The following explanation applies for ScanImage versions 5 or later.
There are two types of triggers exported from ScanImage: Line Trigger (aka Line Clock) and Frame Trigger (aka Frame Clock).
The Fill Fraction Page (see link below) has a nice set of visuals depicting when the acquisition is active and the beams are on/off.
*Line Clock is also referred to as a Beam Clock.
Line Clock: (Resonant Mirror)
Values are exported (Out) on PFI5 (main backboard).
The Line Clock reports information pertaining to the Resonant scanning activity.
The point in time when the beam is on and an acquisition is occurring, the Line Clock value is high.
The point in time when the beam is off and an acquisition is NOT occurring, the Line Clock value is low.
Frame Clock: (Y-Galvo Mirror)
Values are exported (Out) on PFI6.
The Frame Clock reports information pertaining to the Y-Galvo scanning activity.
The Frame Clock value is high at the start of the frame and becomes low when the frame is completed.
Thus, the point in time when the the first pixel on the first scanned line is read (first activated pixel on the first acquisition line)
until the last pixel on the last scan line (last activated pixel on the last acquisition line) is read, the Frame Clock value is high. Otherwise it is low.
When the Frame Clock value is low, the Y-Galvo mirror is re adjusted to the top of the frame. This is what we refer to as Flyback.
Useful ScanImage Links: