Index

Symbols

--directory sl-configure-directory command line option --host sl-configure-server command line option --manager-id sl-manage-session command line option --password sl-configure-server command line option --processed-data-root sl-manage-project command line option sl-manage-session command line option --project-path sl-manage-project command line option --recalculate-checksum sl-manage-session-checksum command line option --reset-tracker sl-manage-session command line option --service sl-configure-server command line option --session-path sl-manage-session command line option --shared-directory sl-configure-server command line option --storage-root sl-configure-server command line option --system sl-configure-system command line option --username sl-configure-server command line option --working-root sl-configure-server command line option

-d sl-configure-directory command line option -h sl-configure-server command line option -id sl-manage-session command line option -p sl-configure-server command line option -pdr sl-manage-project command line option sl-manage-session command line option -pp sl-manage-project command line option -r sl-manage-session command line option -rc sl-manage-session-checksum command line option -s sl-configure-server command line option sl-configure-system command line option -sd sl-configure-server command line option -sp sl-manage-session command line option -sr sl-configure-server command line option -u sl-configure-server command line option -wr sl-configure-server command line option

_

_animal_string (sl_shared_assets.tools.ProjectManifest attribute) _client (sl_shared_assets.server.Server attribute) _command (sl_shared_assets.server.Job attribute) (sl_shared_assets.server.JupyterJob attribute)

_data (sl_shared_assets.tools.ProjectManifest attribute) _open (sl_shared_assets.server.Server attribute)

A

abort() (sl_shared_assets.server.ProcessingTracker method) abort_job() (sl_shared_assets.server.Server method) ABORTED (sl_shared_assets.server.ProcessingStatus attribute) acquire() (sl_shared_assets.data_classes.SessionLock method) acquisition_system (sl_shared_assets.data_classes.SessionData attribute) AcquisitionSystems (class in sl_shared_assets.data_classes) actor_port (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) add_command() (sl_shared_assets.server.Job method)

additional_firmware (sl_shared_assets.data_classes.MesoscopeSystemConfiguration attribute) animal (sl_shared_assets.server.ProcessingPipeline attribute) animal_id (sl_shared_assets.data_classes.SessionData attribute) animals (sl_shared_assets.tools.ProjectManifest property) archive_session() (in module sl_shared_assets.tools) archived_data (sl_shared_assets.data_classes.SessionData attribute) ARCHIVING (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute) auditory_tone_duration_ms (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute)

B

BEHAVIOR (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute) behavior_data_path (sl_shared_assets.data_classes.ProcessedData attribute) (sl_shared_assets.data_classes.RawData attribute)

body_camera_quantization_parameter (sl_shared_assets.data_classes.MesoscopeCameras attribute) buprenorphine_code (sl_shared_assets.data_classes.DrugData attribute) buprenorphine_volume_ml (sl_shared_assets.data_classes.DrugData attribute)

C

cage (sl_shared_assets.data_classes.SubjectData attribute) calculate_directory_checksum() (in module sl_shared_assets.tools) camera_data_path (sl_shared_assets.data_classes.ProcessedData attribute) (sl_shared_assets.data_classes.RawData attribute) cameras (sl_shared_assets.data_classes.MesoscopeSystemConfiguration attribute) CHECKSUM (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute) checksum_path (sl_shared_assets.data_classes.RawData attribute) close() (sl_shared_assets.server.Server method) cm_per_pulse (sl_shared_assets.data_classes.MesoscopeHardwareState attribute)

cm_per_unity_unit (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) command_script (sl_shared_assets.server.Job property) connection_info (sl_shared_assets.server.JupyterJob attribute) connection_info_file (sl_shared_assets.server.JupyterJob attribute) create() (sl_shared_assets.data_classes.SessionData class method) create_directory() (sl_shared_assets.server.Server method) create_job() (sl_shared_assets.server.Server method) create_system_configuration_file() (in module sl_shared_assets.data_classes) cue_map (sl_shared_assets.data_classes.MesoscopeExperimentConfiguration attribute) cue_offset_cm (sl_shared_assets.data_classes.MesoscopeExperimentConfiguration attribute) cue_sequence (sl_shared_assets.data_classes.ExperimentTrial attribute)

D

date_of_birth_us (sl_shared_assets.data_classes.SubjectData attribute) debug (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) delete_directory() (in module sl_shared_assets.tools) dexamethasone_code (sl_shared_assets.data_classes.DrugData attribute) dexamethasone_volume_ml (sl_shared_assets.data_classes.DrugData attribute) dispensed_water_volume_ml (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute)

display_body_camera_frames (sl_shared_assets.data_classes.MesoscopeCameras attribute) display_face_camera_frames (sl_shared_assets.data_classes.MesoscopeCameras attribute) dlc_projects_directory (sl_shared_assets.server.Server property) DrugData (class in sl_shared_assets.data_classes) drugs (sl_shared_assets.data_classes.SurgeryData attribute)

E

ear_punch (sl_shared_assets.data_classes.SubjectData attribute) encoder_port (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) encountered_error (sl_shared_assets.server.ProcessingTracker property) error() (sl_shared_assets.server.ProcessingTracker method) exists() (sl_shared_assets.server.Server method) experiment_configuration_path (sl_shared_assets.data_classes.RawData attribute) experiment_name (sl_shared_assets.data_classes.SessionData attribute) experiment_state_code (sl_shared_assets.data_classes.ExperimentState attribute) experiment_states (sl_shared_assets.data_classes.MesoscopeExperimentConfiguration attribute) experimenter (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) (sl_shared_assets.data_classes.WindowCheckingDescriptor attribute)

experimenter_given_water_volume_ml (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) experimenter_notes (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) (sl_shared_assets.data_classes.WindowCheckingDescriptor attribute) ExperimentState (class in sl_shared_assets.data_classes) ExperimentTrial (class in sl_shared_assets.data_classes)

F

face_camera_index (sl_shared_assets.data_classes.MesoscopeCameras attribute) face_camera_quantization_parameter (sl_shared_assets.data_classes.MesoscopeCameras attribute) FAILED (sl_shared_assets.server.ProcessingStatus attribute) file_path (sl_shared_assets.data_classes.SessionLock attribute) (sl_shared_assets.server.ProcessingTracker attribute)

final_run_duration_threshold_s (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) final_run_speed_threshold_cm_s (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) force_release() (sl_shared_assets.data_classes.SessionLock method) FORGING (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute)

G

generate_manager_id() (in module sl_shared_assets.server) generate_project_manifest() (in module sl_shared_assets.tools) generate_server_credentials() (in module sl_shared_assets.server) genotype (sl_shared_assets.data_classes.SubjectData attribute) get_credentials_file_path() (in module sl_shared_assets.data_classes)

get_session_info() (sl_shared_assets.tools.ProjectManifest method) get_sessions() (sl_shared_assets.tools.ProjectManifest method) get_system_configuration_data() (in module sl_shared_assets.data_classes) get_working_directory() (in module sl_shared_assets.data_classes) google_credentials_path (sl_shared_assets.data_classes.MesoscopePaths attribute) guidance_trigger_location_cm (sl_shared_assets.data_classes.ExperimentTrial attribute)

H

hardware_state_path (sl_shared_assets.data_classes.RawData attribute) harvesters_cti_path (sl_shared_assets.data_classes.MesoscopePaths attribute) headbar_pitch (sl_shared_assets.data_classes.ZaberPositions attribute) headbar_port (sl_shared_assets.data_classes.MesoscopeAdditionalFirmware attribute)

headbar_roll (sl_shared_assets.data_classes.ZaberPositions attribute) headbar_z (sl_shared_assets.data_classes.ZaberPositions attribute) host (sl_shared_assets.server.JupyterJob attribute) (sl_shared_assets.server.Server property) (sl_shared_assets.server.ServerCredentials attribute)

I

id (sl_shared_assets.data_classes.SubjectData attribute) implant (sl_shared_assets.data_classes.ImplantData attribute) implant_ap_coordinate_mm (sl_shared_assets.data_classes.ImplantData attribute) implant_code (sl_shared_assets.data_classes.ImplantData attribute) implant_dv_coordinate_mm (sl_shared_assets.data_classes.ImplantData attribute) implant_ml_coordinate_mm (sl_shared_assets.data_classes.ImplantData attribute) implant_target (sl_shared_assets.data_classes.ImplantData attribute) ImplantData (class in sl_shared_assets.data_classes) implants (sl_shared_assets.data_classes.SurgeryData attribute) incomplete (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) (sl_shared_assets.data_classes.WindowCheckingDescriptor attribute) increase_threshold_ml (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) initial_guided_trials (sl_shared_assets.data_classes.ExperimentState attribute)

