User Stores general information for all researchers and technicians in BRAINCoGS. Being registered in this table is a requirement to add subjects in your behalf Check here for more information. Important fields include, user_id (NETID), active_gui_user & slack_webhook URLS for users (for notifications). Check set slack alerts for more info.
Location All systems associated with rigs, recordings & technician use. All behavior sessions are associated with one of the systems recorded here, each recording (ephys/imaging) is associated with a system recorded here. Check here for more information. Important fields include, user_id (NETID), active_gui_user & slack_webhook (for notifications). Check Configure systems section for more info.
Path Paths for the cup drives in BRAINCoGS. Paths are divided by OS and local or network system types.
AcquisitionType All possible acquisitions modalities in BRAINCoGS. (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 configuration is set for a system is made. Check 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 configuration is set for a system is made. Check DB Access section
InsertionDevice Device types for insertion in subjects. (From ephys electrodes, to optogenetic cannula). Paired with u19_action.SurgeryLocation table.
SlackWebhooks Slack webhooks URLs for general notifications. Check set slack alerts for more info.
Subject Stores general information for all subjects in BRAINCoGS. Being registered in this table is a requirement to train and perform behavior sessions.
LickometerMotorPosition Stores ml, ap, & dv motor coordinates for a subject in a rig with positioning motor installed. Check Set up motor positioning subsection for more information.
CagingStatus Subject-Cage relationship storage.
HealthStatus Daily health assesment for subject. Fields like normal_behavior, posture_grooming, technician_comments etc.
Stores all reference and general information of behavior sessions. Other tables in this DB also stores reference to blocks, trials, manipulation and subtasks of a behavior session.
SessionStarted Reference to all sessions that are started with training GUI. Path to behavior file ia located here.
Session Basic information (performance, experiment code used, etc.) for a behavior session. Record 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. Check manipulation pipeline section for more information.
SessioSubtask Reference to which subtask (if any) was performed for a behavior session. Check subtask pipeline section for more information.
SessionVideo Reference to video adquisition if performed while behavior session. Check Pupillometry Pipeline Guide for more information.
Weighing Records daily weight of subjects. Written by weighingGUI used by technicians.
WaterAdministration Records daily water administration to subjects. Earned water written at the end of training. Supplement water Written by weighingGUI used by technicians.
DaiyPositionData For subjects with automatic motor positioning on rig, stores daily ml,ap & dv coordinates. If cameras are present on rig a lateral and tops reference images are also stored.
Towers Session/Subject ** Psych Group of tables with Psychometric Curves parameters per session, block_type (main, guiding), subject, etc. Check Using psychometric data to know how to use this. Check BRAINCoGS Data viewer to check psychometric curves.
OptogeneticSession Reference to a behavior session that is also an optogenetic session. Stores which protocol and software parameter set were used fot 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 for a subset of optogenetic sessions.
OptogeneticProtocol Describes metadata that will be associated with optogenetic sessions. (e.g. laser wavelength, stimulation frequency, etc.)
Stores all reference to all processing jobs for ephys & imaging on the automation pipeline. Almost all information in this table is shown in the Automation pipeline GUI .
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 Field of View. Stores status_processing, raw_path (recording_process_pre_path), processed_path (recording_process_post_path) for each of these "fragments" of recording.
ProcessingEphysParams Relationship between jobs & which ephys processing parameters were used for that job.
ProcessingImagingParams Relationship between jobs & which imaging processing parameters were used for that job.
LogStatus Stores all status change for processing jobs and corresponding messages & exceptions if applicable.
EphysPipelineSession List of recording_ids that correspond with ephys recordings.
BehaviorSync Synchronization data between ephys recording and behavior session. trial_index_nidq & iteration_index_nidq are trial and iteration # for each sample on the electrophysiology data.
Datajoint element array electrophysiology DB. Database schema is designed to store all data from an ephys recording and subsequent kilosort processing. More info: Datajoint element array electrophysiology docs. For BRAINCoGS ephys_precluster schema was used.
ClusteringParamSet Table that contains a list of parameter dictionaries/structures used for sorting process.
PreClusterparamSet Table that contains a list of parameter dictionaries/structures used for preprocessing steps.
PreClusterparamSteps Table that contains lists of lists of preCluster param Sets that form a preprocessing sequence for recordings. preprocessing steps. (e.g. catgt)
CuratedClusteringUnit Main data for all the units found in sorting process. (spike_times, cluster_quality_label, etc.)
LFPElectrode LFP data for each of the electrodes in recording.
WaveformSetWaveform All waveforms from a unit captured by each electrode in recording.
ProbeInsertion Records which probe was used for the corresponding recording-insertion_number pair. Check 5. u19_pipeline_probe_element.
Datajoint element array electrophysiology DB for probes. Database schema is designed to store probes and electorde configurations used in recordings. More info: Datajoint element array electrophysiology docs. For BRAINCoGS ephys_precluster schema was used.
ImagingPipelineSession List of recording_ids that correspond with imaging recordings.
TiffSplit Identified fields of view for a single recording (regularly 2photon = 1 FOV, mesoscope = 3 FOV). Each FOV is processed separately.
AcquiredTiff TIFF file header metadata for each FOV.
SyncImagingBehavior Synchronization data between imaging recording and behavior session. sync_behav_%%_by_im_frame = Correspoding behavior block, trial and iteration for each imaging frame. sync_im_frame_span_by_behav_%% = Fist and last imaging frame for each behavior block, trial and iteration.
Datajoint element calcium imaging DB. Database schema is designed to store all data from an imaging recording and subsequent segmentation process. More info: Datajoint element calcium imaging docs.
Datajoint element calcium imaging DB. Database schema is designed to store scan info and metadata from imaging files. More info: Datajoint element calcium imaging docs.
Stores all thing related to pupillometry recordings. From reference to behavior sessions to final results. Check Pupillometry Pipeline Guide for more information.
PupillometrySession Reference to behavior session that had pupillometry acquisition.
PupillometryModels Training models ready to use for processing pupillometry data.
PupillometrySyncBehavior Time correspondence between each trial-iteration in behavior file and each video frame.
PupillometrySyncBehavior Time correspondence between each trial-iteration in 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.