Imaging Systems

There are four scan systems available in ScanImage, shown below. An Imaging System can be defined as a collection of previously configured devices whose optical, hardware, and software configuration allow them to be used synchronously for the purpose of imaging.

../_images/ImagingSystems.png

vDAQ Scan System

This is either a Resonant Galvo Galvo (RGG), Resonant Galvo (RG), or Galvo Galvo (GG) Scan System configured with the vDAQ.

NI Resonant Scan System

This is an Resonant Galvo Galvo or Resonant Galvo scan system configured with NI DAQs

NI Linear Scan System

This is a Galvo Galvo system configured with NI DAQs

SLM Scan System

This is a SLM imaging system configured with either vDAQ or NI DAQs

Scanner Configurations will henceforth be denoted by their acronyms - RGG, RG, and GG.

Note

See the Scanner Configurations for a description and visual depiction of each scanning configuration’s technique for scanning Multiple Regions of Interest

vDAQ Scan System

This is either an RGG, RG, or GG Scan System configured with the vDAQ.

Once devices are configured, they can be incorporated into the scan system via navigating to the ScanImage tab and selecting the add +Add Imaging System+ button. Select the Add button under the vDAQ Scan System column. Add a name and continue.

This will take you to the vDAQ Scan System configuration page, shown below.

../_images/vDAQScanSystemConfig.png

DAQ board

Select the vDAQ board for acquisition / device control.

Resonant Scanner

Select the previously configured Resonant Scanner to be associated with this system

X-Galvo (optional)

Select the previously configured Galvo Scanner to be associated with this system’s (fast axis) X-Galvo

Y-Galvo

Select the previously configured Galvo Scanner to be associated with this system’s (slow axis) Y-Galvo

Shutter

Select the previously configured Shutter(s) to be associated with this system

Note: selected shutters will automatically open when an acquisition is started

Beam

Select the previously configured Beam Modulator device(s) to be associated with this system

Note: selected modulators will automatically be activated when an acquisition is started

FastZ

Select the previously configured Fast Focus device to be associated with this system

Note: the selected FastZ device will be used for fast z-stacks.

Channel Invert

Select the Invert checkbox if the input signal for that Channel is inverted (e.g. more negative for increased light signal).

../_images/vDAQScanSystemTriggers.png

Aux trigger 1

Select a DAQ/Port to associate with Aux Trigger 1

Aux trigger 2

Select a DAQ/Port to associate with Aux Trigger 2

Aux trigger 3

Select a DAQ/Port to associate with Aux Trigger 3

Aux trigger 4

Select a DAQ/Port to associate with Aux Trigger 4

Frame clock out

Select a port for outputting the frame clock

The frame clock signals the end of a frame

Line clock out

Select a port for outputting the line clock

The line clock signals the end of a line

Volume clock out

Select a port for outputting the volume clock

The volume clock signals the end of a stack.

../_images/vDAQScanSystemAdv.png

Keep resonant scanner on

Enabling will keep the resonant scanner on once the imaging system is selected from the Configuration Controls window

Tip

After enabling a resonant mirror motor, it slowly warms up. This can result in a slow drift of the resonant frequency over time. Keeping the resonant scanner on allows the motor to reach a thermal equilibrium, which achieves a more stable frequency.

Reverse line read

Flip the image horizontally

Extended RGG FOV

Enables the Resonant mirror and X-Galvo to use their full range of motion for an extended FOV

NI Resonant Scan System

This is either an RGG or RG Scan System configured with NI DAQs.

Once devices are configured, they can be incorporated into the scan system via navigating to the ScanImage tab and selecting the add +Add Imaging System+ button. Select the Add button under the NI Resonant Scan System column. Add a name and continue.

This will take you to the NI Resonant Scan System configuration page, shown below.

../_images/NIRScanSystemBasic.png

Acquisition board

The FPGA/Digitizer combination that will be used for Acquiring fluorescence from the PMTs

Digital I/O board

Select the Auxiliary DAQ board where triggers or other digital signals should be configured

Resonant Scanner

Select the previously configured Resonant Scanner to be associated with this system

X-Galvo

Select the previously configured Galvo Scanner to be associated with this system’s (fast axis) X-Galvo

Y-Galvo

Select the previously configured Galvo Scanner to be associated with this system’s (slow axis) Y-Galvo * - Linear scanner (optional)

Shutter

Select the previously configured Shutter to be associated with this system

Beam

Select the previously configured Beam Modulator device to be associated with this system

FastZ

Select the previously configured Fast Focus device to be associated with this system

Channel Invert

Select the Invert checkbox if the input signal for that Channel is inverted (e.g. more negative for increased light signal).

../_images/NIRScanSystemAdv.png

Laser Trigger In

Select the DI port where the laser trigger signal is connected

Enable AUX triggers

Check to enable AUX triggers that are enabled in the Machine Data File

Keep resonant scanner on

Enabling will keep the resonant scanner on once the imaging system is selected from the Configuration Controls window

Tip

Keeping the resonant scanner on will allow it to achieve a steady state of operation. This prevents variation in the command voltage to mirror amplitude calibration, which is beneficial to experiments where imaging occurs over a long duration

Reverse line read

Flip the image horizontally

Extended RGG FOV

Enables the Resonant mirror and X-Galvo to use their full range of motion for an extended FOV

NI Linear Scan System

This is a GG Scan System configured with NI DAQs.

Once devices are configured, they can be incorporated into the scan system via navigating to the ScanImage tab and selecting the add +Add Imaging System+ button. Select the Add button under the NI Resonant Scan System column. Add a name and continue.

This will take you to the NI Resonant Scan System configuration page, shown below.

../_images/NILScanSystemBasic.png

Acquisition board

The X-Series or FPGA/Digitizer combination that will be used for Acquiring fluorescence from the PMTs.

Note

Legacy S-Series ni boards PCI-6110 and PCI-6115 are also supported for linear scanning

Digital I/O board

Select the Auxiliary DAQ board where triggers or other digital signals should be configured

Resonant Scanner

Select the previously configured Resonant Scanner to be associated with this system

X-Galvo

Select the previously configured Galvo Scanner to be associated with this system’s (fast axis) X-Galvo

Y-Galvo

Select the previously configured Galvo Scanner to be associated with this system’s (slow axis) Y-Galvo * - Linear scanner (optional)

Shutter

Select the previously configured Shutter to be associated with this system

Beam

Select the previously configured Beam Modulator device to be associated with this system

FastZ

Select the previously configured Fast Focus device to be associated with this system

Channel Invert

Select the Invert checkbox if the input signal for that Channel is inverted (e.g. more negative for increased light signal).

../_images/NILScanSystemAdv.png

Enable Striping

Place a check in the box to enable a striping display

Max striping rate [Hz]

The maximum rate at which the stripes are acquired. The higher this is, the thinner the stripes being updated.

Max display rate

The maximum frame rate for displaying on the monitor (regardless of whether striping is enabled)

Laser Trigger In

Select the DI port where the laser trigger signal is connected

SLM Scan System

This is a Scan System utilizing an SLM to control the illumination of ROIs.

Once finished configuring an SLM device, The SLM can be incorporated into an imaging system via the ScanImage tab and selecting the add +Add Imaging System+ button. For a system with an SLM, select the Add button under the SLM Scan System column. Add a name and continue.

../_images/SLMImagingSystem.png

This will take you to the SLM Scan System configuration page, shown below.

../_images/HDMISLMImageSystemBasic.png ../_images/HDMISLMImageSystemAdv.png

DAQ board

Select the Auxiliary DAQ board where triggers or other signals should be configured

SLM medium refractive index

The refractive index of the medium before the SLM array

SLM

Select the SLM device that was configured from the Devices tab

Objective medium refractive index

Refractive index of the medium within the objective lens

Linear scanner (optional)

Select a previously configured Linear Scan System to be used with the SLM.

Note

this assumes the Linear Scan System is downstream of the SLM in the beam path.

Zero order block radius [mm]

The radius of the opaque medium used to block the zero order center of the focal plane.

Focal length [mm]

Enter the intended focal length to operate this SLM in your system

Shutter

Select the shutter in the SLM beam path

Beam

Select the Beam Modulator to be used with the SLM

Channel

Select the Invert checkbox if the input signal for that Channel is inverted (e.g. more negative for increased light signal).