.selected_value
        • spacrCombo.dropdown_menu
        • spacrCombo.draw_rounded_rectangle()
        • spacrCombo.on_click()
        • spacrCombo.open_dropdown()
        • spacrCombo.close_dropdown()
        • spacrCombo.on_select()
        • spacrCombo.set()
      • spacrDropdownMenu
        • spacrDropdownMenu.variable
        • spacrDropdownMenu.options
        • spacrDropdownMenu.command
        • spacrDropdownMenu.text
        • spacrDropdownMenu.size
        • spacrDropdownMenu.font_size
        • spacrDropdownMenu.font_loader
        • spacrDropdownMenu.button_width
        • spacrDropdownMenu.canvas_width
        • spacrDropdownMenu.canvas_height
        • spacrDropdownMenu.canvas
        • spacrDropdownMenu.inactive_color
        • spacrDropdownMenu.active_color
        • spacrDropdownMenu.fg_color
        • spacrDropdownMenu.bg_color
        • spacrDropdownMenu.button_bg
        • spacrDropdownMenu.button_text
        • spacrDropdownMenu.menu
        • spacrDropdownMenu.create_rounded_rectangle()
        • spacrDropdownMenu.on_enter()
        • spacrDropdownMenu.on_leave()
        • spacrDropdownMenu.on_click()
        • spacrDropdownMenu.post_menu()
        • spacrDropdownMenu.on_select()
        • spacrDropdownMenu.update_styles()
      • spacrCheckbutton
        • spacrCheckbutton.text
        • spacrCheckbutton.variable
        • spacrCheckbutton.command
      • spacrProgressBar
        • spacrProgressBar.fg_color
        • spacrProgressBar.bg_color
        • spacrProgressBar.active_color
        • spacrProgressBar.inactive_color
        • spacrProgressBar.font_size
        • spacrProgressBar.font_loader
        • spacrProgressBar.style
        • spacrProgressBar.label
        • spacrProgressBar.operation_type
        • spacrProgressBar.additional_info
        • spacrProgressBar.set_label_position()
        • spacrProgressBar.update_label()
      • spacrSlider
        • spacrSlider.specified_length
        • spacrSlider.knob_radius
        • spacrSlider.thickness
        • spacrSlider.knob_position
        • spacrSlider.slider_line
        • spacrSlider.knob
        • spacrSlider.position
        • spacrSlider.offset
        • spacrSlider.from_
        • spacrSlider.to
        • spacrSlider.value
        • spacrSlider.show_index
        • spacrSlider.command
        • spacrSlider.fg_color
        • spacrSlider.bg_color
        • spacrSlider.active_color
        • spacrSlider.inactive_color
        • spacrSlider.canvas
        • spacrSlider.length
        • spacrSlider.resize_slider()
        • spacrSlider.value_to_position()
        • spacrSlider.position_to_value()
        • spacrSlider.draw_slider()
        • spacrSlider.move_knob()
        • spacrSlider.activate_knob()
        • spacrSlider.release_knob()
        • spacrSlider.set_to()
        • spacrSlider.get()
        • spacrSlider.set()
        • spacrSlider.jump_to_click()
        • spacrSlider.update_slider_from_entry()
      • spacrScrollbarStyle()
      • spacrFrame
        • spacrFrame.scrollable_frame
        • spacrFrame.inactive_color
        • spacrFrame.active_color
        • spacrFrame.fg_color
        • spacrFrame.rounded_rectangle()
      • spacrLabel
        • spacrLabel.text
        • spacrLabel.align
        • spacrLabel.style_out
        • spacrLabel.font_style
        • spacrLabel.font_size
        • spacrLabel.font_family
        • spacrLabel.font_loader
        • spacrLabel.canvas
        • spacrLabel.style
        • spacrLabel.set_text()
      • spacrButton
        • spacrButton.text
        • spacrButton.command
        • spacrButton.icon_name
        • spacrButton.size
        • spacrButton.show_text
        • spacrButton.outline
        • spacrButton.animation
        • spacrButton.font_size
        • spacrButton.font_loader
        • spacrButton.canvas
