Index

A

acquire_images() (microscope_automation.samples.samples.ImagingSystem method), [1] AcquireImage_3() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) Acquisition (class in microscope_automation.connectors.connect_zen_blue_dummy) ActiveExperiment() (microscope_automation.connectors.connect_zen_blue_dummy.Experiments method) ActualPosition() (microscope_automation.connectors.connect_zen_blue_dummy.Focus property) (microscope_automation.connectors.connect_zen_blue_dummy.ObjectiveChanger property) ActualPositionName() (microscope_automation.connectors.connect_zen_blue_dummy.ObjectiveChanger property) ActualPositionX() (microscope_automation.connectors.connect_zen_blue_dummy.Stage property) ActualPositionY() (microscope_automation.connectors.connect_zen_blue_dummy.Stage property) Add() (microscope_automation.connectors.connect_zen_blue_dummy.Documents method) add_attached_image() (microscope_automation.samples.samples.ImagingSystem method), [1] add_barcode() (in module microscope_automation.samples.setup_samples), [1] (microscope_automation.samples.samples.Well method), [1] add_camera_id() (microscope_automation.samples.samples.ImagingSystem method), [1] add_cells() (microscope_automation.samples.samples.Colony method), [1] add_colonies() (in module microscope_automation.samples.setup_samples), [1] (microscope_automation.samples.samples.Well method), [1] add_control_software() (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] add_counter() (microscope_automation.samples.samples.ImmersionDelivery method), [1] add_data() (microscope_automation.util.image_AICS.ImageAICS method), [1] add_last_experiment_object() (microscope_automation.util.software_state.State method), [1] add_meta() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.util.image_AICS.ImageAICS method), [1] add_meta_data_file() (microscope_automation.samples.samples.ImagingSystem method), [1] add_microscope_object() (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1]

add_next_experiment_object() (microscope_automation.util.software_state.State method), [1] add_plates() (microscope_automation.samples.samples.PlateHolder method), [1] add_safe_area() (microscope_automation.hardware.hardware_components.Safety method), [1] add_samples() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.Well method), [1] add_slides() (microscope_automation.samples.samples.PlateHolder method), [1] add_suffix() (in module microscope_automation.util.get_path), [1] add_to_image_dir() (microscope_automation.samples.samples.ImagingSystem method), [1] add_unpickled_objects() (microscope_automation.util.software_state.State method), [1] add_wells() (microscope_automation.samples.samples.Plate method), [1] adjust_image() (microscope_automation.samples.find_cells.CellFinder method), [1] Application (class in microscope_automation.connectors.connect_zen_blue_dummy) Apply() (microscope_automation.connectors.connect_zen_blue_dummy.Focus method) (microscope_automation.connectors.connect_zen_blue_dummy.ObjectiveChanger method) (microscope_automation.connectors.connect_zen_blue_dummy.Stage method) apply_filter() (in module microscope_automation.samples.segmentation_filters) AutoFocus (class in microscope_automation.hardware.hardware_components), [1] AutofocusError (class in microscope_automation.util.automation_exceptions) AutofocusNoReferenceObjectError (class in microscope_automation.util.automation_exceptions) AutofocusNotSetError (class in microscope_automation.util.automation_exceptions) AutofocusObjectiveChangedError (class in microscope_automation.util.automation_exceptions) AutomationError (class in microscope_automation.util.automation_exceptions)

B

Background (class in microscope_automation.samples.samples), [1] background_correction() (microscope_automation.samples.samples.ImagingSystem method), [1] Barcode (class in microscope_automation.samples.samples), [1]

BaseMicroscope (class in microscope_automation.hardware.hardware_control), [1] Braintree (class in microscope_automation.hardware.RS232), [1] (class in microscope_automation.hardware.RS232_dummy)

C

calculate_all_wells_correction() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) calculate_plate_correction() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) calculate_slope_correction() (microscope_automation.samples.samples.ImagingSystem method), [1] calculate_well_correction() (microscope_automation.samples.samples.Well method), [1] CalibrationViewer (class in microscope_automation.samples.find_cells), [1] Camera (class in microscope_automation.hardware.hardware_components), [1] Cell (class in microscope_automation.samples.samples), [1] CellFinder (class in microscope_automation.samples.find_cells), [1] change_magnification() (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] change_objective() (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) change_position() (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] check_box_message() (in module microscope_automation.util.automation_messages_form_layout), [1] choose_imaging_location() (microscope_automation.samples.find_cells.CellFinder method), [1] clear_experiments() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] close() (microscope_automation.samples.find_cells.CalibrationViewer method) close_connection() (microscope_automation.hardware.RS232.Braintree method), [1] (microscope_automation.hardware.RS232_dummy.Braintree method) close_experiment() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) Colony (class in microscope_automation.samples.samples), [1] connect_to_microscope_software() (microscope_automation.hardware.hardware_components.ControlSoftware method), [1] ConnectMicroscope (class in microscope_automation.connectors.connect_slidebook), [1] (class in microscope_automation.connectors.connect_zen_blue) Contains() (microscope_automation.connectors.connect_zen_blue_dummy.Experiments method) control_autofocus() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method)

ControlSoftware (class in microscope_automation.hardware.hardware_components), [1] convert_location_list() (in module microscope_automation.orchestrator.find_positions), [1] convert_to_stage_coords() (microscope_automation.orchestrator.write_zen_tiles_experiment.PositionWriter method), [1] copy_image_position() (in module microscope_automation.orchestrator.find_positions), [1] copy_zero_position() (in module microscope_automation.orchestrator.find_positions), [1] count_and_get_water() (microscope_automation.samples.samples.ImmersionDelivery method), [1] count_experiments() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] CrashDangerError (class in microscope_automation.util.automation_exceptions) create_circular_mask() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) create_edge_image() (in module microscope_automation.samples.find_well_center), [1] create_ellipse() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] create_experiment_path() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) create_file_name() (microscope_automation.util.image_AICS.ImageAICS method), [1] create_output_objects_from_parent_object() (in module microscope_automation.orchestrator.find_positions), [1] create_plate() (in module microscope_automation.samples.samples), [1] create_plate_holder_manually() (in module microscope_automation.samples.samples), [1] create_rect_tile() (in module microscope_automation.samples.samples), [1] create_rectangle() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] create_well_image() (in module microscope_automation.samples.find_well_center), [1] CreateTilePositions (class in microscope_automation.samples.positions_list), [1] current_z_set() (in module microscope_automation.settings.test_zen_experiment)

D

define_load_position() (microscope_automation.hardware.hardware_components.FocusDrive method), [1] define_work_position() (microscope_automation.hardware.hardware_components.FocusDrive method), [1] delete_experiment() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] Devices (class in microscope_automation.connectors.connect_zen_blue_dummy) DiagnosticPickler (class in microscope_automation.util.software_state), [1] display_and_save() (in module microscope_automation.samples.find_cells), [1] display_image() (microscope_automation.samples.find_cells.CalibrationViewer method) Documents (class in microscope_automation.connectors.connect_zen_blue_dummy)

downscale_filter_dictionary() (microscope_automation.samples.well_overview_segmentation.WellSegmentation method) (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) draw_column_labels() (in module microscope_automation.samples.draw_plate), [1] draw_label() (in module microscope_automation.samples.draw_plate), [1] draw_legend() (in module microscope_automation.samples.draw_plate), [1] draw_plate() (in module microscope_automation.samples.draw_plate), [1] draw_row_labels() (in module microscope_automation.samples.draw_plate), [1] draw_well() (in module microscope_automation.samples.draw_plate), [1] draw_wells() (in module microscope_automation.samples.draw_plate), [1]

E

eliminate_unpickled_objects() (microscope_automation.util.software_state.State method), [1] error_dialog() (microscope_automation.util.automation_exceptions.AutofocusError method), [1] (microscope_automation.util.automation_exceptions.AutofocusNoReferenceObjectError method), [1] (microscope_automation.util.automation_exceptions.AutofocusNotSetError method), [1] (microscope_automation.util.automation_exceptions.AutofocusObjectiveChangedError method), [1] (microscope_automation.util.automation_exceptions.CrashDangerError method), [1] (microscope_automation.util.automation_exceptions.ExperimentError method), [1] (microscope_automation.util.automation_exceptions.ExperimentNotExistError method), [1] (microscope_automation.util.automation_exceptions.FileExistsError method), [1] (microscope_automation.util.automation_exceptions.HardwareCommandNotDefinedError method), [1] (microscope_automation.util.automation_exceptions.HardwareDoesNotExistError method), [1] (microscope_automation.util.automation_exceptions.HardwareError method), [1] (microscope_automation.util.automation_exceptions.HardwareNotReadyError method), [1] (microscope_automation.util.automation_exceptions.IOError method), [1] (microscope_automation.util.automation_exceptions.LoadNotDefinedError method), [1] (microscope_automation.util.automation_exceptions.MetaDataNotSavedError method), [1] (microscope_automation.util.automation_exceptions.ObjectiveNotDefinedError method), [1] (microscope_automation.util.automation_exceptions.StopCollectingError method), [1] (microscope_automation.util.automation_exceptions.WorkNotDefinedError method), [1] error_message() (in module microscope_automation.util.automation_messages_form_layout), [1]

Execute() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) execute_experiment() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) (microscope_automation.samples.samples.Cell method), [1] (microscope_automation.samples.samples.Colony method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] Experiment (class in microscope_automation.hardware.hardware_components), [1] experiment_exists() (microscope_automation.settings.slidebook_experiment_info.SlidebookExperiment method), [1] (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1] ExperimentError (class in microscope_automation.util.automation_exceptions) ExperimentNotExistError (class in microscope_automation.util.automation_exceptions) Experiments (class in microscope_automation.connectors.connect_zen_blue_dummy) export_cells() (microscope_automation.samples.find_cells.CellFinder method), [1]

F

failed_image() (microscope_automation.samples.interactive_location_picker_pyqtgraph.ImageLocationPicker method) file_select_dialog() (in module microscope_automation.util.automation_messages_form_layout), [1] FileExistsError (class in microscope_automation.util.automation_exceptions) filter_by_distance() (in module microscope_automation.samples.segmentation_filters) filter_by_size() (in module microscope_automation.samples.segmentation_filters) filter_colonies() (in module microscope_automation.samples.setup_samples), [1] filter_objects() (microscope_automation.samples.find_cells.CellFinder method), [1] filter_small_objects() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) final_edge_detection() (microscope_automation.samples.find_cells.CellFinder method), [1] find_autofocus() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) find_cell_interactive_distance_map() (microscope_automation.samples.samples.Colony method), [1] find_cells() (microscope_automation.samples.find_cells.CellFinder method), [1] find_cells_cell_profiler() (microscope_automation.samples.samples.Colony method), [1] find_cells_distance_map() (microscope_automation.samples.samples.Colony method), [1] find_center_position() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) find_colonies() (microscope_automation.samples.samples.Well method), [1] find_edge_position() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method)

find_edge_ridge_pair() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) find_interactive_distance_map() (in module microscope_automation.orchestrator.find_positions), [1] find_interactive_position() (in module microscope_automation.orchestrator.find_positions), [1] find_positions() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) find_ridge_position() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) find_surface() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] find_well_center() (in module microscope_automation.samples.find_well_center), [1] find_well_center_fine() (in module microscope_automation.samples.find_well_center), [1] (microscope_automation.samples.samples.Well method), [1] FindAutoFocus() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) FindAutoFocus_2() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) FindSurface() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) fixed_pattern_correction() (in module microscope_automation.samples.correct_background), [1] flip_coordinates() (microscope_automation.samples.interactive_location_picker_pyqtgraph.ImageLocationPicker method), [1] Focus (class in microscope_automation.connectors.connect_zen_blue_dummy) FocusDrive (class in microscope_automation.hardware.hardware_components), [1]

G

get_about_command_service() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] get_about_data_service() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] get_abs_pos_from_obj_pos() (microscope_automation.samples.samples.ImagingSystem method), [1] get_abs_position() (microscope_automation.hardware.hardware_components.FocusDrive method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] get_abs_stage_position() (microscope_automation.samples.samples.PlateHolder method), [1] get_abs_zero() (microscope_automation.samples.samples.ImagingSystem method), [1] get_all_objectives() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] get_assigned_diameter() (microscope_automation.samples.samples.Well method), [1] get_attached_image() (microscope_automation.samples.samples.ImagingSystem method), [1] get_auto_focus_id() (microscope_automation.samples.samples.ImagingSystem method), [1] get_autofocus_ready() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.AutoFocus method), [1] get_barcode() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.Plate method), [1] get_barcode_object() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) get_calibration_path() (in module microscope_automation.util.get_path), [1] get_camera_ids() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] get_cell_line() (microscope_automation.samples.samples.Cell method), [1] (microscope_automation.samples.samples.Colony method), [1] get_cells() (microscope_automation.samples.samples.Colony method), [1] get_clone() (microscope_automation.samples.samples.Cell method), [1] (microscope_automation.samples.samples.Colony method), [1] get_colonies() (microscope_automation.samples.samples.Well method), [1] get_colony_data() (in module microscope_automation.samples.setup_samples), [1] get_colony_dir_path() (in module microscope_automation.util.get_path), [1] get_colony_file_path() (in module microscope_automation.util.get_path), [1] get_colony_remote_dir_path() (in module microscope_automation.util.get_path), [1] get_connection() (microscope_automation.hardware.hardware_components.Pump method), [1] get_container() (microscope_automation.samples.samples.ImagingSystem method), [1] get_container_pos_from_obj_pos() (microscope_automation.samples.samples.ImagingSystem method), [1] get_corrected_stage_position() (microscope_automation.samples.samples.PlateHolder method), [1] get_correction() (microscope_automation.samples.samples.ImagingSystem method), [1] get_counter() (microscope_automation.samples.samples.ImmersionDelivery method), [1] get_counter_stop_value() (microscope_automation.samples.samples.ImmersionDelivery method), [1] get_daily_folder() (in module microscope_automation.util.get_path), [1] get_data() (microscope_automation.util.image_AICS.ImageAICS method), [1] get_diameter() (microscope_automation.samples.samples.Well method), [1] get_error_blocking() (in module microscope_automation.util.automation_exceptions), [1] get_experiment() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] get_experiment_dict() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] get_experiment_folder() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) get_experiment_path() (in module microscope_automation.util.get_path), [1] get_failed_image() (microscope_automation.samples.samples.Well method) get_field_rotation() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] get_flip() (microscope_automation.samples.samples.ImagingSystem method), [1] get_focus_id() (microscope_automation.samples.samples.ImagingSystem method), [1] get_focus_pos() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) get_focus_reference_obj_id() (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.util.automation_exceptions.AutofocusError method), [1] get_focus_settings() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Experiment method), [1] (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1] get_from_image_dir() (microscope_automation.samples.samples.ImagingSystem method), [1] get_hardware_settings_path() (in module microscope_automation.util.get_path), [1] get_id() (microscope_automation.hardware.hardware_components.MicroscopeComponent method), [1] get_image() (microscope_automation.samples.samples.ImagingSystem method), [1] get_images() (microscope_automation.samples.samples.ImagingSystem method), [1] get_images_path() (in module microscope_automation.util.get_path), [1] get_immersion_delivery_system() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] get_information() (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.hardware.hardware_components.Camera method), [1] (microscope_automation.hardware.hardware_components.FocusDrive method), [1] (microscope_automation.hardware.hardware_components.MicroscopeComponent method), [1] (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] (microscope_automation.hardware.hardware_components.Stage method), [1] (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) get_init_experiment() (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.hardware.hardware_components.MicroscopeComponent method), [1] get_last_known_focus_position() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) get_load_position() (microscope_automation.hardware.hardware_components.FocusDrive method), [1] (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] get_log_file_path() (in module microscope_automation.util.get_path), [1] get_measured_diameter() (microscope_automation.samples.samples.Well method), [1] get_meta() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.util.image_AICS.ImageAICS method), [1]

