ScanImage 2018 : Configuring ResScan (Resonant Scanning)

Created by Georg Jaindl on May 26, 2017
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To use the ResScan Imaging System it must be defined as a Scanning System in the General ScanImage Settings section of the ScanImage Machine Configuration Editor.

The ScanImage Machine Configuration Editor can be accessed by selecting the Machine Configuration... option in the File Menu on the Main Controls panel.

 

 

ResScan Acquisition System

The ResScan acquisition system is the minimum hardware required 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 an analog output on the breakout for the scan control DAQ.
  • Connect the control line for the Y Mirror to an analog output on the breakout for the scan control DAQ.
  • Connect any necessary Acquisition Triggering (Start, Next, Loop) to PFI1-4.  These connections are configured using the Triggers Contol.
  • To configure a Shutter for ResScan, review the article Shutter Configuration

 


 

ResScan 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.

The settings for the routing of triggers are accessed in the Power Modulation (Beams) section of the ScanImage Machine Configuration Editor.

In this case, select "PFI0" for the Line Clock Input Terminal:

 

 

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The Pockels Cell (Beams) control task is a timed Daqmx Task. Due to Daqmx limitations on timing resources this requires the Pockels Cell to run on a Daq card by itself. Other timed tasks such as Galvo control or FastZ piezo control must run on separate Daq boards.

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.

The settings for the automatic routing of the frame clock trigger for Fast Z is accessed in the FastZ Actuator Setup section of the ScanImage Machine Configuration Editor.

In this case, select "PFI0" for the Frame Clock Input Terminal:

 

 

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The FastZ Piezo control task is a timed Daqmx Task. Due to Daqmx limitations on timing resources this requires the FastZ Piezo to run on a Daq card by itself. Other timed tasks such as Galvo control or Pockels Cell control control must run on separate Daq boards.

 

 

 

Fast Z: Using a PXI based DAQ

Fast Z: Using a PCIe based DAQ

 

Signals Summary

Timing Signals  (DigitalIODevice)

Inputs (to DigitalIODeviceName)

SignalDescriptionDAQ Terminal
Period TriggerProvided by resonant mirror driver as critical synchronization signal used for image formation.PFI 0
Start TriggerA TTL transition will cause a running Acquisition Mode to start it's first Acquisition.Specifed in Triggers
Next File TriggerA TTL transition will cause a LOOP to start the next Acquisition.Specifed in Triggers 
Stop TriggerA TTL transition will cause a running Acquisition to end.Specifed in Triggers 

Outputs (from DigitalIODeviceName)

SignalDescription

DAQ Terminal

Beam ClockA TTL pulse generated on each line that controls when waveforms driving the Pockels cells begin.PFI 5

Frame Clock

A TTL pulse generated at the start of each frame.PFI 6
Acq Trigger

A TTL pulse generated when an acquisition starts. Useful for responding to software-triggered acquisitions.

PFI 7

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 2016 system:

Wire the Thor ECU and ScanImage 2016 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 2016 system
  • Connect the ECU's USB cable to the ScanImage 2016 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.

       

 

Start ScanImage

Start ScanImage 2016 and select the option to create a new machine data file.

Configure ScanImage

The ScanImage Machine Configuration Editor will be started. Beginning with the General ScanImage Settings section, enter settings information appropriately.  
As sections are configured, modify them appropriately then press Next. When the Additional Components section is reached, you can press Finish or Finish and Run ScanImage to save configured information to the given machine data file.
Machine configuration can be updated at a later time by selecting the Machine Configuration... option on the File Menu on the Main Controls panel.

Integrate ThorLabs ECU and/or BScope 2 into ScanImage

To configure ThorLabs ECU and/or BScope 2, they must first be added within the ScanImage Machine Configuration Editor.

In the General ScanImage Settings section, add "Thorlabs ECU 1" and/or "Thorlabs B-Scope 2" to the Additional Components and PlugIns table, depending on your hardware.

The ScanImage Machine Configuration Editor will add settings sections, accordingl
A  Thorlabs ECU Scanner Settings section is added if "Thorlabs ECU 1" is selected as an additional component; and a ThorLabs BScope2 Setup section is added if "Thorlabs B-Scope 2" is selected as an additional component.

 

Configure Thorlabs ECU Scanner

Select the ThorLabs ECU Scanner section In the ScanImage Machine Configuration Editor.

 

Select the resonant scanning system you defined in the General ScanImage Settings section. Only scanners that have a "Resonant" Scanner Type are available in the Scanner Name dropdown list.

Recap:

 

Select the ECU COM Port of USB to serial adapter that installs when USB cord was plugged in. Use the device manager to determine this.

 

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The Digital I/O device where triggers are wired is configured in the Resonant Scanning system section.

Since the scanner control DAQ board is wired directly to the Thorlabs ECU, a separate board must be used. This can be found in NI MAX. (ex: 'PXI1Slot3').

 

Configure Thorlabs B-Scope 2

Select the ThorLabs BScope2 Setup section In the ScanImage Machine Configuration Editor. 


 


Select the resonant scanning system you defined in the General ScanImage Settings section. Only scanners that have a "Resonant" Scanner Type are available in the Scanner Name dropdown list.

Recap:

 

Select the appropriate COM Ports for ECU, Galvo-Galvo Flipper mirror, Resonant-Galvo Flipper mirror, and Camera PMT Flipper mirror.

 

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Select the ECU COM Port of USB to serial adapter that installs when USB cord was plugged in. Use the device manager to determine this.

 

See ThorLabs BScope2 Settings for additional setup information.

 

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The FlexRIO Device is configured in the Resonant Scanning system settings section.

The available selections in the  Signal Acquisition DAQ dropdown list are obtained from configured devices in NI MAX.

 

Configure Resonant Scanning System

Select the Scanner Settings section for the defined Resonant scanning system, In the ScanImage Machine Configuration Editor. The defined scanning system will appear in the section name.

Enter the additional Resonant and Galvo mirror configuration.

 

Resonant Mirror settings

Select the name of the DAQ device where Thorlabs ECU is plugged in (found in NI MAX. (ex: 'PXI1Slot3')) in the Zoom Control DAQ.

Defaults are provided by the system. Change default entries as needed.

 

Galvo Mirror settings

Defaults are provided by the system. Change default entries as needed.

 

 



 

 

Attachments:

wiringFastZPCIe.png (image/png)
wiringBeamsPCIe.png (image/png)
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