Icon

This documentation is for a legacy ScanImage version. The current documentation is ScanImage 2019.

Skip to end of metadata
Go to start of metadata

Primary Acquisition System

The primary acquisition system is the minimum hardware required to for raster image scanning.

It consists of a PXIe chassis which is connected to a PC via a PCI Express card.  The PXIe chassis has at least two cards installed:

For Thorlabs systems, see Thorlabs Scope Wiring below

For all other systems, connect according to the schematic at right:

  • Connect lines from PMT amplifiers to the analog inputs on the digitizer module.
  • Connect the resonant mirror's Period Trigger to PFI0 on the breakout for the scan control DAQ.
  • Connect the control line for the X Zoom to AO0 on the breakout for the scan control DAQ.
  • Connect the control line for the Y Mirror to AO1 on the breakout for the scan control DAQ.
  • Connect any necessary Acquisition Triggers (Start, Next, Loop) to PFI1-4.  These connections are configured using the Triggers Control.
  • Connect the shutter control line to PFI12.
Contents

Icon

The device and terminal for many signals may be set in the Machine Data File. Acquisition Triggers are configured in the Trigger Controls.

Primary Acquisition System


 

Beams

The Beams subsystem requires its own DAQ module.  There are two supported configurations.

For both:

  • connect calibration inputs to the desired analog input terminals.  
  • connect control lines to the desired analog outputs.

PXI-based

The relevant timing signals are communicated through the PXI backplane; no extra wiring is needed.

PCIe-based

Connect PFI5 of the scan control DAQ breakout box to the PFI terminal on the Beam DAQ board configured in the Beams section of the Machine Data File (see the beamModifiedLineClockIn property).

Example (PCIe-based):
Icon

Please review the article Wiring ScanImage analog input terminals if you are using a NI screw terminal (SCB-68(A) or USB DAQ device) as the breakout box for the beams board.

Beams: Using PXI based DAQ

Beams: Using PCIe based DAQ


 

Fast Z

The Fast Z subsystem requires its own DAQ module.  There are two supported configurations.

For both: 

  • connect the control line to the desired analog output.

PXI-based

The relevant timing signals are communicated through the PXI backplane; no extra wiring is needed.

PCIe-based

Connect PFI6 of the scan control DAQ breakout box to the PFI terminal on the FastZ DAQ board configured in Fast Z section of the Machine Data File (see the frameClockIn property).

Example (PCIe-based):
Icon

Please review the article Wiring ScanImage analog input terminals if you are using a NI screw terminal (SCB-68(A) or USB DAQ device) as the breakout box for the FastZ board.

 

 

 

Fast Z: Using a PXI based DAQ

Fast Z: Using a PCIe based DAQ


 

Signals Summary

Timing Signals  (DigitalIODevice)

Digital Inputs (to DigitalIODeviceName)

SignalDescriptionDAQ Terminal
Period TriggerProvided by resonant mirror driver as critical synchronization signal used for image formation.PFI 0
Start TriggerStarts an acquisition of N frames (within 1 sample period). See Acquisition Triggers.Specifed in Triggers
Next File TriggerStarts a new file within an ongoing acquisition without any gap in data
(new file begins at start of next frame or volume). See Acquisition Triggers.
Specifed in Triggers 
Stop TriggerStops an ongoing acquisition, arming ScanImage for the next Start Trigger. See Acquisition Triggers.Specifed in Triggers 

Digital Outputs (from DigitalIODeviceName)

SignalDescription

DAQ Terminal

Beam Clock

Waveform generated that is HI during the active acquisition time for each line.
Signal is HI for additional time to allow for beam device (e.g. Pockels cell) settling time.

Useful as a 'line active' clock signal for external experiment devices.

PFI 5

Frame Clock

Pulses generated at the start of each frame.

Useful as a 'frame active' clock signal for external experiment devices.

PFI 6
Acq Trigger

Pulses generated when an acquisition starts.

Useful as an exported signal, for ScanImage self-triggered acquisitions.

PFI 7
ShutterA TTL level that opens/closes an external shutter in the beam's pathPFI 12

Analog Inputs

SignalDescription
Channels 1-4Voltage inputs used for imaging, typically from the PMTs.
BeamsVoltage from a photodiode reporting the transmission through a Pockels cell. For calibration. Each Pockels cell requires an analog input channel.