get_meta_data_file() (microscope_automation.samples.samples.ImagingSystem method), [1] get_meta_data_path() (in module microscope_automation.util.get_path), [1] get_microscope() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] get_microscope_name() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) get_mode_c_points() (microscope_automation.samples.well_overview_segmentation.WellSegmentation method) get_module_version() (in module microscope_automation) get_name() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.Well method), [1] get_next_experiment() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] get_next_pos_name() (microscope_automation.orchestrator.write_zen_tiles_experiment.PositionWriter method), [1] get_number_positions() (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] get_obj_pos_from_container_pos() (microscope_automation.samples.samples.ImagingSystem method), [1] get_objective_changer_id() (microscope_automation.samples.samples.ImagingSystem method), [1] get_objective_information() (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] get_objective_is_ready() (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) get_objective_magnification() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] get_objective_name() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) get_objective_offsets() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) get_objective_position() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Experiment method), [1] (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1] get_objective_position_from_experiment_file() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) get_objectives_dict() (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] get_original_data() (microscope_automation.samples.find_cells.CellFinder method), [1] get_parent_prefs() (microscope_automation.settings.preferences.Preferences method), [1] get_plates() (microscope_automation.samples.samples.PlateHolder method), [1] get_pos_from_abs_pos() (microscope_automation.samples.samples.ImagingSystem method), [1] get_pos_list() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] get_position_csv_path() (in module microscope_automation.util.get_path), [1] get_pref() (microscope_automation.settings.preferences.Preferences method), [1] get_pref_as_meta() (microscope_automation.settings.preferences.Preferences method), [1] get_pump_id() (microscope_automation.samples.samples.ImmersionDelivery method), [1] get_recovery_settings_path() (in module microscope_automation.util.get_path), [1] get_reference_object() (microscope_automation.samples.samples.ImagingSystem method), [1] get_reference_position() (microscope_automation.samples.samples.ImagingSystem method), [1] get_references_path() (in module microscope_automation.util.get_path), [1] get_safe() (microscope_automation.samples.samples.ImagingSystem method), [1] get_safe_area() (microscope_automation.hardware.hardware_components.Safety method), [1] get_safety_id() (microscope_automation.samples.samples.ImagingSystem method), [1] get_sample_type() (microscope_automation.samples.samples.ImagingSystem method), [1] get_samples() (microscope_automation.samples.samples.Well method), [1] get_single_slice() (in module microscope_automation.orchestrator.find_positions), [1] get_slides() (microscope_automation.samples.samples.PlateHolder method), [1] get_stage_id() (microscope_automation.samples.samples.ImagingSystem method), [1] get_stage_pos() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) get_tag_value() (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1] get_tile_number() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] get_tile_positions_list() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.Well method), [1] get_tile_size() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] get_tile_type() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] get_time() (microscope_automation.hardware.hardware_components.Pump method), [1] get_use_autofocus() (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] get_valid_path_from_prefs() (in module microscope_automation.util.get_path), [1] get_water() (microscope_automation.samples.samples.ImmersionDelivery method), [1] get_well() (microscope_automation.samples.samples.Plate method), [1] get_well_edge_path() (in module microscope_automation.util.get_path) get_well_object() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.Well method), [1] get_well_position_numeric() (microscope_automation.samples.samples.Well method), [1] get_well_position_string() (microscope_automation.samples.samples.Well method), [1] get_wells() (microscope_automation.samples.samples.Plate method), [1] get_wells_by_type() (microscope_automation.samples.samples.Plate method), [1] get_work_position() (microscope_automation.hardware.hardware_components.FocusDrive method), [1] get_z_position() (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) get_zero() (microscope_automation.samples.samples.ImagingSystem method), [1] GetActiveObject (class in microscope_automation.connectors.connect_zen_blue_dummy) GetByName() (microscope_automation.connectors.connect_zen_blue_dummy.Experiments method) GetMagnificationByPosition() (microscope_automation.connectors.connect_zen_blue_dummy.ObjectiveChanger method) GetNameByPosition() (microscope_automation.connectors.connect_zen_blue_dummy.ObjectiveChanger method) goto_load() (microscope_automation.hardware.hardware_components.FocusDrive method), [1] (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] goto_work() (microscope_automation.hardware.hardware_components.FocusDrive method), [1]

H

HardwareCommandNotDefinedError (class in microscope_automation.util.automation_exceptions) HardwareDoesNotExistError (class in microscope_automation.util.automation_exceptions)

HardwareError (class in microscope_automation.util.automation_exceptions) HardwareNotReadyError (class in microscope_automation.util.automation_exceptions)

