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Three types of connections between/among DAQ Boards and the external hardware they interface with are required:

  1. Clock Synchronization is required whenever 2 (or more) boards are used by ScanImage.
  2. Triggering is required to synchronize the start of ScanImage's various input and output data streams; in addition, External Triggering can also be used to synchronize these data streams with external software.
  3. Hardware Signals must be connected between the boards' Analog Output/Input channels and the external hardware.

The Clock Synchronization connection(s) are typically made inside the computer case.

The Triggering and Hardware Signal connections are made at the breakout panel/box terminals/connectors. The Typical Wiring Diagrams illustrate these connections for typical ScanImage installations.

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ClockSync
ClockSync

Clock Synchronization

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If 2 or more boards are used by ScanImage (as is needed when using a Pockels Cell, or equivalent light modulator), it is required that the clocks of these boards be synchronized to ensure that their respective signals remain phase locked during acquisition (e.g. that Pockels flyback blanking remain phase locked with the mirror command signals).

Synchronization occurs via the terminal RTSI 7. Additionally, the digital ground (DGND) terminal for each board should also be wired together.

(info) RTSI (Real Time Synchronization Interface) connectors are present on the edge of National Instruments DAQ boards.
(info) Note that RTSI7/DGND (also referred to as RTSIOSC on older boards) are the last pair of pins, nearest to the slot cover

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titleConnect Them All

Users can also achieve clock synchronization by connecting all the RTSI pins on each of the DAQ boards by using a suitable 40-pin ribbon cable. National Instruments offers such cables as RTSI Bus Connectors. Note that the Extended Length RTSI Bus Cable should be selected as S series boards are full-length PCI boards.

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Triggering
Triggering

Triggering

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Excerpt Include
Acquisition Triggering (r3.6)
Acquisition Triggering (r3.6)
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HWSignals
HWSignals

Hardware Signals

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Physical microscope hardware used by ScanImage must be connected to appropriate National Instruments Analog and Digital Output/Input physical channels.

Core (Minimum) Hardware

At minimum, ScanImage employs:

  • X/Y Mirrors: 2 Analog Output (AO) channels for controlling an X/Y mirror pair. The INI value identifies the NI board (e.g. 'Dev1') on which both these physical AO channels reside (physical channels AO0 and AO1).
  • Image Inputs: 1-4 Analog Input (AI) input channels which receive the image input signals (e.g. amplified PMT signals reporting on measured fluorescence). Each signal is referred to as a ScanImage Channel. The INI value identifies the NI board (e.g. 'Dev1') on which all of these AI physical channels reside. The ScanImage Channels 1-4 correspond to physical channels AI0-AI3 on this board.

(info) At the present time, the and INI values must be identical, i.e. the AO/AI channels for the input signals and mirror control signals must reside on the same NI board.
(info) If the rig requires less than 4 image input channels, then the remaining AI physical channels on the board specified by can be used as photodiode input channels, as described below.

Optional Hardware

In addition, the following optional microscope hardware components must be connected (after being enabled in the INI file):

  • Pockels Cells: 1-3 AO channels to control Pockels Cells (or other light modulators). These comprise ScanImage Beams. The AO physical channels are specified by the INI variables and , where N is the Beam number (from 1-3).
  • Photodiodes: 1-3 AI channels, associated with each ScanImage Beam, to connect to photodiodes (or other light detectors) used for calibrating the Pockels/light-modulator operation. For each Beam, the INI variables and specify the (optional) photodiode input physical channel.
  • Shutter: 1 Digital Output (DO) channel to control a shutter (or other digitally controlled device) to be open during acquisition, and closed otherwise. The INI variables and specify the physical channel used. The variable specifies the digital level (0=LO;1=HI) which corresponds to the shutter being open.

(tick) The INI variable must be set to 1 for the Pockels/photodiode channel(s) to be employed by ScanImage.
(tick) The INI variable must be set to 1 for the shutter channel to be employed by ScanImage

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TypWiring
TypWiring

Typical Wiring Diagrams

Typical Terminal Block Connections

As described above, ScanImage allows a primary and optional external trigger input terminal ( and INI values, respectively) to be specified as the trigger signal 'listener'. These terminals are programmable function interface (PFI) terminals and the values apply to all boards used by ScanImage. By default terminals PFI0 and PFI1 default are used for the and , respectively.

In FOCUS mode and other scan modes by default, ScanImage generates a trigger source signal on the digital output terminal specified by the and INI values.

If the default trigger source and trigger input lines/terminals are used, the 'typical' board wiring depicted in the panels below applies:

Typical BNC Connections

With the terminal blocks wired as above, two typical wirings of the BNC connectors are shown here:

Typical Wiring Scenario 1
This scenario applies where the second board ('Dev 2') is a multifunction DAQ board from either the M or E series (e.g. PCI-6251, PCI-6259, or the PCI-6040E)

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  • [Cyan] USER1 on the first board ('Dev 1') is connected to PFI 0 on both boards. Thus all boards (and their subsystems) receive their primary trigger input signal from the same trigger signal (generated by ScanImage on P0.0 of 'Dev 1').
  • [Green] USER2 is connected on both boards to the external trigger source (if desired). Thus all boards (and their subsystems) can respond to the same external trigger signal.
  • 'Dev 2' is used for both the PMT outputs and the photodiode inputs

(tick) If 3 'beams' (Pockels Cells) are used, the NI 6259 has 2 additional AO channels which can be connected via an additional (third) breakout box, without requiring an additional board. (The NI 6259 has 2 connectors, allowing connection to 2 breakout boxes). The connections to PFI0 and USER2 (PFI 1) would not be required on the additional breakout box.

Typical Wiring Scenario 2
This scenario applies where the second board ('Dev 2') is an Analog Output (AO) board (e.g. PCI-6711 or PCI-6713 )

Center

  • Connections are the same as in Scenario 1, except that the photodiode inputs are connected to 'Dev 1'

(tick) This scenario applies when the number of PMT inputs and calibrated 'beams' (i.e. photodiode inputs) totals less than 4 – which is the number of AI inputs available on the S Series boards used for 'Dev 1'
(info) If 3 'beams' are required, a third Pockels Cell output can be connected at the ACH7 connector. However, there are typically not enough AI channels on 'Dev 1' to account for the number of PMT and photodiode inputs. Then, either the use of a third board, or Scenario 1 (with the NI 6259) is recommended.