Index

Symbols

--animal sl-experiment command line option sl-lick-train command line option sl-run-train command line option --animal_weight sl-experiment command line option sl-lick-train command line option sl-run-train command line option --duration_step sl-run-train command line option --errors sl-devices command line option --experiment sl-experiment command line option --increase_threshold sl-run-train command line option --initial_duration sl-run-train command line option --initial_speed sl-run-train command line option --maximum_delay sl-lick-train command line option --maximum_time sl-lick-train command line option sl-run-train command line option --maximum_volume sl-lick-train command line option sl-run-train command line option --minimum_delay sl-lick-train command line option --path sl-experiment command line option --project sl-experiment command line option, [1] sl-lick-train command line option sl-maintain-vr command line option sl-run-train command line option --remove_telomere sl-experiment command line option --remove_ubiquitin sl-experiment command line option --session-path sl-experiment command line option --speed_step sl-run-train command line option --string sl-crc command line option --user sl-experiment command line option sl-lick-train command line option sl-run-train command line option

-a sl-experiment command line option sl-lick-train command line option sl-run-train command line option -ds sl-run-train command line option -e sl-devices command line option sl-experiment command line option -i sl-crc command line option -id sl-run-train command line option -is sl-run-train command line option -it sl-run-train command line option -max sl-lick-train command line option -min sl-lick-train command line option -p sl-experiment command line option, [1], [2] sl-lick-train command line option sl-maintain-vr command line option sl-run-train command line option -s sl-experiment command line option -ss sl-run-train command line option -t sl-experiment command line option sl-lick-train command line option sl-run-train command line option -u sl-experiment command line option, [1] sl-lick-train command line option sl-run-train command line option -v sl-lick-train command line option sl-run-train command line option -w sl-experiment command line option sl-lick-train command line option sl-run-train command line option

_

__del__() (sl_experiment.experiment._KeyboardListener method) (sl_experiment.google_sheet_tools.SurgerySheet method) (sl_experiment.google_sheet_tools.WaterSheetData method) (sl_experiment.module_interfaces.EncoderInterface method) (sl_experiment.module_interfaces.LickInterface method) (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method) (sl_experiment.visualizers.BehaviorVisualizer method) (sl_experiment.zaber_bindings.ZaberAxis method) (sl_experiment.zaber_bindings.ZaberConnection method) __post_init__() (sl_experiment.data_classes.SessionData method) __repr__() (sl_experiment.zaber_bindings.ZaberAxis method) (sl_experiment.zaber_bindings.ZaberConnection method) (sl_experiment.zaber_bindings.ZaberDevice method) _actor (sl_experiment.binding_classes.MicroControllerInterfaces attribute) _animals (sl_experiment.google_sheet_tools.SurgerySheet attribute) (sl_experiment.google_sheet_tools.WaterSheetData attribute) _attempt_connection() (in module sl_experiment.zaber_bindings) _axis (sl_experiment.zaber_bindings.ZaberDevice attribute) _BehaviorTraining (class in sl_experiment.experiment) _body_cameras_started (sl_experiment.binding_classes.VideoSystems attribute) _calculate_file_checksum() (in module sl_experiment.packaging_tools) _calculator (sl_experiment.zaber_bindings.CRCCalculator attribute) _calibration_cov (sl_experiment.module_interfaces.ValveInterface attribute) _cameras (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._MesoscopeExperiment attribute) _capacity_in_newtons_cm (sl_experiment.module_interfaces.TorqueInterface attribute) _change_vr_state() (sl_experiment.experiment._MesoscopeExperiment method) _check_stack_size() (in module sl_experiment.data_preprocessing) _cm_per_pulse (sl_experiment.module_interfaces.EncoderInterface attribute) _communication (sl_experiment.module_interfaces.EncoderInterface attribute) (sl_experiment.module_interfaces.LickInterface attribute) _connection (sl_experiment.zaber_bindings.ZaberConnection attribute) _convert_date_time_to_timestamp() (in module sl_experiment.google_sheet_tools) _convert_index_to_column_letter() (in module sl_experiment.google_sheet_tools) _crc_calculator (sl_experiment.zaber_bindings.ZaberDevice attribute) _currently_pressed (sl_experiment.experiment._KeyboardListener attribute) _cycle_timer (sl_experiment.module_interfaces.ValveInterface attribute) _data_array (sl_experiment.experiment._KeyboardListener attribute) _debug (sl_experiment.module_interfaces.BreakInterface attribute) (sl_experiment.module_interfaces.EncoderInterface attribute) (sl_experiment.module_interfaces.LickInterface attribute) (sl_experiment.module_interfaces.ScreenInterface attribute) (sl_experiment.module_interfaces.TorqueInterface attribute) (sl_experiment.module_interfaces.TTLInterface attribute) (sl_experiment.module_interfaces.ValveInterface attribute) _delete_directory() (in module sl_experiment.data_preprocessing) _device (sl_experiment.zaber_bindings.ZaberDevice attribute) _devices (sl_experiment.zaber_bindings.ZaberConnection attribute) _distance_tracker (sl_experiment.module_interfaces.EncoderInterface attribute) (sl_experiment.visualizers.BehaviorVisualizer attribute) _duration_threshold_line (sl_experiment.visualizers.BehaviorVisualizer attribute) _duration_threshold_text (sl_experiment.visualizers.BehaviorVisualizer attribute) _encoder (sl_experiment.binding_classes.MicroControllerInterfaces attribute) _ensure_call_padding() (sl_experiment.zaber_bindings.ZaberAxis method) _experiment_configuration (sl_experiment.experiment._MesoscopeExperiment attribute) _experiment_state (sl_experiment.experiment._MesoscopeExperiment attribute) _extract_coordinate_value() (in module sl_experiment.google_sheet_tools) _face_camera_started (sl_experiment.binding_classes.VideoSystems attribute) _figure (sl_experiment.visualizers.BehaviorVisualizer attribute) _find_date_row() (sl_experiment.google_sheet_tools.WaterSheetData method) _force_per_adc_unit (sl_experiment.module_interfaces.TorqueInterface attribute) _force_per_pwm (sl_experiment.module_interfaces.BreakInterface attribute) _format_device_info() (in module sl_experiment.zaber_bindings) _generate_ops() (in module sl_experiment.data_preprocessing) _get_column_id() (sl_experiment.google_sheet_tools.SurgerySheet method) _get_cue_sequence() (sl_experiment.experiment._MesoscopeExperiment method) _get_stack_number() (in module sl_experiment.data_preprocessing) _headbar (sl_experiment.binding_classes.HeadBar attribute) _headbar_pitch (sl_experiment.binding_classes.HeadBar attribute) _headbar_roll (sl_experiment.binding_classes.HeadBar attribute) _headbar_z (sl_experiment.binding_classes.HeadBar attribute) _headers (sl_experiment.google_sheet_tools.SurgerySheet attribute) (sl_experiment.google_sheet_tools.WaterSheetData attribute) _id (sl_experiment.zaber_bindings.ZaberDevice attribute) _initially_on (sl_experiment.module_interfaces.ScreenInterface attribute) _is_connected (sl_experiment.zaber_bindings.ZaberConnection attribute) _keyboard_process (sl_experiment.experiment._KeyboardListener attribute) _KeyboardListener (class in sl_experiment.experiment) _label (sl_experiment.zaber_bindings.ZaberDevice attribute) _left_camera (sl_experiment.binding_classes.VideoSystems attribute) _lick_axis (sl_experiment.visualizers.BehaviorVisualizer attribute) _lick_data (sl_experiment.visualizers.BehaviorVisualizer attribute) _lick_line (sl_experiment.visualizers.BehaviorVisualizer attribute) _lick_threshold (sl_experiment.module_interfaces.LickInterface attribute) _lick_tracker (sl_experiment.module_interfaces.LickInterface attribute) (sl_experiment.visualizers.BehaviorVisualizer attribute) _lick_training (sl_experiment.experiment._BehaviorTraining attribute) _lickport (sl_experiment.binding_classes.LickPort attribute) _lickport_x (sl_experiment.binding_classes.LickPort attribute) _lickport_y (sl_experiment.binding_classes.LickPort attribute) _lickport_z (sl_experiment.binding_classes.LickPort attribute) _linear (sl_experiment.zaber_bindings.ZaberAxis attribute) _logger (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._MesoscopeExperiment attribute) _max_limit (sl_experiment.zaber_bindings.ZaberAxis attribute) _maximum_break_strength (sl_experiment.module_interfaces.BreakInterface attribute) _MesoscopeExperiment (class in sl_experiment.experiment) _microcontrollers (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._MesoscopeExperiment attribute)

_min_limit (sl_experiment.zaber_bindings.ZaberAxis attribute) _minimum_break_strength (sl_experiment.module_interfaces.BreakInterface attribute) _motion_topic (sl_experiment.module_interfaces.EncoderInterface attribute) _motor (sl_experiment.zaber_bindings.ZaberAxis attribute) _mount_position (sl_experiment.zaber_bindings.ZaberAxis attribute) _name (sl_experiment.zaber_bindings.ZaberAxis attribute) (sl_experiment.zaber_bindings.ZaberDevice attribute) _newton_per_gram_centimeter (sl_experiment.module_interfaces.BreakInterface attribute) (sl_experiment.module_interfaces.TorqueInterface attribute) _nonlinearity_exponent (sl_experiment.module_interfaces.ValveInterface attribute) _object_diameter (sl_experiment.module_interfaces.EncoderInterface attribute) _on_press() (sl_experiment.experiment._KeyboardListener method) _on_release() (sl_experiment.experiment._KeyboardListener method) _once (sl_experiment.visualizers.BehaviorVisualizer attribute) _park_position (sl_experiment.zaber_bindings.ZaberAxis attribute) _parse_stereotactic_coordinates() (in module sl_experiment.google_sheet_tools) _plt_line_styles() (in module sl_experiment.visualizers) _plt_palette() (in module sl_experiment.visualizers) _port (sl_experiment.zaber_bindings.ZaberConnection attribute) _ppr (sl_experiment.module_interfaces.EncoderInterface attribute) _preprocess_google_sheet_data() (in module sl_experiment.data_preprocessing) _preprocess_log_directory() (in module sl_experiment.data_preprocessing) _preprocess_mesoscope_directory() (in module sl_experiment.data_preprocessing) _preprocess_video_names() (in module sl_experiment.data_preprocessing) _previous_distance (sl_experiment.visualizers.BehaviorVisualizer attribute) _previous_lick_count (sl_experiment.visualizers.BehaviorVisualizer attribute) _previous_positions (sl_experiment.binding_classes.HeadBar attribute) (sl_experiment.binding_classes.LickPort attribute) _previous_state (sl_experiment.module_interfaces.ValveInterface attribute) _previous_valve_count (sl_experiment.visualizers.BehaviorVisualizer attribute) _previous_volume (sl_experiment.binding_classes.MicroControllerInterfaces attribute) _process_invariant_metadata() (in module sl_experiment.data_preprocessing) _process_stack() (in module sl_experiment.data_preprocessing) _project_name (sl_experiment.google_sheet_tools.SurgerySheet attribute) _pull_mesoscope_data() (in module sl_experiment.data_preprocessing) _pulse_tracker (sl_experiment.module_interfaces.TTLInterface attribute) _push_data() (in module sl_experiment.data_preprocessing) _replace_empty_values() (in module sl_experiment.google_sheet_tools) _report_pulses (sl_experiment.module_interfaces.TTLInterface attribute) _reset_pad_timer() (sl_experiment.zaber_bindings.ZaberAxis method) _resolve_telomere_markers() (in module sl_experiment.data_preprocessing) _resolve_ubiquitin_markers() (in module sl_experiment.data_preprocessing) _reward_topic (sl_experiment.module_interfaces.ValveInterface attribute) _right_camera (sl_experiment.binding_classes.VideoSystems attribute) _run_keyboard_listener() (sl_experiment.experiment._KeyboardListener method) _running_speed (sl_experiment.visualizers.BehaviorVisualizer attribute) _sample_data() (sl_experiment.visualizers.BehaviorVisualizer method) _scale_coefficient (sl_experiment.module_interfaces.ValveInterface attribute) _scan_active_ports() (in module sl_experiment.zaber_bindings) _screen_state (sl_experiment.binding_classes.MicroControllerInterfaces attribute) _sensor (sl_experiment.binding_classes.MicroControllerInterfaces attribute) _sensor_topic (sl_experiment.module_interfaces.LickInterface attribute) _service (sl_experiment.google_sheet_tools.SurgerySheet attribute) (sl_experiment.google_sheet_tools.WaterSheetData attribute) _session_data (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._MesoscopeExperiment attribute) _sheet_id (sl_experiment.google_sheet_tools.SurgerySheet attribute) (sl_experiment.google_sheet_tools.WaterSheetData attribute) _sheet_id_numeric (sl_experiment.google_sheet_tools.WaterSheetData attribute) _shutdown_flag (sl_experiment.zaber_bindings.ZaberAxis attribute) (sl_experiment.zaber_bindings.ZaberDevice attribute) _source_id (sl_experiment.experiment._MesoscopeExperiment attribute) _speed_axis (sl_experiment.visualizers.BehaviorVisualizer attribute) _speed_data (sl_experiment.visualizers.BehaviorVisualizer attribute) _speed_line (sl_experiment.visualizers.BehaviorVisualizer attribute) _speed_threshold_line (sl_experiment.visualizers.BehaviorVisualizer attribute) _speed_threshold_text (sl_experiment.visualizers.BehaviorVisualizer attribute) _speed_timer (sl_experiment.visualizers.BehaviorVisualizer attribute) _start_mesoscope() (sl_experiment.experiment._MesoscopeExperiment method) _started (sl_experiment.binding_classes.MicroControllerInterfaces attribute) (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._KeyboardListener attribute) (sl_experiment.experiment._MesoscopeExperiment attribute) _state_map (sl_experiment.experiment._MesoscopeExperiment attribute) _time_step (sl_experiment.visualizers.BehaviorVisualizer attribute) _time_window (sl_experiment.visualizers.BehaviorVisualizer attribute) _timer (sl_experiment.zaber_bindings.ZaberAxis attribute) _timestamp_timer (sl_experiment.experiment._MesoscopeExperiment attribute) _timestamps (sl_experiment.visualizers.BehaviorVisualizer attribute) _to_path() (sl_experiment.data_classes.ProjectConfiguration method) _torque_per_adc_unit (sl_experiment.module_interfaces.TorqueInterface attribute) _torque_per_pwm (sl_experiment.module_interfaces.BreakInterface attribute) _transfer_file() (in module sl_experiment.transfer_tools) _units (sl_experiment.zaber_bindings.ZaberAxis attribute) _unity_unit_per_pulse (sl_experiment.module_interfaces.EncoderInterface attribute) _update_timer (sl_experiment.visualizers.BehaviorVisualizer attribute) _valve_axis (sl_experiment.visualizers.BehaviorVisualizer attribute) _valve_data (sl_experiment.visualizers.BehaviorVisualizer attribute) _valve_line (sl_experiment.visualizers.BehaviorVisualizer attribute) _valve_position (sl_experiment.zaber_bindings.ZaberAxis attribute) _valve_tracker (sl_experiment.module_interfaces.ValveInterface attribute) (sl_experiment.visualizers.BehaviorVisualizer attribute) _verify_data() (sl_experiment.data_classes.ProjectConfiguration method) _volt_per_adc_unit (sl_experiment.module_interfaces.LickInterface attribute) _vr_state (sl_experiment.experiment._MesoscopeExperiment attribute) _write_value() (sl_experiment.google_sheet_tools.WaterSheetData method) _ZaberSettings (class in sl_experiment.zaber_bindings) _ZaberUnits (class in sl_experiment.zaber_bindings)

A

acceleration_units (sl_experiment.zaber_bindings._ZaberUnits property) actor_port (sl_experiment.data_classes.ProjectConfiguration attribute) animal_id (sl_experiment.data_classes.SessionData attribute) animals (sl_experiment.google_sheet_tools.SurgerySheet property) (sl_experiment.google_sheet_tools.WaterSheetData property) axis (sl_experiment.zaber_bindings.ZaberDevice property) axis_acceleration (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_calibration_position (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_information (sl_experiment.zaber_bindings.ZaberDevice property)

axis_inversion (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_linear_flag (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_maximum_limit (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_maximum_speed (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_minimum_limit (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_mount_position (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_park_position (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_position (sl_experiment.zaber_bindings._ZaberSettings attribute) axis_temperature (sl_experiment.zaber_bindings._ZaberSettings attribute)

B

BehaviorVisualizer (class in sl_experiment.visualizers) BreakInterface (class in sl_experiment.module_interfaces)

buprenorphine_code (sl_experiment.data_classes.DrugData attribute) buprenorphine_volume_ml (sl_experiment.data_classes.DrugData attribute) bytes_checksum() (sl_experiment.zaber_bindings.CRCCalculator method)

C

cage (sl_experiment.data_classes.SubjectData attribute) calculate_directory_checksum() (in module sl_experiment.packaging_tools) calibrate() (sl_experiment.module_interfaces.ValveInterface method) calibrate_position() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) calibrate_valve() (sl_experiment.binding_classes.MicroControllerInterfaces method) calibration_covariance (sl_experiment.module_interfaces.ValveInterface property) camera_frames_path (sl_experiment.data_classes.SessionData property) change_experiment_state() (sl_experiment.experiment._MesoscopeExperiment method) check_state() (sl_experiment.module_interfaces.EncoderInterface method) (sl_experiment.module_interfaces.LickInterface method) (sl_experiment.module_interfaces.TorqueInterface method) (sl_experiment.module_interfaces.TTLInterface method)

close() (sl_experiment.visualizers.BehaviorVisualizer method) close_valve() (sl_experiment.binding_classes.MicroControllerInterfaces method) cm_per_pulse (sl_experiment.data_classes.HardwareConfiguration attribute) (sl_experiment.module_interfaces.EncoderInterface property) connect() (sl_experiment.zaber_bindings.ZaberConnection method) CRCCalculator (class in sl_experiment.zaber_bindings) credentials_path (sl_experiment.data_classes.ProjectConfiguration attribute) (sl_experiment.data_classes.SessionData attribute) cue_map (sl_experiment.data_classes.ExperimentConfiguration attribute) (sl_experiment.data_classes.HardwareConfiguration attribute)

D

date_of_birth_us (sl_experiment.data_classes.SubjectData attribute) deliver_reward() (sl_experiment.binding_classes.MicroControllerInterfaces method) (sl_experiment.experiment._BehaviorTraining method) delivered_volume (sl_experiment.module_interfaces.ValveInterface property) descriptor (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._MesoscopeExperiment attribute) device_code (sl_experiment.zaber_bindings._ZaberSettings attribute) device_count (sl_experiment.zaber_bindings.ZaberConnection property) device_information (sl_experiment.zaber_bindings.ZaberConnection property) device_shutdown_flag (sl_experiment.zaber_bindings._ZaberSettings attribute) device_temperature (sl_experiment.zaber_bindings._ZaberSettings attribute) dexamethasone_code (sl_experiment.data_classes.DrugData attribute) dexamethasone_volume_ml (sl_experiment.data_classes.DrugData attribute) disable_break() (sl_experiment.binding_classes.MicroControllerInterfaces method) disable_encoder_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method) disable_lick_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method)

disable_mesoscope_frame_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method) disable_torque_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method) disable_vr_screens() (sl_experiment.binding_classes.MicroControllerInterfaces method) disconnect() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) (sl_experiment.zaber_bindings.ZaberConnection method) discover_zaber_devices() (in module sl_experiment.zaber_bindings) dispensed_water_volume_ml (sl_experiment.data_classes.LickTrainingDescriptor attribute) (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.RunTrainingDescriptor attribute) displacement_units (sl_experiment.zaber_bindings._ZaberUnits property) distance_tracker (sl_experiment.binding_classes.MicroControllerInterfaces property) (sl_experiment.module_interfaces.EncoderInterface property) DrugData (class in sl_experiment.data_classes) drugs (sl_experiment.data_classes.SurgeryData attribute) duration_modifier (sl_experiment.experiment._KeyboardListener property)

E

ear_punch (sl_experiment.data_classes.SubjectData attribute) enable_break() (sl_experiment.binding_classes.MicroControllerInterfaces method) enable_encoder_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method) enable_lick_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method) enable_mesoscope_frame_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method) enable_torque_monitoring() (sl_experiment.binding_classes.MicroControllerInterfaces method) enable_vr_screens() (sl_experiment.binding_classes.MicroControllerInterfaces method) encoder_port (sl_experiment.data_classes.ProjectConfiguration attribute) EncoderInterface (class in sl_experiment.module_interfaces) exit_signal (sl_experiment.experiment._KeyboardListener property) experiment_configuration_path (sl_experiment.data_classes.SessionData property) experiment_name (sl_experiment.data_classes.SessionData attribute) experiment_state_code (sl_experiment.data_classes.ExperimentState attribute)

experiment_states (sl_experiment.data_classes.ExperimentConfiguration attribute) ExperimentConfiguration (class in sl_experiment.data_classes) experimenter (sl_experiment.data_classes.LickTrainingDescriptor attribute) (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.RunTrainingDescriptor attribute) experimenter_given_water_volume_ml (sl_experiment.data_classes.LickTrainingDescriptor attribute) (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.RunTrainingDescriptor attribute) experimenter_notes (sl_experiment.data_classes.LickTrainingDescriptor attribute) (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.RunTrainingDescriptor attribute) ExperimentState (class in sl_experiment.data_classes) extract_animal_data() (sl_experiment.google_sheet_tools.SurgerySheet method)

F

face_camera_index (sl_experiment.data_classes.ProjectConfiguration attribute) face_camera_log_path (sl_experiment.binding_classes.VideoSystems property) final_run_duration_threshold_s (sl_experiment.data_classes.RunTrainingDescriptor attribute)

final_run_speed_threshold_cm_s (sl_experiment.data_classes.RunTrainingDescriptor attribute) force_per_adc_unit (sl_experiment.module_interfaces.TorqueInterface property) force_per_pwm (sl_experiment.module_interfaces.BreakInterface property) from_path() (sl_experiment.data_classes.SessionData class method)

G

genotype (sl_experiment.data_classes.SubjectData attribute) get_adc_units_from_torque() (sl_experiment.module_interfaces.TorqueInterface method) get_adc_units_from_volts() (sl_experiment.module_interfaces.LickInterface method) get_device() (sl_experiment.zaber_bindings.ZaberConnection method) get_duration_from_volume() (sl_experiment.module_interfaces.ValveInterface method)

get_position() (sl_experiment.zaber_bindings.ZaberAxis method) get_positions() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) get_ppr() (sl_experiment.module_interfaces.EncoderInterface method) get_pwm_from_torque() (sl_experiment.module_interfaces.BreakInterface method)

H

hardware_configuration_path (sl_experiment.data_classes.SessionData property) HardwareConfiguration (class in sl_experiment.data_classes) harvesters_cti_path (sl_experiment.data_classes.ProjectConfiguration attribute) HeadBar (class in sl_experiment.binding_classes) (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._MesoscopeExperiment attribute)

headbar_pitch (sl_experiment.data_classes.ZaberPositions attribute) headbar_port (sl_experiment.data_classes.ProjectConfiguration attribute) headbar_roll (sl_experiment.data_classes.ZaberPositions attribute) headbar_z (sl_experiment.data_classes.ZaberPositions attribute) headers (sl_experiment.google_sheet_tools.SurgerySheet property) (sl_experiment.google_sheet_tools.WaterSheetData property) home() (sl_experiment.zaber_bindings.ZaberAxis method)

I

id (sl_experiment.data_classes.SubjectData attribute) (sl_experiment.zaber_bindings.ZaberDevice property) implant (sl_experiment.data_classes.ImplantData attribute) implant_ap_coordinate_mm (sl_experiment.data_classes.ImplantData attribute) implant_code (sl_experiment.data_classes.ImplantData attribute) implant_dv_coordinate_mm (sl_experiment.data_classes.ImplantData attribute) implant_ml_coordinate_mm (sl_experiment.data_classes.ImplantData attribute) implant_target (sl_experiment.data_classes.ImplantData attribute) ImplantData (class in sl_experiment.data_classes) implants (sl_experiment.data_classes.SurgeryData attribute) increase_threshold_ml (sl_experiment.data_classes.RunTrainingDescriptor attribute) initial_run_duration_threshold_s (sl_experiment.data_classes.RunTrainingDescriptor attribute) initial_run_speed_threshold_cm_s (sl_experiment.data_classes.RunTrainingDescriptor attribute) initialize_remote_assets() (sl_experiment.module_interfaces.BreakInterface method) (sl_experiment.module_interfaces.EncoderInterface method) (sl_experiment.module_interfaces.LickInterface method) (sl_experiment.module_interfaces.ScreenInterface method) (sl_experiment.module_interfaces.TorqueInterface method) (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method)

initially_on (sl_experiment.module_interfaces.ScreenInterface property) injection (sl_experiment.data_classes.InjectionData attribute) injection_ap_coordinate_mm (sl_experiment.data_classes.InjectionData attribute) injection_code (sl_experiment.data_classes.InjectionData attribute) injection_dv_coordinate_mm (sl_experiment.data_classes.InjectionData attribute) injection_ml_coordinate_mm (sl_experiment.data_classes.InjectionData attribute) injection_target (sl_experiment.data_classes.InjectionData attribute) injection_volume_nl (sl_experiment.data_classes.InjectionData attribute) InjectionData (class in sl_experiment.data_classes) injections (sl_experiment.data_classes.SurgeryData attribute) inversion (sl_experiment.zaber_bindings.ZaberAxis property) is_busy (sl_experiment.zaber_bindings.ZaberAxis property) is_connected (sl_experiment.zaber_bindings.ZaberConnection property) is_homed (sl_experiment.zaber_bindings.ZaberAxis property) is_parked (sl_experiment.zaber_bindings.ZaberAxis property)

K

ketoprofen_code (sl_experiment.data_classes.DrugData attribute)

ketoprofen_volume_ml (sl_experiment.data_classes.DrugData attribute)

L

label (sl_experiment.zaber_bindings.ZaberDevice property) lactated_ringers_solution_code (sl_experiment.data_classes.DrugData attribute) lactated_ringers_solution_volume_ml (sl_experiment.data_classes.DrugData attribute) left_camera_index (sl_experiment.data_classes.ProjectConfiguration attribute) left_camera_log_path (sl_experiment.binding_classes.VideoSystems property) lick (sl_experiment.binding_classes.MicroControllerInterfaces attribute) lick_threshold (sl_experiment.data_classes.HardwareConfiguration attribute) (sl_experiment.module_interfaces.LickInterface property) lick_tracker (sl_experiment.binding_classes.MicroControllerInterfaces property) (sl_experiment.module_interfaces.LickInterface property) lick_train_state() (sl_experiment.experiment._BehaviorTraining method) lick_training_logic() (in module sl_experiment.experiment) LickInterface (class in sl_experiment.module_interfaces)

LickPort (class in sl_experiment.binding_classes) (sl_experiment.experiment._BehaviorTraining attribute) (sl_experiment.experiment._MesoscopeExperiment attribute) lickport_port (sl_experiment.data_classes.ProjectConfiguration attribute) lickport_x (sl_experiment.data_classes.ZaberPositions attribute) lickport_y (sl_experiment.data_classes.ZaberPositions attribute) lickport_z (sl_experiment.data_classes.ZaberPositions attribute) LickTrainingDescriptor (class in sl_experiment.data_classes) load() (sl_experiment.data_classes.ProjectConfiguration class method) local_experiment_configuration_path (sl_experiment.data_classes.SessionData property) local_metadata_path (sl_experiment.data_classes.SessionData property) local_root_directory (sl_experiment.data_classes.ProjectConfiguration attribute) (sl_experiment.data_classes.SessionData attribute) location_housed (sl_experiment.data_classes.SubjectData attribute)

M

maximum_break_strength (sl_experiment.data_classes.HardwareConfiguration attribute) (sl_experiment.module_interfaces.BreakInterface property) maximum_limit (sl_experiment.zaber_bindings.ZaberAxis property) maximum_reward_delay_s (sl_experiment.data_classes.LickTrainingDescriptor attribute) maximum_training_time_m (sl_experiment.data_classes.LickTrainingDescriptor attribute) (sl_experiment.data_classes.RunTrainingDescriptor attribute) maximum_water_volume_ml (sl_experiment.data_classes.LickTrainingDescriptor attribute) (sl_experiment.data_classes.RunTrainingDescriptor attribute) mesoscope_fast_z_position (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.MesoscopePositions attribute) mesoscope_frame (sl_experiment.binding_classes.MicroControllerInterfaces attribute) mesoscope_frame_count (sl_experiment.binding_classes.MicroControllerInterfaces property) mesoscope_persistent_path (sl_experiment.data_classes.SessionData property) mesoscope_roll_position (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.MesoscopePositions attribute) mesoscope_root_directory (sl_experiment.data_classes.ProjectConfiguration attribute) (sl_experiment.data_classes.SessionData attribute) mesoscope_root_path (sl_experiment.data_classes.SessionData property) mesoscope_start (sl_experiment.binding_classes.MicroControllerInterfaces attribute) mesoscope_stop (sl_experiment.binding_classes.MicroControllerInterfaces attribute) mesoscope_tilt_position (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.MesoscopePositions attribute) mesoscope_tip_position (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.MesoscopePositions attribute) mesoscope_x_position (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.MesoscopePositions attribute) mesoscope_y_position (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.MesoscopePositions attribute) mesoscope_z_position (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.MesoscopePositions attribute)

MesoscopeExperimentDescriptor (class in sl_experiment.data_classes) MesoscopePositions (class in sl_experiment.data_classes) MicroControllerInterfaces (class in sl_experiment.binding_classes) minimum_break_strength (sl_experiment.data_classes.HardwareConfiguration attribute) (sl_experiment.module_interfaces.BreakInterface property) minimum_limit (sl_experiment.zaber_bindings.ZaberAxis property) minimum_reward_delay (sl_experiment.data_classes.LickTrainingDescriptor attribute) module sl_experiment.binding_classes sl_experiment.cli sl_experiment.data_classes sl_experiment.data_preprocessing sl_experiment.experiment sl_experiment.google_sheet_tools sl_experiment.module_interfaces sl_experiment.packaging_tools sl_experiment.transfer_tools sl_experiment.visualizers sl_experiment.zaber_bindings mount_position (sl_experiment.zaber_bindings.ZaberAxis property) mount_position() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) mouse_weight_g (sl_experiment.data_classes.LickTrainingDescriptor attribute) (sl_experiment.data_classes.MesoscopeExperimentDescriptor attribute) (sl_experiment.data_classes.RunTrainingDescriptor attribute) move() (sl_experiment.zaber_bindings.ZaberAxis method) mqtt_topic (sl_experiment.module_interfaces.EncoderInterface property) (sl_experiment.module_interfaces.LickInterface property) (sl_experiment.module_interfaces.ValveInterface property)

N

name (sl_experiment.zaber_bindings.ZaberAxis property) (sl_experiment.zaber_bindings.ZaberDevice property) nas_metadata_path (sl_experiment.data_classes.SessionData property)

nas_root_directory (sl_experiment.data_classes.ProjectConfiguration attribute) (sl_experiment.data_classes.SessionData attribute) nas_root_path (sl_experiment.data_classes.SessionData property) nonlinearity_exponent (sl_experiment.module_interfaces.ValveInterface property)

O

open_valve() (sl_experiment.binding_classes.MicroControllerInterfaces method)