Analog Outputs

SignalDescription
X ZoomControl voltage specifying the scan amplitude of the resonant mirror.
Y MirrorControl voltage specifying the deflection of the Y mirror.
BeamsControl voltage specifying for controlling a Pockels cell. Each Pockels cell requires one analog output channel.
Fast ZControl voltage specifying the deflection of an objective positioner used for fast volume imaging.

 

Thorlabs Scope Wiring 

Steps to integrate a Thorlabs ECU1 or ECU2 (BScope 2) into a ScanImage 5 system:

  1. Wire the Thor ECU and the ScanImage 5 system. Use the image below as a guide. Items in black apply to both ECU1 and ECU2/BScope 2 while items in red apply only to the ECU2/BScope 2.
    • Loop the ECU's line clock output terminal back to the ECU's line clock input terminal
    • Connect the Thor ECU to the scanner system
      • For ECU1, connect the single DVI connector to the resonant/galvo scanner assembly
      • For ECU2/BScope 2, connect all cables for PMT and scanner controls. There will be a 25 pin D-sub for each of the two parallel scan paths and two round cables for each PMT
    • If using a BScope 2, connect the MCM5000 controller. For each stage axis (X, Y, fine Z, coarse Z, rotation) there will be two D-sub cables, one for the motor and one for the encoder. There will also be three round mirror control cables
    • Connect the 68pin DAQ connector to the scanner control DAQ board of the ScanImage 5 system
    • Connect the ECU's USB cable to the ScanImage 5 PC. Windows will automatically download the drivers (requires an Internet connection) and register a USB serial port.
    • If using a BScope 2, also connect the USB cable to the MCM5000 controller. An unknown device should appear in the device manager. Use device manager to update the device driver and choose the option to manually select driver location. Locate the BScope_ControlV3 driver package from Thorlabs. After installing, a second USB serial port should appear in the device manager.
       
     
  2. Start ScanImage 5 and create a new machine data file.
     
  3. As sections are added to the machine data file, modify them appropriately, save the file, then click ok at the prompt. Use the following settings under the specified headings. Populate the rest of the machine data file according to your acquisition hardware setup.

    1. %% ScanImage
      • scannerHardwareType: 'ecu1' or 'bscope' depending on your hardware
      • primaryPxiChassisNum: Number of the PXI chassis with the FPGA and DAQ boards. This can be found in NI MAX.
      • digitalIODeviceName: The name of the DAQ device where triggers are wired. Since the scanner control DAQ board is wired directly to the Thorlabs ECU, another board must be used. This can be found in NI MAX. (ex: 'PXI1Slot4')

    2. %% ResonantAcq
      • pathToBitfile: Appropriate FPGA bitfile for your FPGA/digitizer combination.
      • rioDeviceID: FPGA device name. This can be found in NI MAX. (ex: 'RIO0')
         
    3. %% ResScanCtrl
      • scanCtrlDeviceName: Name of the DAQ device where Thorlabs ECU is plugged in. This can be found in NI MAX. (ex: 'PXI1Slot3')
      • resonantZoomAOChanID = 0;
      • galvoAOChanID = 1;
      • chanCtrMeasResPeriod = 0;

      • galvoVoltsPerOpticalDegree = 1.0;

      • rScanVoltsPerOpticalDegree = 0.33;
      • refAngularRange = 15;
      • resonantScannerSettleTime = 0;
         
    4. %% Thor ECU1 (this section only appears is you chose 'ecu1' in the %% ScanImage section)
      • comPort: Numeric ID of COM port (ie "1" for COM1) of USB to serial adapter that installs when USB cord was plugged in. Use the device manager to determine this.
         
    5. %% Thor BScope (this section only appears is you chose 'bscope' in the %% ScanImage section)
      • ecu2ComPort: Numeric ID of COM port (ie "1" for COM1) of USB to serial adapter that installs when USB cord was plugged in from ECU. Use the device manager to determine this.
      • mcm5000ComPort: Numeric ID of COM port (ie "1" for COM1) of USB to serial adapter that installs when USB cord was plugged in from MCM5000 controller. Use the device manager to determine this.
      • hasRotation: Set to true if your BScope stage controller includes the rotation axis. Otherwise set to false.
      • acqStatusUpdateInterval: Rate at which PMT statuses are polled during an ongoing acquisition. Change if the default value causes performance issues.