Imaging: Terminology

Due to the divergent development process, some different terminology has evolved between the imaging and ephys pipelines, although attempts have been made to unify the terminology wherever possible. This page, and it’s Ephys twin, will cover some of the distinctions.

Session and Recordings

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

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

A Recording is a single group of data (tiff stacks, tracking etc) generated by a microscope. A Recording 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 Recording (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”.

Systems 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 SystemConfig 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 System 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 single physical object are used to keep track of the date of calibration data.

Both Systems and Scopes are given nicknames for easier discussion. These nicknames do not encode full information about every part of themselves, they are just pointers to the group documentation where that information can be found. Scopes are named as synonyms of either “fast” (for high speed scanners), or “large” (for wide field of view scanners). Systems are named after shades of green.