initial_run_duration_threshold_s (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) initial_run_speed_threshold_cm_s (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) injection (sl_shared_assets.data_classes.InjectionData attribute) injection_ap_coordinate_mm (sl_shared_assets.data_classes.InjectionData attribute) injection_code (sl_shared_assets.data_classes.InjectionData attribute) injection_dv_coordinate_mm (sl_shared_assets.data_classes.InjectionData attribute) injection_ml_coordinate_mm (sl_shared_assets.data_classes.InjectionData attribute) injection_target (sl_shared_assets.data_classes.InjectionData attribute) injection_volume_nl (sl_shared_assets.data_classes.InjectionData attribute) InjectionData (class in sl_shared_assets.data_classes) injections (sl_shared_assets.data_classes.SurgeryData attribute) is_complete (sl_shared_assets.server.ProcessingTracker property) is_locked (sl_shared_assets.data_classes.SessionLock property) is_running (sl_shared_assets.server.ProcessingPipeline property) (sl_shared_assets.server.ProcessingTracker property)

J

Job (class in sl_shared_assets.server) job_complete() (sl_shared_assets.server.Server method) job_id (sl_shared_assets.server.Job attribute)

job_name (sl_shared_assets.server.Job attribute) jobs (sl_shared_assets.server.ProcessingPipeline attribute) JupyterJob (class in sl_shared_assets.server)

K

keep_job_logs (sl_shared_assets.server.ProcessingPipeline attribute)

ketoprofen_code (sl_shared_assets.data_classes.DrugData attribute) ketoprofen_volume_ml (sl_shared_assets.data_classes.DrugData attribute)

L

lactated_ringers_solution_code (sl_shared_assets.data_classes.DrugData attribute) lactated_ringers_solution_volume_ml (sl_shared_assets.data_classes.DrugData attribute) laser_power_mw (sl_shared_assets.data_classes.MesoscopePositions attribute) launch_jupyter_server() (sl_shared_assets.server.Server method) left_camera_index (sl_shared_assets.data_classes.MesoscopeCameras attribute) lick_averaging_pool_size (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) lick_delta_threshold_adc (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) lick_signal_threshold_adc (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) lick_threshold (sl_shared_assets.data_classes.MesoscopeHardwareState attribute)

lick_threshold_adc (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) LICK_TRAINING (sl_shared_assets.data_classes.SessionTypes attribute) lickport_port (sl_shared_assets.data_classes.MesoscopeAdditionalFirmware attribute) lickport_x (sl_shared_assets.data_classes.ZaberPositions attribute) lickport_y (sl_shared_assets.data_classes.ZaberPositions attribute) lickport_z (sl_shared_assets.data_classes.ZaberPositions attribute) LickTrainingDescriptor (class in sl_shared_assets.data_classes) load() (sl_shared_assets.data_classes.SessionData class method) local_tracker_path (sl_shared_assets.server.ProcessingPipeline attribute) location_housed (sl_shared_assets.data_classes.SubjectData attribute)

M

make_directories() (sl_shared_assets.data_classes.ProcessedData method) (sl_shared_assets.data_classes.RawData method) (sl_shared_assets.data_classes.TrackingData method) manager_id (sl_shared_assets.server.ProcessingPipeline attribute) MANIFEST (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute) maximum_break_strength (sl_shared_assets.data_classes.MesoscopeHardwareState attribute) maximum_break_strength_g_cm (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) maximum_idle_time_s (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) maximum_reward_delay_s (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) maximum_training_time_m (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) maximum_unconsumed_rewards (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) maximum_water_volume_ml (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) mesoscope_data_path (sl_shared_assets.data_classes.ProcessedData attribute) (sl_shared_assets.data_classes.RawData attribute) mesoscope_directory (sl_shared_assets.data_classes.MesoscopePaths attribute) MESOSCOPE_EXPERIMENT (sl_shared_assets.data_classes.SessionTypes attribute) mesoscope_fast_z (sl_shared_assets.data_classes.MesoscopePositions attribute) mesoscope_positions_path (sl_shared_assets.data_classes.RawData attribute) mesoscope_roll (sl_shared_assets.data_classes.MesoscopePositions attribute) mesoscope_tilt (sl_shared_assets.data_classes.MesoscopePositions attribute) mesoscope_tip (sl_shared_assets.data_classes.MesoscopePositions attribute)