P

park() (sl_experiment.zaber_bindings.ZaberAxis method) park_position (sl_experiment.zaber_bindings.ZaberAxis property) park_position() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) parse_mqtt_command() (sl_experiment.module_interfaces.BreakInterface method) (sl_experiment.module_interfaces.EncoderInterface method) (sl_experiment.module_interfaces.LickInterface method) (sl_experiment.module_interfaces.ScreenInterface method) (sl_experiment.module_interfaces.TorqueInterface method) (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method) port (sl_experiment.zaber_bindings.ZaberConnection property) post_op_notes (sl_experiment.data_classes.ProcedureData attribute) prepare_motors() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) preprocess_session_data() (in module sl_experiment.data_preprocessing)

previous_mesoscope_positions_path (sl_experiment.data_classes.SessionData property) previous_zaber_positions_path (sl_experiment.data_classes.SessionData property) procedure (sl_experiment.data_classes.SurgeryData attribute) ProcedureData (class in sl_experiment.data_classes) process_received_data() (sl_experiment.module_interfaces.BreakInterface method) (sl_experiment.module_interfaces.EncoderInterface method) (sl_experiment.module_interfaces.LickInterface method) (sl_experiment.module_interfaces.ScreenInterface method) (sl_experiment.module_interfaces.TorqueInterface method) (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method) project_name (sl_experiment.data_classes.SessionData attribute) ProjectConfiguration (class in sl_experiment.data_classes) protocol (sl_experiment.data_classes.ProcedureData attribute) pulse_count (sl_experiment.module_interfaces.TTLInterface property) purge_redundant_data() (in module sl_experiment.data_preprocessing)

R

raw_data_path (sl_experiment.data_classes.SessionData property) recorded_mesoscope_ttl (sl_experiment.data_classes.HardwareConfiguration attribute) reference_valve() (sl_experiment.binding_classes.MicroControllerInterfaces method) replace_root_path() (in module sl_experiment.data_classes) reset_pulse_count() (sl_experiment.module_interfaces.EncoderInterface method) restore_position() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) reward_signal (sl_experiment.experiment._KeyboardListener property)

right_camera_index (sl_experiment.data_classes.ProjectConfiguration attribute) right_camera_log_path (sl_experiment.binding_classes.VideoSystems property) run_duration_increase_step_s (sl_experiment.data_classes.RunTrainingDescriptor attribute) run_experiment_logic() (in module sl_experiment.experiment) run_speed_increase_step_cm_s (sl_experiment.data_classes.RunTrainingDescriptor attribute) run_train_logic() (in module sl_experiment.experiment) run_train_state() (sl_experiment.experiment._BehaviorTraining method) running_speed (sl_experiment.visualizers.BehaviorVisualizer property) RunTrainingDescriptor (class in sl_experiment.data_classes)

S

save_body_camera_frames() (sl_experiment.binding_classes.VideoSystems method) save_face_camera_frames() (sl_experiment.binding_classes.VideoSystems method) scale_coefficient (sl_experiment.module_interfaces.ValveInterface property) ScreenInterface (class in sl_experiment.module_interfaces) screens (sl_experiment.binding_classes.MicroControllerInterfaces attribute) screens_initially_on (sl_experiment.data_classes.HardwareConfiguration attribute) send_pulse() (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method) sensor_port (sl_experiment.data_classes.ProjectConfiguration attribute) server_metadata_path (sl_experiment.data_classes.SessionData property) server_root_directory (sl_experiment.data_classes.ProjectConfiguration attribute) (sl_experiment.data_classes.SessionData attribute) server_root_path (sl_experiment.data_classes.SessionData property) session_descriptor_path (sl_experiment.data_classes.SessionData property) session_name (sl_experiment.data_classes.SessionData attribute) session_type (sl_experiment.data_classes.SessionData attribute) SessionData (class in sl_experiment.data_classes) set_breaking_power() (sl_experiment.module_interfaces.BreakInterface method) set_parameters() (sl_experiment.module_interfaces.BreakInterface method) (sl_experiment.module_interfaces.EncoderInterface method) (sl_experiment.module_interfaces.LickInterface method) (sl_experiment.module_interfaces.ScreenInterface method) (sl_experiment.module_interfaces.TorqueInterface method) (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method) sex (sl_experiment.data_classes.SubjectData attribute) shutdown() (sl_experiment.experiment._KeyboardListener method) (sl_experiment.zaber_bindings.ZaberAxis method) (sl_experiment.zaber_bindings.ZaberDevice method) sl-crc command line option --string -i sl-devices command line option --errors -e sl-experiment command line option --animal --animal_weight --experiment --path --project, [1] --remove_telomere --remove_ubiquitin --session-path --user -a -e -p, [1], [2] -s -t -u, [1] -w sl-lick-train command line option --animal --animal_weight --maximum_delay --maximum_time --maximum_volume --minimum_delay --project --user -a -max -min -p -t -u -v -w sl-maintain-vr command line option --project -p