        • spacrButton.inactive_color
        • spacrButton.bg_color
        • spacrButton.active_color
        • spacrButton.fg_color
        • spacrButton.is_zoomed_in
        • spacrButton.load_icon()
        • spacrButton.get_icon_path()
        • spacrButton.on_enter()
        • spacrButton.on_leave()
        • spacrButton.on_click()
        • spacrButton.create_rounded_rectangle()
        • spacrButton.update_description()
        • spacrButton.clear_description()
        • spacrButton.animate_zoom()
        • spacrButton.zoom_icon()
      • spacrSwitch
        • spacrSwitch.text
        • spacrSwitch.variable
        • spacrSwitch.command
        • spacrSwitch.canvas
        • spacrSwitch.switch_bg
        • spacrSwitch.switch
        • spacrSwitch.label
        • spacrSwitch.toggle()
        • spacrSwitch.update_switch()
        • spacrSwitch.animate_switch()
        • spacrSwitch.animate_movement()
        • spacrSwitch.get()
        • spacrSwitch.set()
        • spacrSwitch.create_rounded_rectangle()
      • spacrToolTip
        • spacrToolTip.widget
        • spacrToolTip.text
        • spacrToolTip.tooltip_window
        • spacrToolTip.show_tooltip()
        • spacrToolTip.hide_tooltip()
      • standardize_figure()
      • modify_figure_properties()
      • save_figure_as_format()
      • modify_figure()
      • generate_dna_matrix()
  • GUI Utilities
    • Module Contents
      • initialize_cuda()
      • set_high_priority()
      • set_cpu_affinity()
      • proceed_with_app()
      • load_app()
      • parse_list()
      • create_input_field()
      • process_stdout_stderr()
      • WriteToQueue
        • WriteToQueue.q
        • WriteToQueue.write()
        • WriteToQueue.flush()
      • cancel_after_tasks()
      • load_next_app()
      • convert_settings_dict_for_gui()
      • spacrFigShow()
      • function_gui_wrapper()
      • run_function_gui()
      • hide_all_settings()
      • setup_frame()
      • download_hug_dataset()
      • download_dataset()
      • ensure_after_tasks()
      • display_gif_in_plot_frame()
      • display_media_in_plot_frame()
      • print_widget_structure()
      • get_screen_dimensions()
      • convert_to_number()

Sequencing & Submodules

  • Sequencing
    • Module Contents
      • map_sequences_to_names()
      • save_df_to_hdf5()
      • save_unique_combinations_to_csv()
      • save_qc_df_to_csv()
      • extract_sequence_and_quality()
      • create_consensus()
      • get_consensus_base()
      • reverse_complement()
      • process_chunk()
      • saver_process()
      • paired_read_chunked_processing()
      • single_read_chunked_processing()
      • generate_barecode_mapping()
      • barecodes_reverse_complement()
      • graph_sequencing_stats()
  • Toxoplasma Tools
    • Module Contents
      • custom_volcano_plot()
      • go_term_enrichment_by_column()
      • plot_gene_phenotypes()
      • plot_gene_heatmaps()
      • generate_score_heatmap()
  • Submodules
    • Module Contents
      • CellposeLazyDataset
        • CellposeLazyDataset.normalize
        • CellposeLazyDataset.percentiles
        • CellposeLazyDataset.target_size
        • CellposeLazyDataset.augment
        • CellposeLazyDataset.__len__()
        • CellposeLazyDataset.apply_augmentation()
        • CellposeLazyDataset.__getitem__()
      • train_cellpose()
      • test_cellpose_model()
      • apply_cellpose_model()
      • plot_cellpose_batch()
      • analyze_percent_positive()
      • analyze_recruitment()
      • analyze_plaques()
      • count_phenotypes()
      • compare_reads_to_scores()
      • interperate_vision_model()
      • analyze_endodyogeny()
      • analyze_class_proportion()
      • generate_score_heatmap()
      • post_regression_analysis()
  • API Reference
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