MESOSCOPE_VR (sl_shared_assets.data_classes.AcquisitionSystems attribute) mesoscope_x (sl_shared_assets.data_classes.MesoscopePositions attribute) mesoscope_y (sl_shared_assets.data_classes.MesoscopePositions attribute) mesoscope_z (sl_shared_assets.data_classes.MesoscopePositions attribute) MesoscopeAdditionalFirmware (class in sl_shared_assets.data_classes) MesoscopeCameras (class in sl_shared_assets.data_classes) MesoscopeExperimentConfiguration (class in sl_shared_assets.data_classes) MesoscopeExperimentDescriptor (class in sl_shared_assets.data_classes) MesoscopeHardwareState (class in sl_shared_assets.data_classes) MesoscopeMicroControllers (class in sl_shared_assets.data_classes) MesoscopePaths (class in sl_shared_assets.data_classes) MesoscopePositions (class in sl_shared_assets.data_classes) MesoscopeSystemConfiguration (class in sl_shared_assets.data_classes) microcontrollers (sl_shared_assets.data_classes.MesoscopeSystemConfiguration attribute) minimum_break_strength (sl_shared_assets.data_classes.MesoscopeHardwareState attribute) minimum_break_strength_g_cm (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) minimum_reward_delay_s (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) module sl_shared_assets.data_classes sl_shared_assets.server sl_shared_assets.tools mouse_weight_g (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) MULTIDAY (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute)

N

name (sl_shared_assets.data_classes.MesoscopeSystemConfiguration attribute) nas_directory (sl_shared_assets.data_classes.MesoscopePaths attribute)

nk_path (sl_shared_assets.data_classes.RawData attribute) notebook_dir (sl_shared_assets.server.JupyterJob attribute)

O

owner (sl_shared_assets.data_classes.SessionLock property)

P

parse_connection_info() (sl_shared_assets.server.JupyterJob method) password (sl_shared_assets.server.ServerCredentials attribute) paths (sl_shared_assets.data_classes.MesoscopeSystemConfiguration attribute) pause_dispensed_water_volume_ml (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) pipeline_status (sl_shared_assets.server.ProcessingPipeline attribute) pipeline_type (sl_shared_assets.server.ProcessingPipeline attribute) port (sl_shared_assets.server.JupyterJob attribute) post_op_notes (sl_shared_assets.data_classes.ProcedureData attribute) preferred_session_water_volume_ml (sl_shared_assets.data_classes.LickTrainingDescriptor attribute) (sl_shared_assets.data_classes.MesoscopeExperimentDescriptor attribute) (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) PREPARATION (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute) prepare_session() (in module sl_shared_assets.tools) print_connection_info() (sl_shared_assets.server.JupyterJob method) print_data() (sl_shared_assets.tools.ProjectManifest method) print_notes() (sl_shared_assets.tools.ProjectManifest method) print_summary() (sl_shared_assets.tools.ProjectManifest method)

procedure (sl_shared_assets.data_classes.SurgeryData attribute) ProcedureData (class in sl_shared_assets.data_classes) processed_data (sl_shared_assets.data_classes.SessionData attribute) processed_data_path (sl_shared_assets.data_classes.ProcessedData attribute) processed_data_root (sl_shared_assets.server.Server property) (sl_shared_assets.server.ServerCredentials attribute) ProcessedData (class in sl_shared_assets.data_classes) ProcessingPipeline (class in sl_shared_assets.server) ProcessingPipelines (class in sl_shared_assets.server) ProcessingStatus (class in sl_shared_assets.server) ProcessingTracker (class in sl_shared_assets.server) project (sl_shared_assets.server.ProcessingPipeline attribute) project_name (sl_shared_assets.data_classes.SessionData attribute) ProjectManifest (class in sl_shared_assets.tools) protocol (sl_shared_assets.data_classes.ProcedureData attribute) pull_directory() (sl_shared_assets.server.Server method) pull_file() (sl_shared_assets.server.Server method) push_directory() (sl_shared_assets.server.Server method) push_file() (sl_shared_assets.server.Server method) python_version (sl_shared_assets.data_classes.SessionData attribute)

R

raw_data (sl_shared_assets.data_classes.SessionData attribute) raw_data_path (sl_shared_assets.data_classes.RawData attribute) raw_data_root (sl_shared_assets.server.Server property) (sl_shared_assets.server.ServerCredentials attribute) RawData (class in sl_shared_assets.data_classes) recorded_mesoscope_ttl (sl_shared_assets.data_classes.MesoscopeHardwareState attribute) recovery_failed_trial_threshold (sl_shared_assets.data_classes.ExperimentState attribute) recovery_guided_trials (sl_shared_assets.data_classes.ExperimentState attribute) red_dot_alignment_z (sl_shared_assets.data_classes.MesoscopePositions attribute) release() (sl_shared_assets.data_classes.SessionLock method) remote_script_path (sl_shared_assets.server.Job attribute) remote_tracker_path (sl_shared_assets.server.ProcessingPipeline attribute) remove() (sl_shared_assets.server.Server method) resolve_checksum() (in module sl_shared_assets.tools) resolve_paths() (sl_shared_assets.data_classes.ProcessedData method) (sl_shared_assets.data_classes.RawData method) (sl_shared_assets.data_classes.TrackingData method)

reward_zone_end_cm (sl_shared_assets.data_classes.ExperimentTrial attribute) reward_zone_start_cm (sl_shared_assets.data_classes.ExperimentTrial attribute) right_camera_index (sl_shared_assets.data_classes.MesoscopeCameras attribute) root_directory (sl_shared_assets.data_classes.MesoscopePaths attribute) root_path (sl_shared_assets.data_classes.ProcessedData attribute) (sl_shared_assets.data_classes.RawData attribute) run_duration_increase_step_s (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) run_speed_increase_step_cm_s (sl_shared_assets.data_classes.RunTrainingDescriptor attribute) RUN_TRAINING (sl_shared_assets.data_classes.SessionTypes attribute) RUNNING (sl_shared_assets.server.ProcessingStatus attribute) runtime_cycle() (sl_shared_assets.server.ProcessingPipeline method) runtime_initialized() (sl_shared_assets.data_classes.SessionData method) RunTrainingDescriptor (class in sl_shared_assets.data_classes)

S

save() (sl_shared_assets.data_classes.MesoscopeSystemConfiguration method) (sl_shared_assets.data_classes.SessionData method) screen_trigger_pulse_duration_ms (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) screens_initially_on (sl_shared_assets.data_classes.MesoscopeHardwareState attribute) sensor_polling_delay_ms (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) sensor_port (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) Server (class in sl_shared_assets.server) server (sl_shared_assets.server.ProcessingPipeline attribute) server_storage_directory (sl_shared_assets.data_classes.MesoscopePaths attribute) server_working_directory (sl_shared_assets.data_classes.MesoscopePaths attribute) ServerCredentials (class in sl_shared_assets.server) session (sl_shared_assets.server.ProcessingPipeline attribute) session_data_path (sl_shared_assets.data_classes.RawData attribute) session_descriptor_path (sl_shared_assets.data_classes.RawData attribute) session_lock_path (sl_shared_assets.data_classes.TrackingData attribute) session_name (sl_shared_assets.data_classes.SessionData attribute) session_type (sl_shared_assets.data_classes.SessionData attribute) SessionData (class in sl_shared_assets.data_classes) SessionLock (class in sl_shared_assets.data_classes) sessions (sl_shared_assets.tools.ProjectManifest property) SessionTypes (class in sl_shared_assets.data_classes) set_working_directory() (in module sl_shared_assets.data_classes) sex (sl_shared_assets.data_classes.SubjectData attribute) shared_directory_name (sl_shared_assets.server.ServerCredentials attribute) sheets (sl_shared_assets.data_classes.MesoscopeSystemConfiguration attribute) sl-configure-directory command line option --directory -d sl-configure-server command line option --host --password --service --shared-directory --storage-root --username --working-root -h -p -s -sd -sr -u -wr sl-configure-system command line option --system -s sl-manage-project command line option --processed-data-root --project-path -pdr -pp

