BRAIN CoGS Mini VR Rigs

Database Organization ​

The following sections describe all databases on the BRAIN CoGS host (datajoint00.pni.princeton.edu). The databases fall into these categories:

  1. Lab, subject & schedule DBs
  2. Behavior DBs
  3. Ephys & imaging DBs

Lab, Subject & Schedule DBs ​

1. u19_lab ​

  • Stores general information that applies across all BRAIN CoGS projects, including information about researchers.

Main tables ​

  • User Stores general information for all researchers and technicians in BRAIN CoGS. You must be registered in this table to have subjects added under your name (see here for more information). Important fields include user_id (NETID), active_gui_user, and slack_webhook URLs for users (for notifications). See Slack alerts for more information.
  • Location All systems associated with rigs, recordings, and technician use. Every behavior session is associated with one of the systems recorded here, and each recording (ephys/imaging) is associated with a system recorded here.
  • Path Paths for the cup drives in BRAIN CoGS. Paths are divided by OS and by local or network system type.
  • AcquisitionType All possible acquisition modalities in BRAIN CoGS (each location in Path is associated with one modality as well). Modalities include behavior, electrophysiology, 2photon, mesoscope, etc.
  • DjCustomVariables Configuration variables for DataJoint, mainly paths for special directories. This table is used in the background when DB access is configured for a system (see the DB access section).
  • DjStores External storage path locations on the network drives (cup) for several DataJoint tables. This table is used in the background when DB access is configured for a system (see the DB access section).
  • InsertionDevice Device types for insertion in subjects (from ephys electrodes to optogenetic cannulae). Paired with the u19_action.SurgeryLocation table.
  • SlackWebhooks Slack webhook URLs for general notifications. See Slack alerts for more information.

2. u19_subject ​

  • Stores all general information for subjects (mice) registered for experiments.

Main tables ​

  • Subject Stores general information for all subjects in BRAIN CoGS. Being registered in this table is a requirement to train and run behavior sessions.
  • LickometerMotorPosition Stores ml, ap, and dv motor coordinates for a subject in a rig with a positioning motor installed. See the motor positioning setup for more information.
  • CagingStatus Subject-cage relationship storage.
  • HealthStatus Daily health assessment for a subject. Fields include normal_behavior, posture_grooming, technician_comments, etc.
  • Allele All subjects' genotypes in BRAIN CoGS.
  • Cage Cage list for subjects.

3. u19_scheduler ​

  • Stores everything related to scheduling future sessions for subjects in the "NewTrainingGUI" model .
  • It includes current rig IOs, training profiles for all experiments, and the schedule calendar for future sessions.

Main tables ​

  • Schedule Records which subjects are scheduled to train, on which date, on which rig, and which training profile they are assigned.
  • TrainingProfile All variables for a given experiment (e.g. experiment world, protocol, rewardFactor). See the Rig Tester documentation for more information.
  • InputOutputRig All IO "types" defined for every rig (e.g. Reward, LeftAirPuff, Arduino). See the Rig Tester documentation for more information.
  • InputOutputRigParameters All RigParameters.m parameters needed for a given IO.
  • InputOutputProfile Defines which IOs are needed for a specific rig and/or task.

Behavior DBs ​

1. u19_acquisition: ​

  • Stores all reference and general information for behavior sessions. Other tables in this database also store references to the blocks, trials, manipulations, and subtasks of a behavior session.

Main tables ​

  • SessionStarted Reference to all sessions started with the training GUI. The path to the behavior file is located here.
  • Session Basic information (performance, experiment code used, etc.) for a behavior session. The record is written after training is finished.
  • SessionBlock Basic reference to all blocks from all behavior sessions.
  • SessionBlockTrial Basic reference to all trials from all behavior sessions.
  • SessionManipulation Reference to which manipulation (if any) was performed for a behavior session. See the manipulation pipeline section for more information.
  • SessionSubtask Reference to which subtask (if any) was performed for a behavior session. See the subtask pipeline section for more information.
  • SessionVideo Reference to video acquisition, if performed during a behavior session. See the Pupillometry Pipeline Guide for more information.