I

illumination_correction() (in module microscope_automation.samples.correct_background), [1] Image (class in microscope_automation.connectors.connect_zen_blue_dummy) ImageAICS (class in microscope_automation.util.image_AICS), [1] ImageLocationPicker (class in microscope_automation.samples.interactive_location_picker_pyqtgraph), [1] ImagingSystem (class in microscope_automation.samples.samples), [1] ImmersionDelivery (class in microscope_automation.samples.samples), [1] improve_initial_edges() (microscope_automation.samples.find_cells.CellFinder method), [1] information_message() (in module microscope_automation.util.automation_messages_form_layout), [1] initial_edge_detection() (microscope_automation.samples.find_cells.CellFinder method), [1] initialize() (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.hardware.hardware_components.FocusDrive method), [1] (microscope_automation.hardware.hardware_components.MicroscopeComponent method), [1] (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] (microscope_automation.hardware.hardware_components.Stage method), [1] initialize_hardware() (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method)

initialize_microscope() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) IOError (class in microscope_automation.util.automation_exceptions) is_outlier() (microscope_automation.samples.find_cells.CellFinder static method), [1] is_safe_move_from_to() (microscope_automation.hardware.hardware_components.Safety method), [1] is_safe_position() (microscope_automation.hardware.hardware_components.Safety method), [1] is_safe_travel_path() (microscope_automation.hardware.hardware_components.Safety method), [1] is_tile_scan() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Experiment method), [1] (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1] is_z_stack() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Experiment method), [1] (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1] iter_all_strings() (microscope_automation.orchestrator.write_zen_tiles_experiment.PositionWriter method)

K

keyPressEvent() (microscope_automation.samples.interactive_location_picker_pyqtgraph.KeyPressWindow method), [1]

KeyPressWindow (class in microscope_automation.samples.interactive_location_picker_pyqtgraph), [1]

L

label_gen() (microscope_automation.orchestrator.write_zen_tiles_experiment.PositionWriter method) live_mode() (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) live_mode_start() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Camera method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] live_mode_stop() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Camera method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1]

load_image() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] (microscope_automation.util.load_image_czi.LoadImageCzi method), [1] LoadImageCzi (class in microscope_automation.util.load_image_czi), [1] LoadNotDefinedError (class in microscope_automation.util.automation_exceptions) location_to_object() (in module microscope_automation.orchestrator.find_positions), [1] log_message() (in module microscope_automation.hardware.hardware_components), [1] log_method() (in module microscope_automation.hardware.hardware_components), [1] log_warning() (in module microscope_automation.hardware.hardware_components), [1]

M

main() (in module microscope_automation.orchestrator.microscope_automation) MetaDataFile (class in microscope_automation.settings.meta_data_file), [1] MetaDataNotSavedError (class in microscope_automation.util.automation_exceptions) microscope_automation module microscope_automation() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) microscope_automation.connectors module microscope_automation.connectors.connect_slidebook module microscope_automation.connectors.connect_zen_blue module microscope_automation.connectors.connect_zen_blue_dummy module microscope_automation.hardware module microscope_automation.hardware.hardware_components module microscope_automation.hardware.hardware_control module microscope_automation.hardware.hardware_control_3i module microscope_automation.hardware.hardware_control_zeiss module microscope_automation.hardware.RS232 module microscope_automation.hardware.RS232_dummy module microscope_automation.hardware.setup_microscope module microscope_automation.imports module microscope_automation.imports.intelligent_imaging_innovations module microscope_automation.orchestrator module microscope_automation.orchestrator.find_positions module microscope_automation.orchestrator.microscope_automation module microscope_automation.orchestrator.write_zen_tiles_experiment module microscope_automation.samples module microscope_automation.samples.correct_background module microscope_automation.samples.draw_plate module microscope_automation.samples.find_cells module microscope_automation.samples.find_well_center module microscope_automation.samples.interactive_location_picker_pyqtgraph module microscope_automation.samples.positions_list module microscope_automation.samples.samples module microscope_automation.samples.segmentation_filters module microscope_automation.samples.setup_samples module microscope_automation.samples.tile_images module microscope_automation.samples.well_overview_segmentation module microscope_automation.samples.well_segmentation_refined module microscope_automation.settings module microscope_automation.settings.meta_data_file module microscope_automation.settings.preferences module microscope_automation.settings.slidebook_experiment_info module microscope_automation.settings.test_zen_experiment module microscope_automation.settings.zen_experiment_info module microscope_automation.util module microscope_automation.util.automation_exceptions module microscope_automation.util.automation_messages_form_layout module microscope_automation.util.error_handling module

microscope_automation.util.get_path module microscope_automation.util.image_AICS module microscope_automation.util.load_image_czi module microscope_automation.util.software_state module microscope_is_ready() (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) (microscope_automation.samples.samples.ImagingSystem method), [1] MicroscopeAutomation (class in microscope_automation.orchestrator.microscope_automation) MicroscopeComponent (class in microscope_automation.hardware.hardware_components), [1] MicroscopeStatus (class in microscope_automation.connectors.connect_zen_blue_dummy) module microscope_automation microscope_automation.connectors microscope_automation.connectors.connect_slidebook microscope_automation.connectors.connect_zen_blue microscope_automation.connectors.connect_zen_blue_dummy microscope_automation.hardware microscope_automation.hardware.hardware_components microscope_automation.hardware.hardware_control microscope_automation.hardware.hardware_control_3i microscope_automation.hardware.hardware_control_zeiss microscope_automation.hardware.RS232 microscope_automation.hardware.RS232_dummy microscope_automation.hardware.setup_microscope microscope_automation.imports microscope_automation.imports.intelligent_imaging_innovations microscope_automation.orchestrator microscope_automation.orchestrator.find_positions microscope_automation.orchestrator.microscope_automation microscope_automation.orchestrator.write_zen_tiles_experiment microscope_automation.samples microscope_automation.samples.correct_background microscope_automation.samples.draw_plate microscope_automation.samples.find_cells microscope_automation.samples.find_well_center microscope_automation.samples.interactive_location_picker_pyqtgraph microscope_automation.samples.positions_list microscope_automation.samples.samples microscope_automation.samples.segmentation_filters microscope_automation.samples.setup_samples microscope_automation.samples.tile_images microscope_automation.samples.well_overview_segmentation microscope_automation.samples.well_segmentation_refined microscope_automation.settings microscope_automation.settings.meta_data_file microscope_automation.settings.preferences microscope_automation.settings.slidebook_experiment_info microscope_automation.settings.test_zen_experiment microscope_automation.settings.zen_experiment_info microscope_automation.util microscope_automation.util.automation_exceptions microscope_automation.util.automation_messages_form_layout microscope_automation.util.error_handling microscope_automation.util.get_path microscope_automation.util.image_AICS microscope_automation.util.load_image_czi microscope_automation.util.software_state move_delta_xyz() (microscope_automation.samples.samples.ImagingSystem method), [1] move_focus_to() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) move_focus_to_load() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) move_focus_to_work() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) move_stage_to() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) move_to_abs_pos() (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) move_to_abs_position() (microscope_automation.samples.samples.ImagingSystem method), [1] move_to_position() (microscope_automation.hardware.hardware_components.FocusDrive method), [1] (microscope_automation.hardware.hardware_components.Stage method), [1] move_to_r_phi() (microscope_automation.samples.samples.ImagingSystem method), [1] move_to_safe() (microscope_automation.samples.samples.ImagingSystem method), [1] move_to_well() (microscope_automation.samples.samples.Plate method), [1] move_to_xyz() (microscope_automation.samples.samples.ImagingSystem method), [1] move_to_zero() (microscope_automation.samples.samples.ImagingSystem method), [1] MoveTo() (microscope_automation.connectors.connect_zen_blue_dummy.Focus method)

N

not_implemented() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1]

number_cells() (microscope_automation.samples.samples.Colony method)

O

objective_name() (microscope_automation.connectors.connect_zen_blue_dummy.MicroscopeStatus property) objective_position() (microscope_automation.connectors.connect_zen_blue_dummy.MicroscopeStatus property) ObjectiveChanger (class in microscope_automation.connectors.connect_zen_blue_dummy) (class in microscope_automation.hardware.hardware_components), [1]

ObjectiveNotDefinedError (class in microscope_automation.util.automation_exceptions) operate_message() (in module microscope_automation.util.automation_messages_form_layout), [1]

P

parse_file_template() (microscope_automation.util.image_AICS.ImageAICS method), [1] Pause() (microscope_automation.connectors.connect_zen_blue_dummy.Application method) Plate (class in microscope_automation.samples.samples), [1] PlateHolder (class in microscope_automation.samples.samples), [1] plot_points() (microscope_automation.samples.interactive_location_picker_pyqtgraph.ImageLocationPicker method), [1] point_locations() (microscope_automation.samples.well_overview_segmentation.WellSegmentation property) (microscope_automation.samples.well_segmentation_refined.WellSegmentation property) PositionWriter (class in microscope_automation.orchestrator.write_zen_tiles_experiment), [1]

post_experiment() (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] Preferences (class in microscope_automation.settings.preferences), [1] preprocessing_image() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) print_prefs() (microscope_automation.settings.preferences.Preferences method) process_colonies() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) prune_object_dict() (microscope_automation.util.software_state.State method), [1] pull_down_select_dialog() (in module microscope_automation.util.automation_messages_form_layout), [1] Pump (class in microscope_automation.hardware.hardware_components), [1]

R

read_barcode() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) (microscope_automation.samples.samples.Barcode method), [1] read_barcode_data_acquisition() (microscope_automation.samples.samples.Barcode method), [1] read_first_barcode_from_plateholderobject() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) read_string() (in module microscope_automation.util.automation_messages_form_layout), [1] recall_focus() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] RecallFocus() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) recover_focus() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) recover_hardware() (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) recover_objects() (microscope_automation.util.software_state.State method), [1] recover_previous_settings() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) reference_position() (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method)

rehydrate_removed_references() (microscope_automation.util.software_state.State method), [1] remove_all() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) remove_images() (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] RemoveAll() (microscope_automation.connectors.connect_zen_blue_dummy.Documents method) reset_counter() (microscope_automation.samples.samples.ImmersionDelivery method), [1] rotate_pos_list() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] round_locations() (microscope_automation.samples.interactive_location_picker_pyqtgraph.ImageLocationPicker method) run_macro() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) RunMacro() (microscope_automation.connectors.connect_zen_blue_dummy.Application method) RunMacro_2() (microscope_automation.connectors.connect_zen_blue_dummy.Application method)