sl-manage-session command line option --manager-id --processed-data-root --reset-tracker --session-path -id -pdr -r -sp sl-manage-session-checksum command line option --recalculate-checksum -rc sl_experiment_version (sl_shared_assets.data_classes.SessionData attribute) sl_shared_assets.data_classes module sl_shared_assets.server module sl_shared_assets.tools module source_data (sl_shared_assets.data_classes.SessionData attribute) start() (sl_shared_assets.server.ProcessingTracker method) state_duration_s (sl_shared_assets.data_classes.ExperimentState attribute) status (sl_shared_assets.data_classes.SubjectData attribute) (sl_shared_assets.server.ProcessingPipeline property) stop() (sl_shared_assets.server.ProcessingTracker method) storage_root (sl_shared_assets.server.ServerCredentials attribute) subject (sl_shared_assets.data_classes.SurgeryData attribute) SubjectData (class in sl_shared_assets.data_classes) submit_job() (sl_shared_assets.server.Server method) SUCCEEDED (sl_shared_assets.server.ProcessingStatus attribute) SUITE2P (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute) suite2p_configurations_directory (sl_shared_assets.server.Server property) surgeon (sl_shared_assets.data_classes.ProcedureData attribute) surgery_end_us (sl_shared_assets.data_classes.ProcedureData attribute) surgery_metadata_path (sl_shared_assets.data_classes.RawData attribute) surgery_notes (sl_shared_assets.data_classes.ProcedureData attribute) surgery_quality (sl_shared_assets.data_classes.ProcedureData attribute) (sl_shared_assets.data_classes.WindowCheckingDescriptor attribute) surgery_start_us (sl_shared_assets.data_classes.ProcedureData attribute) SurgeryData (class in sl_shared_assets.data_classes) system_configuration_path (sl_shared_assets.data_classes.RawData attribute) system_state_code (sl_shared_assets.data_classes.ExperimentState attribute) system_state_codes (sl_shared_assets.data_classes.MesoscopeHardwareState attribute)

T

telomere_path (sl_shared_assets.data_classes.RawData attribute) torque_averaging_pool_size (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) torque_baseline_voltage_adc (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) torque_delta_threshold_adc (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) torque_maximum_voltage_adc (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) torque_per_adc_unit (sl_shared_assets.data_classes.MesoscopeHardwareState attribute) torque_report_ccw (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) torque_report_cw (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) torque_sensor_capacity_g_cm (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute)

torque_signal_threshold_adc (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) TrackerFileNames (class in sl_shared_assets.server) tracking_data (sl_shared_assets.data_classes.SessionData attribute) tracking_data_path (sl_shared_assets.data_classes.TrackingData attribute) TrackingData (class in sl_shared_assets.data_classes) transfer_directory() (in module sl_shared_assets.tools) trial_length_cm (sl_shared_assets.data_classes.ExperimentTrial attribute) trial_reward_size_ul (sl_shared_assets.data_classes.ExperimentTrial attribute) trial_structures (sl_shared_assets.data_classes.MesoscopeExperimentConfiguration attribute)

U

ubiquitin_path (sl_shared_assets.data_classes.RawData attribute) unity_ip (sl_shared_assets.data_classes.MesoscopeAdditionalFirmware attribute) unity_port (sl_shared_assets.data_classes.MesoscopeAdditionalFirmware attribute) unity_scene_name (sl_shared_assets.data_classes.MesoscopeExperimentConfiguration attribute) user (sl_shared_assets.server.JupyterJob attribute) (sl_shared_assets.server.Server property)

user_data_root (sl_shared_assets.server.Server property) (sl_shared_assets.server.ServerCredentials attribute) user_working_root (sl_shared_assets.server.Server property) (sl_shared_assets.server.ServerCredentials attribute) username (sl_shared_assets.server.ServerCredentials attribute)

V

valve_calibration_data (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) valve_calibration_pulse_count (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) valve_nonlinearity_exponent (sl_shared_assets.data_classes.MesoscopeHardwareState attribute)

valve_scale_coefficient (sl_shared_assets.data_classes.MesoscopeHardwareState attribute) VIDEO (sl_shared_assets.server.ProcessingPipelines attribute) (sl_shared_assets.server.TrackerFileNames attribute)

W

weight_g (sl_shared_assets.data_classes.SubjectData attribute) wheel_diameter_cm (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) wheel_encoder_delta_threshold_pulse (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) wheel_encoder_polling_delay_us (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) wheel_encoder_ppr (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) wheel_encoder_report_ccw (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute)

wheel_encoder_report_cw (sl_shared_assets.data_classes.MesoscopeMicroControllers attribute) wheel_port (sl_shared_assets.data_classes.MesoscopeAdditionalFirmware attribute) wheel_x (sl_shared_assets.data_classes.ZaberPositions attribute) WINDOW_CHECKING (sl_shared_assets.data_classes.SessionTypes attribute) window_screenshot_path (sl_shared_assets.data_classes.RawData attribute) WindowCheckingDescriptor (class in sl_shared_assets.data_classes) working_root (sl_shared_assets.server.ServerCredentials attribute)

Z

zaber_positions_path (sl_shared_assets.data_classes.RawData attribute)

ZaberPositions (class in sl_shared_assets.data_classes)