sl-run-train command line option --animal --animal_weight --duration_step --increase_threshold --initial_duration --initial_speed --maximum_time --maximum_volume --project --speed_step --user -a -ds -id -is -it -p -ss -t -u -v -w sl_experiment.binding_classes module sl_experiment.cli module sl_experiment.data_classes module sl_experiment.data_preprocessing module sl_experiment.experiment module sl_experiment.google_sheet_tools module sl_experiment.module_interfaces module sl_experiment.packaging_tools module sl_experiment.transfer_tools module sl_experiment.visualizers module sl_experiment.zaber_bindings module speed_modifier (sl_experiment.experiment._KeyboardListener property) start() (sl_experiment.binding_classes.MicroControllerInterfaces method) (sl_experiment.experiment._BehaviorTraining method) (sl_experiment.experiment._MesoscopeExperiment method) start_body_cameras() (sl_experiment.binding_classes.VideoSystems method) start_face_camera() (sl_experiment.binding_classes.VideoSystems method) start_mesoscope() (sl_experiment.binding_classes.MicroControllerInterfaces method) state_duration_s (sl_experiment.data_classes.ExperimentState attribute) status (sl_experiment.data_classes.SubjectData attribute) stop() (sl_experiment.binding_classes.MicroControllerInterfaces method) (sl_experiment.binding_classes.VideoSystems method) (sl_experiment.experiment._BehaviorTraining method) (sl_experiment.experiment._MesoscopeExperiment method) (sl_experiment.zaber_bindings.ZaberAxis method) stop_mesoscope() (sl_experiment.binding_classes.MicroControllerInterfaces method) string_checksum() (sl_experiment.zaber_bindings.CRCCalculator method) subject (sl_experiment.data_classes.SurgeryData attribute) SubjectData (class in sl_experiment.data_classes) surgeon (sl_experiment.data_classes.ProcedureData attribute) surgery_end_us (sl_experiment.data_classes.ProcedureData attribute) surgery_notes (sl_experiment.data_classes.ProcedureData attribute) surgery_sheet_id (sl_experiment.data_classes.ProjectConfiguration attribute) (sl_experiment.data_classes.SessionData attribute) surgery_start_us (sl_experiment.data_classes.ProcedureData attribute) SurgeryData (class in sl_experiment.data_classes) SurgerySheet (class in sl_experiment.google_sheet_tools)

T

terminate_remote_assets() (sl_experiment.module_interfaces.BreakInterface method) (sl_experiment.module_interfaces.EncoderInterface method) (sl_experiment.module_interfaces.LickInterface method) (sl_experiment.module_interfaces.ScreenInterface method) (sl_experiment.module_interfaces.TorqueInterface method) (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method) to_path() (sl_experiment.data_classes.SessionData method) toggle() (sl_experiment.module_interfaces.BreakInterface method) (sl_experiment.module_interfaces.ScreenInterface method) (sl_experiment.module_interfaces.TTLInterface method) (sl_experiment.module_interfaces.ValveInterface method)

torque (sl_experiment.binding_classes.MicroControllerInterfaces attribute) torque_per_adc_unit (sl_experiment.data_classes.HardwareConfiguration attribute) (sl_experiment.module_interfaces.TorqueInterface property) torque_per_pwm (sl_experiment.module_interfaces.BreakInterface property) TorqueInterface (class in sl_experiment.module_interfaces) total_delivered_volume (sl_experiment.binding_classes.MicroControllerInterfaces property) trackers (sl_experiment.experiment._BehaviorTraining property) (sl_experiment.experiment._MesoscopeExperiment property) transfer_directory() (in module sl_experiment.transfer_tools) TTLInterface (class in sl_experiment.module_interfaces)

U

unit_type (sl_experiment.zaber_bindings._ZaberUnits attribute) unity_ip (sl_experiment.data_classes.ProjectConfiguration attribute) unity_port (sl_experiment.data_classes.ProjectConfiguration attribute)

unpark() (sl_experiment.zaber_bindings.ZaberAxis method) update() (sl_experiment.visualizers.BehaviorVisualizer method) update_speed_thresholds() (sl_experiment.visualizers.BehaviorVisualizer method) update_water_log() (sl_experiment.google_sheet_tools.WaterSheetData method)

V

valve (sl_experiment.binding_classes.MicroControllerInterfaces attribute) valve_calibration_data (sl_experiment.data_classes.ProjectConfiguration attribute) valve_nonlinearity_exponent (sl_experiment.data_classes.HardwareConfiguration attribute) valve_position (sl_experiment.zaber_bindings.ZaberAxis property) valve_scale_coefficient (sl_experiment.data_classes.HardwareConfiguration attribute) valve_tracker (sl_experiment.binding_classes.MicroControllerInterfaces property) (sl_experiment.module_interfaces.ValveInterface property)

ValveInterface (class in sl_experiment.module_interfaces) velocity_units (sl_experiment.zaber_bindings._ZaberUnits property) VideoSystems (class in sl_experiment.binding_classes) volts_per_adc_unit (sl_experiment.module_interfaces.LickInterface property) vr_maintenance_logic() (in module sl_experiment.experiment) vr_rest() (sl_experiment.experiment._MesoscopeExperiment method) vr_run() (sl_experiment.experiment._MesoscopeExperiment method) vr_state_code (sl_experiment.data_classes.ExperimentState attribute)

W

wait_until_idle() (sl_experiment.binding_classes.HeadBar method) (sl_experiment.binding_classes.LickPort method) water_log_sheet_id (sl_experiment.data_classes.ProjectConfiguration attribute) (sl_experiment.data_classes.SessionData attribute)

WaterSheetData (class in sl_experiment.google_sheet_tools) weight_g (sl_experiment.data_classes.SubjectData attribute) wheel_break (sl_experiment.binding_classes.MicroControllerInterfaces attribute) wheel_encoder (sl_experiment.binding_classes.MicroControllerInterfaces attribute)

Z

zaber_positions_path (sl_experiment.data_classes.SessionData property) zaber_units_conversion (sl_experiment.zaber_bindings._ZaberUnits attribute) ZaberAxis (class in sl_experiment.zaber_bindings)

ZaberConnection (class in sl_experiment.zaber_bindings) ZaberDevice (class in sl_experiment.zaber_bindings) ZaberPositions (class in sl_experiment.data_classes)