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The role of acquisition triggers during a LOOP

Overview

ScanImage consists of continuous (gap-free) numbered acquisitions, which are:

  • Started by an Acquisition Start Trigger
  • Ended when either:
    • An Acquisition Stop Trigger is detected
    • Specified set of {# Frames, # Slices, # Volumes} is completed, as entered in the Main Controls and FastZ Controls (if enabled)
  • Numerically incremented, without a gap, by Next File Markers, with data logging into separate files

The Acquisition Start Trigger, Acquisition Stop Trigger,and Next File Markers are TTL edge input signals to ScanImage.

External timing signals can be used to control the timing of ScanImage acquisitions. Destinations for each of these trigger sources are routed to the Scan Control DAQ and configured on the Trigger Controls.

(tick) External timing signals provide great flexibility to synchronize imaging and image files with experiment signals external to ScanImage, e.g. signals associated with behavior, physiology, or stimulus data streams.

The Acquisition Start Trigger is mandatory: a trigger is self-generated by ScanImage if an external source is not provided. 

Acquisition Start Trigger

 The start trigger can be configured to use an external input.  Otherwise ScanImage configures generates this trigger signal connected Without an externally supplied start trigger, generated trigger is used.

The acquisition starts listening for the start trigger after a GRAB or LOOP is initiated from the Main Controls.  If the acquisition is software triggered, the trigger is immediately generated as soon as the hardware is ready; acquisition starts right away.

When the appropriate TTL edge is observed, the acquisition system transitions into an acquiring state and begins producing data.

Start triggers that occur while the system is actively acquiring are ignored.

Next File Marker

The next file marker signals that logging should begin saving to the next file beginning on the very next frame.

When this event is observed, the counter is incremented indicating another acquisition has started (see Main Controls for more information).

This is especially useful for aligning ScanImage image file numbers to behavioral/physiological epochs defined by external software. 

Acquisition Stop Trigger

The stop trigger signals that acquisition should immediately stop after the current frame is done being acquired, even before the full specified set of {# Frames, # Slices, # Volumes} is completed.