Index A | B | C | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z A add_prev_trained_model() (scripts.ImportFiles.ImportFilePanel method) add_species() (scripts.ImportFiles.ImportFilePanel method) apply_gating() (in module scripts.helpers) AXIS_SELECTION (scripts.GUIhelpers.GuiMessages attribute) axis_selection_label (scripts.Prediction.PredictionPanel attribute) axis_selectors (scripts.Prediction.PredictionPanel attribute) AxisSelector (class in scripts.GUIhelpers) B basic_stains() (scripts.GUIhelpers.LiveDeadDebrisSelectors method) batch_combo (scripts.TrainingModel.TrainModelPanel attribute) best_model (scripts.TrainingModel.TrainModelPanel attribute) blank_button (scripts.ImportFiles.ImportFilePanel attribute) blank_files (scripts.ImportFiles.ImportFilePanel attribute) BLANKS_MULTIFILES (scripts.GUIhelpers.GuiMessages attribute) build_model() (in module scripts.nn) build_stain_inputs() (scripts.Prediction.PredictionPanel method) button_style() (in module scripts.helpers) C calculate_threshold() (in module scripts.nn) channel (scripts.helpers.Stain attribute) channels_on_stain_buttons() (scripts.Prediction.PredictionPanel method) choose_coculture_file() (scripts.Prediction.PredictionPanel method) choose_coculture_file_button (scripts.Prediction.PredictionPanel attribute) cleaned_data (scripts.TrainingModel.TrainModelPanel attribute) COLUMN_NAMES_ERROR (scripts.GUIhelpers.GuiMessages attribute) combo (scripts.GUIhelpers.AxisSelector attribute) (scripts.GUIhelpers.LabeledComboBox attribute) (scripts.GUIhelpers.StainSelector attribute) create_color_map() (in module scripts.illustrations) create_file_path() (in module scripts.helpers) create_shape_map() (in module scripts.illustrations) cs_uncertainty_threshold (scripts.TrainingModel.TrainModelPanel attribute) E epochs_combo (scripts.TrainingModel.TrainModelPanel attribute) error_signal (scripts.Prediction.WorkerPredict attribute) (scripts.TrainingModel.WorkerProcessFiles attribute) event_combo (scripts.TrainingModel.TrainModelPanel attribute) event_label (scripts.TrainingModel.TrainModelPanel attribute) F file_panel (scripts.Prediction.PredictionPanel attribute) (scripts.TrainingModel.TrainModelPanel attribute) file_settings_group (scripts.TrainingModel.TrainModelPanel attribute) file_types (scripts.ImportFiles.ImportFilePanel attribute) finished_signal (scripts.Prediction.WorkerPredict attribute) (scripts.TrainingModel.WorkerProcessFiles attribute) fire_predict() (scripts.Prediction.PredictionPanel method) G GATING_CHECHBOX (scripts.GUIhelpers.GuiMessages attribute) gating_checkbox() (scripts.GUIhelpers.GatingCheckBox method) gating_plot() (in module scripts.illustrations) GATING_THRESHOLD (scripts.GUIhelpers.GuiMessages attribute) GatingCheckBox (class in scripts.GUIhelpers) GatingMixin (class in scripts.GUIhelpers) get_abs_path() (in module scripts.helpers) get_app_dir() (in module scripts.helpers) get_host_class_name() (scripts.GUIhelpers.GatingMixin method) get_model_components() (in module scripts.run_prediction) get_stains_from_panel() (in module scripts.helpers) GuiMessages (class in scripts.GUIhelpers) H hetero_mini_batch() (in module scripts.run_prediction) hetero_simple() (in module scripts.run_prediction) heterogeneity_bar_plot() (in module scripts.illustrations) heterogeneity_pie_chart() (in module scripts.illustrations) I ImportFilePanel (class in scripts.ImportFiles) init_species_layout() (scripts.ImportFiles.ImportFilePanel method) iterate_stains() (in module scripts.GUIhelpers) K kfold_combo (scripts.TrainingModel.TrainModelPanel attribute) L label (scripts.GUIhelpers.AxisSelector attribute) (scripts.GUIhelpers.LabeledComboBox attribute) (scripts.GUIhelpers.LabeledSpinBox attribute) (scripts.GUIhelpers.StainSelector attribute) (scripts.helpers.Stain attribute) LabeledComboBox (class in scripts.GUIhelpers) LabeledSpinBox (class in scripts.GUIhelpers) layout (scripts.ImportFiles.ImportFilePanel attribute) (scripts.Prediction.PredictionPanel attribute) (scripts.TrainingModel.TrainModelPanel attribute) le (scripts.TrainingModel.TrainModelPanel attribute) LiveDeadDebrisSelectors (class in scripts.GUIhelpers) load_fcs_file() (in module scripts.GUIhelpers) load_model_from_files() (in module scripts.helpers) M merge_prediction_results() (in module scripts.run_prediction) model (scripts.ImportFiles.ImportFilePanel attribute) model_loaded (scripts.ImportFiles.ImportFilePanel attribute) model_settings_group (scripts.TrainingModel.TrainModelPanel attribute) module scripts scripts.apply_umap scripts.GUIhelpers scripts.helpers scripts.illustrations scripts.ImportFiles scripts.nn scripts.Prediction scripts.run_prediction scripts.TrainingModel N new_stain_button (scripts.Prediction.PredictionPanel attribute) nn_blank_combo (scripts.TrainingModel.TrainModelPanel attribute) nn_group (scripts.TrainingModel.TrainModelPanel attribute) nn_nonblank_combo (scripts.TrainingModel.TrainModelPanel attribute) O on_error() (scripts.Prediction.PredictionPanel method) (scripts.TrainingModel.TrainModelPanel