2. u19_action: ​

  • Stores daily, recurrent, and specific actions performed on subjects.

Main tables ​

  • Weighing Records the daily weight of subjects. Written by the weighingGUI used by technicians.
  • WaterAdministration Records daily water administration to subjects. Earned water is written at the end of training. Supplement water is written by the weighingGUI used by technicians.
  • Surgery Records of surgeries performed on subjects. Written by the ephys/imaging automation pipeline.
  • SurgeryLocation Records device locations implanted in subjects during surgeries (e.g. Neuropixels probes). Written by the ephys/imaging automation pipeline.
  • DailyPositionData For subjects with automatic motor positioning on a rig, stores daily ml, ap, and dv coordinates. If cameras are present on the rig, lateral and top reference images are also stored.

3. u19_behavior: ​

  • Stores detailed data for behavior sessions. Built to support Towers Task data, but stores data from all behavior sessions.

Main tables ​

  • TowersBlock Specific block data from behavior sessions (level, main_level, block_performance, etc.).
  • TowersBlockTrial Specific trial data from behavior sessions (tower positions, trial_type, choice, position, velocity, etc.).
  • SpatialTimeBlobs Efficient time, position, and velocity storage (per session, not per trial). See get_full_trial_data with SpatialTimeBlobs to learn how to use it.
  • Towers Session/Subject Psych Group of tables with psychometric curve parameters per session, block_type (main, guiding), subject, etc. View psychometric curves in the BRAIN CoGS data viewer.

4. u19_behavior_subtask: ​

5. u19_optogenetics ​

Main tables ​

  • OptogeneticSession Reference to a behavior session that is also an optogenetic session. Stores which protocol and software parameter set were used for the session.
  • OptogeneticSessionTrial Stores specific optogenetic data on a trial-by-trial basis.
  • OptogeneticSoftwareParameters MATLAB structure with parameters to be used during the behavior session, specific to a subset of optogenetic sessions.
  • OptogeneticProtocol Describes metadata associated with optogenetic sessions (e.g. laser wavelength, stimulation frequency, etc.).

6. u19_thermal ​

7. u19_puffs ​

  • Air puff task session-specific data.

Main tables ​

  • PuffsSession Reference to a behavior session that is also a puff session.
  • PuffsSessionTrial Stores specific puffs data on a trial-by-trial basis.

Ephys/Imaging DBs ​

1. u19_recording: ​

Main tables ​

  • Recording Reference to all recordings. Stores information such as location, status_recording, and recording directory on the network drives.
  • RecordingBehaviorSessions Relationship between recordings and behavior sessions. (recording_id <-> session_key (subject, date, #)
  • RecordingRecordingSession Relationship between recordings and subject/date. Used when no behavior is attached to a recording.
  • Modality List of all possible modalities supported by the automation pipeline.

2. u19_recording_process: ​

  • Stores all references to processing jobs for ephys and imaging in the automation pipeline. Almost all information in this table is shown in the automation pipeline GUI.

Main tables ​

  • Processing Reference to all processing jobs. For ephys, it has a one-to-one relationship with recording probes. For imaging, it has a one-to-one relationship with the field of view. Stores status_processing, raw_path (recording_process_pre_path), processed_path (recording_process_post_path) for each of these "fragments" of a recording.
  • ProcessingEphysParams Relationship between jobs and which ephys processing parameters were used for each job.
  • ProcessingImagingParams Relationship between jobs and which imaging processing parameters were used for each job.
  • LogStatus Stores all status changes for processing jobs, along with the corresponding messages and exceptions if applicable.

3. u19_ephys_pipeline: ​

  • Basic reference to recordings and behavior synchronization data.

Main tables ​

  • EphysPipelineSession List of recording_ids that correspond to ephys recordings.
  • BehaviorSync Synchronization data between the ephys recording and the behavior session. trial_index_nidq & iteration_index_nidq are the trial and iteration # for each sample in the electrophysiology data.

