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Excerpt

Composition Setup

...

ScanImage 
...
 utilizes 
...
 various 
...
 data 
...
 acquisitions 
...
subsystems
...
 (each 
...
 bank 
...
 of 
...
 Analog 
...
 Input 
...
 and 
...
 Output 
...
 channels 
...
 per 
...
 board 
...
 comprises 
...
 a 
...
 subsystem) 
...
 during 
...
 its 
...
 operation. 
...
 The 
...
 start 
...
 time(s) 
...
 of 
...
 the 
...
 data 
...
 streams 
...
 on 
...
 each 
...
 of 
...
 these 
...
 subsystems 
...
 must 
...
 be 
...
 synchronized 
...
 for 
...
 each 
...
 acquisition. 
...
 This 
...
 requires 
...
 that 
...
 each 
...
 of 
...
 the 
...
 subsystems 
...
 'listen' 
...
 for 
...
 a 
...
 common 
...
Start 
...
 Trigger
...
 signal 
...
 (i.e. 
...
 a 
...
 digital 
...
 rising/falling 
...
 edge) 
...
 which 
...
 initiates 
...
 the 
...
 acquisition/generation. 
...
To 
...
 accomplish 
...
 this, 
...
 ScanImage 
...
 identifies 
...
 a 
...
National 
...
 Instruments
...
 'programmable 
...
 function 
...
 interface' 
...
 (PFI) 
...
 terminal 
...
 (e.g. 
...
 PFI0, 
...
 PFI1, 
...
 etc) 
...
 which 
...
 can 
...
 serve 
...
 as 
...
 a 
...
 'listener' 
...
 for 
...
 a 
...
Start 
...
 Trigger
...
 input 
...
 signal. 
...

 (info) Note that all subsystems on each board use the same physical PFI terminal as their trigger input source. 
 (info) Note that all boards used by ScanImage must use the same PFI terminal number value for a particular acquisition (i.e., 
...
 if 
...
 PFI0 
...
 is 
...
 used, 
...
 it 
...
 must 
...
 be 
...
 used/connected 
...
 on 
...
 all 
...
 boards).
...
Start 
...
 Triggering 
...
 Modes
...
Every 
...
 ScanImage 
...
 acquisition 
...
 requires 
...
 a 
...
Start 
...
 Trigger
...
 – this 
...
 can 
...
 be 
...
 either 
...
Internal
...
 or 
...
External
...
.
...
 Panel
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Internal Start Triggering (REQUIRED)
The 'Internal' start triggering mode is the default. In this mode, ScanImage itself generates a single Start Trigger signal that serves as the trigger source for acquisitions. 
  • This rising-edge Start Trigger output signal is generated by ScanImage on the digital output line specified by the and values in the INI file.
     (info) Port 0 is assumed, i.e. line X implies the digital output P0.X
  • The INI value specifies the input PFI terminal on which to receive the 'Internal' Start Trigger, typically PFI0. This input terminal, on all boards, must be connected to the Start Trigger output generated by ScanImage.
External Start Triggering (OPTIONAL)
ScanImage also allows an external trigger source to be used, allowing ScanImage to be 'slaved' to external software, such as that for electrophysiology, sensory stimulation, or behavioral control/monitoring.
  • The toggle control on the Main Controls is used to specify that ScanImage should 'listen' for an external, rather than the default 'internal' trigger source.
     (info) The setting only applies for GRAB and LOOP acquisitions - excluding Image Stack acquisitions. Otherwise, it is ignored and 'internal' triggering is used.
  • The value specified on the Triggers panel specifies the input PFI terminal number on which to receive the 'Internal' Start Trigger. This input PFI terminal, on all boards, must be connected to the Start Trigger output generated by ScanImage.
Trigger Time Logging
The time at which the Start Trigger arrives, initiating an acquisition, is stored as part of the image file header, to aid with analysis, e.g. for aligning image data to separately obtained physiology/stimulus/behavior data. The following header fields are stored: