Imaging: Terminology

Due to the divergent development process, some different terminology has evolved between the imaging and ephys pipelines. This page, and it’s Ephys twin, will cover some of the distinctions.

MetaSessions and Sessions

In the Imaging pipeline, the top level object for grouping data together is the MetaSession, approximately equal to the Session in the Ephys pipeline. It is not completely identical.

A MetaSession collectively labels one or more sets of imaging and tracking data together. All imaging data in a MetaSession is analysed as a single group within Suite2P, and unit IDs are consistent within that MetaSession.

A Session is a single group of data (tiff stacks, tracking etc) generated by a microscope. A Session is associated with a single arena, a single tracking system, and so on.

A BaseFolder is the physical location on disk where your data is stored, created by ScanImage, and is the key to ingesting data via the Imaging Web GUI. Data in a single BaseFolder does not necessarily correspond to a single MetaSession (see the discussion of the combined in the Imaging Web GUI page).

Data Sets

The Imaging pipeline keeps track of data files stored in the BaseFolder. If changes are made to the data in the BaseFolder (e.g. curating units identified by Suite2P), you should re-ingest the BaseFolder via the Web GUI. Only files that have changed will be re-ingested.

A Data Set may consist of one or more physical files relating to a specific kind of data. For example, “Tif” or “Tracking” or “DLC”.

Setups and Scopes

As part of the metadata stored about acquired data, the imaging pipeline keeps track of the physical hardware used, and its most recent calibration data. This “hardware tracking” (mostly) occurs under the Scope and Setup tables.

  • A Scope describes the microscope objective and scanner, corresponding to specific fields of view, warping/dewarping proceedures etc. This is relevant only for the experimental miniscopes, as the Femontics system, the Scope cannot be changed.

  • A Setup describes the majority of the experimental hardware, photodetectors, lasers, calibrations, etc. In general, it describes everything else in the recording room except the Scope, the arena and the subject.

Entries in these tables describe and refer to a single, unique, physical object. Multiple copies of the same design of hardware should have one (or more) entries each. Multiple entries per physical object are used to keep track of the date of calibration data.