4. u19_pipeline_ephys_element: ​

  • DataJoint element array electrophysiology DB. The database schema is designed to store all data from an ephys recording and the subsequent Kilosort processing. More info: DataJoint Element Array Electrophysiology docs. For BRAIN CoGS, the ephys_precluster schema was used.

Main tables ​

  • ClusteringParamSet Contains a list of parameter dictionaries/structures used for the sorting process.
  • PreClusterparamSet Contains a list of parameter dictionaries/structures used for preprocessing steps.
  • PreClusterparamSteps Contains lists of PreCluster param sets that form a sequence of preprocessing steps for recordings (e.g. CatGT).
  • CuratedClusteringUnit Main data for all the units found in the sorting process (spike_times, cluster_quality_label, etc.).
  • LFPElectrode LFP data for each of the electrodes in a recording.
  • WaveformSetWaveform All waveforms from a unit captured by each electrode in a recording.
  • ProbeInsertion Records which probe was used for the corresponding recording-insertion_number pair. Check 5. u19_pipeline_probe_element.

5. u19_pipeline_probe_element: ​

  • DataJoint element array electrophysiology DB for probes. The database schema is designed to store the probes and electrode configurations used in recordings. More info: DataJoint Element Array Electrophysiology docs. For BRAIN CoGS, the ephys_precluster schema was used.

Main tables ​

  • Probe Contains all physical probes used in recordings.
  • ProbeTypeElectrode Contains coordinates, shank #, and id for each electrode in a probe.

6. u19_imaging_pipeline: ​

  • Reference to all imaging recordings and the subsequent fields of view (FOV) identification and splitting for processing.

Main tables ​

  • ImagingPipelineSession List of recording_ids that correspond to imaging recordings.
  • TiffSplit Identified fields of view for a single recording (typically 2photon = 1 FOV, mesoscope = 3 FOV). Each FOV is processed separately.
  • AcquiredTiff TIFF file header metadata for each FOV.
  • SyncImagingBehavior Synchronization data between the imaging recording and the behavior session. sync_behav_%%_by_im_frame = corresponding behavior block, trial, and iteration for each imaging frame. sync_im_frame_span_by_behav_%% = first and last imaging frame for each behavior block, trial, and iteration.

7. u19_pipeline_imaging_element: ​

  • DataJoint element calcium imaging DB. The database schema is designed to store all data from an imaging recording and the subsequent segmentation process. More info: DataJoint Element Calcium Imaging docs.

Main tables ​

  • ProcessingParamSet Contains a list of parameter dictionaries/structures used for the segmentation process.
  • ActivityTrace Activity trace signals for all masks identified in the segmentation process.
  • FluorescenceTrace Fluorescence trace signals for all masks identified in the segmentation process.
  • MaskClassificationMaskType Mask types (soma, blob, doughnut, etc.) and confidence for each mask identified in the segmentation process.
  • MotionCorrection(non)RigidMotionCorrection Motion correction details (shifts, outlier_frames, etc.) performed during processing.
  • MotionCorrectionSummary Summary (average, correlation, max_proj) images for each field and channel after motion correction.

8. u19_pipeline_scan_element: ​

Main tables ​

  • ScanInfo Similar to u19_imaging_pipeline.AcquiredTiff. General data and metadata from scans.
  • ScanInfoField Data specific to each of the fields of the scan.
  • ScanInfoScanFile All files that are part of a scan.

9. u19_pupillometry: ​

  • Stores everything related to pupillometry recordings, from references to behavior sessions to final results. See the Pupillometry Pipeline Guide for more information.

Main tables ​

  • PupillometrySession Reference to a behavior session that had pupillometry acquisition.
  • PupillometryModels Training models ready to use for processing pupillometry data.
  • PupillometrySyncBehavior Time correspondence between each trial-iteration in the behavior file and each video frame.
  • PupillometrySessionModel Reference to which model was used to process a behavior session (more than one model can be used to process data from a session).
  • PupillometrySessionModelData Status of pupillometry processing and final result storage.

Made by BRAIN CoGS at Princeton Neuroscience Institute