method) on_finished() (scripts.TrainingModel.TrainModelPanel method) P patience_combo (scripts.TrainingModel.TrainModelPanel attribute) predict() (in module scripts.run_prediction) predict_panel (scripts.Prediction.PredictionPanel attribute) predict_panel_layout (scripts.Prediction.PredictionPanel attribute) predict_species() (in module scripts.run_prediction) predict_validation() (in module scripts.nn) prediction_completed() (scripts.Prediction.PredictionPanel method) PredictionPanel (class in scripts.Prediction) PredictPanel (scripts.Prediction.WorkerPredict attribute) prepare_for_training() (in module scripts.nn) PREVIOUSLY_TRAINED_MODEL (scripts.GUIhelpers.GuiMessages attribute) previously_trained_model_button (scripts.ImportFiles.ImportFilePanel attribute) process_button (scripts.TrainingModel.TrainModelPanel attribute) process_file() (in module scripts.apply_umap) process_files() (in module scripts.apply_umap) R relation (scripts.GUIhelpers.StainSelector attribute) run_heterogeneity() (in module scripts.run_prediction) run_predict() (scripts.Prediction.WorkerPredict method) run_prediction_button (scripts.Prediction.PredictionPanel attribute) run_process_files() (scripts.TrainingModel.WorkerProcessFiles method) S save_gating_results() (in module scripts.helpers) save_heterogeneity_plots() (in module scripts.run_prediction) save_prediction_results() (in module scripts.run_prediction) save_train_stats() (in module scripts.nn) scaler (scripts.TrainingModel.TrainModelPanel attribute) scaling_constant (scripts.ImportFiles.ImportFilePanel attribute) (scripts.TrainingModel.TrainModelPanel attribute) scripts module scripts.apply_umap module scripts.GUIhelpers module scripts.helpers module scripts.illustrations module scripts.ImportFiles module scripts.nn module scripts.Prediction module scripts.run_prediction module scripts.TrainingModel module select_blank_files() (scripts.ImportFiles.ImportFilePanel method) select_blanks_message (scripts.ImportFiles.ImportFilePanel attribute) select_directory() (scripts.ImportFiles.ImportFilePanel method) select_species_files() (scripts.ImportFiles.ImportFilePanel method) set_items() (scripts.GUIhelpers.AxisSelector method) (scripts.GUIhelpers.StainSelector method) sign (scripts.helpers.Stain attribute) species_files (scripts.ImportFiles.ImportFilePanel attribute) species_plot() (in module scripts.illustrations) species_widgets (scripts.ImportFiles.ImportFilePanel attribute) spin_box (scripts.GUIhelpers.LabeledSpinBox attribute) Stain (class in scripts.helpers) stain_sannity_check() (in module scripts.helpers) StainSelector (class in scripts.GUIhelpers) start_loading_cursor() (scripts.Prediction.PredictionPanel method) (scripts.TrainingModel.TrainModelPanel method) start_training_process() (scripts.TrainingModel.TrainModelPanel method) stop_loading_cursor() (scripts.Prediction.PredictionPanel method) (scripts.TrainingModel.TrainModelPanel method) T threshold (scripts.GUIhelpers.StainSelector attribute) time_based_dir() (in module scripts.helpers) toggle_const_scaling() (scripts.ImportFiles.ImportFilePanel method) toggle_gating_options() (scripts.GUIhelpers.GatingMixin method) toggle_uncertainty_filterint_options() (scripts.Prediction.PredictionPanel method) train_gating (scripts.TrainingModel.TrainModelPanel attribute) train_gating_layout (scripts.TrainingModel.TrainModelPanel attribute) train_neural_network() (in module scripts.nn) train_panel (scripts.Prediction.PredictionPanel attribute) train_wrapper() (in module scripts.nn) TrainModelPanel (class in scripts.TrainingModel) (scripts.TrainingModel.WorkerProcessFiles attribute) U umap_group (scripts.TrainingModel.TrainModelPanel attribute) umap_mindist_combo (scripts.TrainingModel.TrainModelPanel attribute) umap_nneighbors_combo (scripts.TrainingModel.TrainModelPanel attribute) umap_plot() (in module scripts.illustrations) UNCERTAINTY_CHECKBOX (scripts.GUIhelpers.GuiMessages attribute) uncertainty_filtering_checkbox (scripts.Prediction.PredictionPanel attribute) uncertainty_plot() (in module scripts.illustrations) uncertainty_threshold (scripts.Prediction.PredictionPanel attribute) uncertainty_threshold_label (scripts.Prediction.PredictionPanel attribute) uncertainty_threshold_layout (scripts.Prediction.PredictionPanel attribute) UNCERTAINTY_TOOLTIP (scripts.GUIhelpers.GuiMessages attribute) update_uncertainty_threshold() (scripts.Prediction.PredictionPanel method) USER_STAIN_TOOLTIP (scripts.GUIhelpers.GuiMessages attribute) V value (scripts.helpers.Stain attribute) W WorkerPredict (class in scripts.Prediction) WorkerProcessFiles (class in scripts.TrainingModel) working_directory (scripts.ImportFiles.ImportFilePanel attribute) X X (scripts.TrainingModel.TrainModelPanel attribute) x_axis_selector (scripts.Prediction.PredictionPanel attribute) Y y (scripts.TrainingModel.TrainModelPanel attribute) y_axis_selector (scripts.Prediction.PredictionPanel attribute) Z z_axis_selector (scripts.Prediction.PredictionPanel attribute)