Data Pipeline

Each node in the following diagram represents the analysis code in the workflow and the corresponding table in the database. Within the workflow, Element Miniscope connects to upstream Elements including Lab, Animal, Session, and Event. For more detailed documentation on each table, see the API docs for the respective schemas.

Table descriptions

reference schema

• For further details see the reference schema API docs

Table	Description
Equipment	Scanner metadata

subject schema

• Although not required, most choose to connect the Session table to a Subject table.

• For further details see the subject schema API docs

Table	Description
Subject	Basic information of the research subject.

session schema

• For further details see the session schema API docs

Table	Description
Session	Unique experimental session identifier.

miniscope schema

• Tables related to importing and analyzing miniscope data.

• For further details see the miniscope schema API docs

Table	Description
AcquisitionSoftware	Software used for miniscope acquisition
Channel	Number of channels in the miniscope recording
Recording	Information about the equipment used (e.g. the acquisition hardware information).
RecordingLocation	Brain location of the miniscope recording
RecordingInfo	Metadata about this recording from the Miniscope DAQ software (e.g. frame rate, number of channels, frames, etc.)
RecordingInfo.File	Relative file paths for the recording files
ProcessingMethod	Available analysis suites that can be used in processing of the miniscope datasets
ProcessingParamSet	All parameters required to process a miniscope dataset
MaskType	All possible classifications of a segmented mask
ProcessingTask	Task defined by a combination of Recording and ProcessingParamSet
Processing	The core table that executes a ProcessingTask
Curation	Curated results
MotionCorrection	Results of the motion correction procedure
MotionCorrection.RigidMotionCorrection	Details of the rigid motion correction performed on the miniscope data
MotionCorrection.NonRigidMotionCorrection	Details of nonrigid motion correction performed on the miniscope data
MotionCorrection.NonRigidMotionCorrection.Block	Results of non-rigid motion correction for each block
MotionCorrection.Summary	Summary images for each field and channel after motion correction
Segmentation	Results of the segmentation
Segmentation.Mask	Masks identified in the segmentation procedure
MaskClassificationMethod	Method used in the mask classification procedure
MaskClassification	Result of the mask classification procedure
MaskClassification.MaskType	Classification type assigned to each mask (e.g. soma, axon, dendrite, artifact, etc.)
Fluorescence	Fluorescence measurements
Fluorescence.Trace	Fluorescence trace for each region of interest
ActivityExtractionMethod	Method used in activity extraction
Activity	Inferred neural activity
Activity.Trace	Inferred neural activity for each fluorescence trace
ProcessingQualityMetrics	Quality metrics used to evaluate the results of the calcium imaging analysis pipeline
ProcessingQualityMetrics.Mask	Quality metrics used to evaluate the masks
ProcessingQualityMetrics.Trace	Quality metrics used to evaluate the fluorescence traces

miniscope_report schema

• Tables that provide summary reports of the processed miniscope data.

• For further details see the miniscope_report API docs

Table	Description
QualityMetrics	A table containing information about CaImAn estimates: + r_values: Space correlation + snr: Trace SNR + cnn_preds: CNN predictions