S

Safety (class in microscope_automation.hardware.hardware_components), [1] Sample (class in microscope_automation.samples.samples), [1] save() (microscope_automation.util.software_state.DiagnosticPickler method) Save_2() (microscope_automation.connectors.connect_zen_blue_dummy.Image method) save_as_tiff() (microscope_automation.util.image_AICS.ImageAICS method), [1] save_image() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) (microscope_automation.samples.samples.PlateHolder method), [1] save_segmented_image() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) save_state() (microscope_automation.util.software_state.State method), [1] save_state_and_exit() (microscope_automation.util.software_state.State method), [1] scan_all_objects() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) scan_plate() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) scan_samples() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) scan_single_ROI() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) scan_wells_zero() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) segment() (in module microscope_automation.samples.find_cells), [1] segment_and_find_positions() (microscope_automation.samples.well_overview_segmentation.WellSegmentation method) (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) segment_colonies() (microscope_automation.samples.well_segmentation_refined.WellSegmentation method) segment_dir() (in module microscope_automation.samples.find_cells), [1] segment_image() (microscope_automation.samples.find_cells.CellFinder method), [1] segment_wells() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) segmentation() (in module microscope_automation.orchestrator.find_positions), [1] select_message() (in module microscope_automation.util.automation_messages_form_layout), [1] set_assigned_diameter() (microscope_automation.samples.samples.Well method), [1] set_autofocus_not_ready() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) set_autofocus_ready() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) set_barcode() (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.Plate method), [1] set_calibration() (microscope_automation.samples.find_cells.CellFinder method) set_cell_line() (microscope_automation.samples.samples.Cell method), [1] (microscope_automation.samples.samples.Colony method), [1] set_clone() (microscope_automation.samples.samples.Cell method), [1] (microscope_automation.samples.samples.Colony method), [1] set_component() (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.hardware.hardware_components.MicroscopeComponent method), [1] set_connection() (microscope_automation.hardware.hardware_components.Pump method), [1] set_container() (microscope_automation.samples.samples.ImagingSystem method), [1] set_correction() (microscope_automation.samples.samples.ImagingSystem method), [1] set_counter_stop_value() (microscope_automation.samples.samples.ImmersionDelivery method), [1] set_diameter() (microscope_automation.samples.samples.Well method), [1] set_error_blocking() (in module microscope_automation.util.automation_exceptions), [1] set_experiment() (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) set_field_rotation() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] set_flip() (microscope_automation.samples.samples.ImagingSystem method), [1] set_focus_load_position() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) set_focus_reference_obj_id() (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.util.automation_exceptions.AutofocusError method), [1] set_focus_work_position() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) set_hardware() (microscope_automation.samples.samples.ImagingSystem method), [1] set_id() (microscope_automation.hardware.hardware_components.MicroscopeComponent method), [1] set_image() (microscope_automation.samples.samples.ImagingSystem method), [1] set_init_experiment() (microscope_automation.hardware.hardware_components.MicroscopeComponent method), [1] set_interactive_positions() (microscope_automation.samples.samples.Cell method), [1] (microscope_automation.samples.samples.Colony method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.Well method), [1] set_last_known_focus_position() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) set_measured_diameter() (microscope_automation.samples.samples.Well method), [1] set_microscope() (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) set_name() (microscope_automation.samples.samples.ImagingSystem method), [1] set_number_positions() (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] set_objective_is_ready() (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) set_objective_offset() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) set_plate_holder_pos_to_zero() (microscope_automation.samples.samples.PlateHolder method), [1] set_pref() (microscope_automation.settings.preferences.Preferences method) set_pump_id() (microscope_automation.samples.samples.ImmersionDelivery method), [1]

set_reference_object() (microscope_automation.samples.samples.ImagingSystem method), [1] set_reference_position() (microscope_automation.samples.samples.ImagingSystem method), [1] set_safe() (microscope_automation.samples.samples.ImagingSystem method), [1] set_stage_position() (microscope_automation.samples.samples.PlateHolder method), [1] set_tile_number() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] set_tile_size() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] set_tile_type() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] set_time() (microscope_automation.hardware.hardware_components.Pump method), [1] set_up_koehler() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) set_up_objectives() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) set_up_settings_folders() (in module microscope_automation.util.get_path) set_up_subfolders() (in module microscope_automation.util.get_path), [1] set_use_autofocus() (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] set_well_position_numeric() (microscope_automation.samples.samples.Well method), [1] set_well_position_string() (microscope_automation.samples.samples.Well method), [1] set_zero() (microscope_automation.samples.samples.ImagingSystem method), [1] setup_autofocus() (in module microscope_automation.hardware.setup_microscope), [1] setup_cameras() (in module microscope_automation.hardware.setup_microscope), [1] setup_focus_drive() (in module microscope_automation.hardware.setup_microscope), [1] setup_immersion_system() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) setup_logger() (in module microscope_automation.util.error_handling), [1] setup_message() (in module microscope_automation.util.automation_messages_form_layout), [1] setup_microscope() (in module microscope_automation.hardware.setup_microscope), [1] setup_microscope_for_initialization() (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) setup_obj_changer() (in module microscope_automation.hardware.setup_microscope), [1] setup_plate() (in module microscope_automation.samples.setup_samples), [1] setup_pump() (in module microscope_automation.hardware.setup_microscope), [1] setup_safe_areas() (in module microscope_automation.hardware.setup_microscope), [1] setup_slide() (in module microscope_automation.samples.setup_samples), [1] setup_stages() (in module microscope_automation.hardware.setup_microscope), [1] show() (microscope_automation.samples.positions_list.CreateTilePositions method), [1] (microscope_automation.samples.samples.Plate method), [1] (microscope_automation.util.image_AICS.ImageAICS method), [1] show_debug_image() (in module microscope_automation.samples.find_well_center), [1] show_debug_summary() (in module microscope_automation.samples.find_well_center), [1] show_hist() (in module microscope_automation.samples.find_well_center), [1] show_image() (in module microscope_automation.connectors.connect_slidebook) (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) show_safe_areas() (microscope_automation.hardware.hardware_components.Safety method), [1] sigKeyPress (microscope_automation.samples.interactive_location_picker_pyqtgraph.KeyPressWindow attribute) Slide (class in microscope_automation.samples.samples), [1] SlidebookExperiment (class in microscope_automation.settings.slidebook_experiment_info), [1] snap_image() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Camera method), [1] SpinningDisk3i (class in microscope_automation.hardware.hardware_control_3i) SpinningDiskZeiss (class in microscope_automation.hardware.hardware_control_zeiss) Stage (class in microscope_automation.connectors.connect_zen_blue_dummy) (class in microscope_automation.hardware.hardware_components), [1] start_pump() (microscope_automation.hardware.RS232.Braintree method), [1] (microscope_automation.hardware.RS232_dummy.Braintree method) StartLive() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) StartLive_2() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) State (class in microscope_automation.util.software_state), [1] stop() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) stop_microscope() (in module microscope_automation.hardware.hardware_control_3i.SpinningDisk3i) (in module microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss) (microscope_automation.hardware.hardware_control_3i.SpinningDisk3i method) (microscope_automation.hardware.hardware_control_zeiss.SpinningDiskZeiss method) stop_pump() (microscope_automation.hardware.RS232.Braintree method), [1] (microscope_automation.hardware.RS232_dummy.Braintree method) stop_script() (in module microscope_automation.util.automation_messages_form_layout), [1] StopCollectingError (class in microscope_automation.util.automation_exceptions) StopLive() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) StopLive_2() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) store_focus() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.AutoFocus method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] (microscope_automation.samples.samples.PlateHolder method), [1] StoreFocus() (microscope_automation.connectors.connect_zen_blue_dummy.Acquisition method) switch_objective() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method)

T

TAG_PATH_TILE_CENTER_XY (microscope_automation.settings.zen_experiment_info.ZenExperiment attribute) TAG_PATH_TILE_CENTER_Z (microscope_automation.settings.zen_experiment_info.ZenExperiment attribute) test_connect_zen_blue() (in module microscope_automation.connectors.connect_zen_blue), [1] test_definite_focus() (in module microscope_automation.connectors.connect_zen_blue), [1] test_FocusSetup() (in module microscope_automation.settings.test_zen_experiment) test_ImageLocationPicker() (in module microscope_automation.samples.interactive_location_picker_pyqtgraph) test_offline() (in module microscope_automation.samples.interactive_location_picker_pyqtgraph) test_online() (in module microscope_automation.samples.interactive_location_picker_pyqtgraph)

tile_images() (in module microscope_automation.samples.tile_images), [1] (microscope_automation.samples.samples.ImagingSystem method), [1] trigger_pump() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Pump method), [1] (microscope_automation.hardware.hardware_control.BaseMicroscope method), [1] (microscope_automation.samples.samples.ImmersionDelivery method), [1] twofold_distance_map() (microscope_automation.samples.find_cells.CellFinder method), [1]

U

update_correction() (microscope_automation.samples.samples.ImagingSystem method), [1] update_flip() (microscope_automation.samples.samples.ImagingSystem method), [1] update_objective_offset() (microscope_automation.hardware.hardware_components.ObjectiveChanger method), [1] update_plate_z_zero() (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method) update_tag_value() (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1] update_tile_positions() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Experiment method), [1] (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1]

update_zero() (microscope_automation.samples.samples.Colony method), [1] (microscope_automation.samples.samples.ImagingSystem method), [1]

V

validate() (microscope_automation.samples.find_cells.CellFinder method), [1] validate_experiment() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Experiment method), [1] (microscope_automation.orchestrator.microscope_automation.MicroscopeAutomation method)

value_calibration_form() (in module microscope_automation.util.automation_messages_form_layout), [1]

W

wait_for_experiment() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) wait_for_objective() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) wait_message() (in module microscope_automation.util.automation_messages_form_layout), [1] Well (class in microscope_automation.samples.samples), [1]

WellSegmentation (class in microscope_automation.samples.well_overview_segmentation) (class in microscope_automation.samples.well_segmentation_refined) WorkNotDefinedError (class in microscope_automation.util.automation_exceptions) write() (microscope_automation.orchestrator.write_zen_tiles_experiment.PositionWriter method), [1] write_csv() (microscope_automation.settings.meta_data_file.MetaDataFile method), [1] write_meta() (microscope_automation.settings.meta_data_file.MetaDataFile method), [1]

X

xPos() (microscope_automation.connectors.connect_zen_blue_dummy.MicroscopeStatus property)

Y

yPos() (microscope_automation.connectors.connect_zen_blue_dummy.MicroscopeStatus property)

Z

z_down_relative() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) z_relative_move() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) z_stack_range() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) (microscope_automation.hardware.hardware_components.Experiment method), [1] (microscope_automation.settings.zen_experiment_info.ZenExperiment method), [1]

z_up_relative() (in module microscope_automation.connectors.connect_zen_blue.ConnectMicroscope) (microscope_automation.connectors.connect_slidebook.ConnectMicroscope method), [1] (microscope_automation.connectors.connect_zen_blue.ConnectMicroscope method) ZenExperiment (class in microscope_automation.settings.zen_experiment_info), [1] zPos() (microscope_automation.connectors.connect_zen_blue_dummy.MicroscopeStatus property)