Scan2D Subclasses

Scan2D: Imaging Systems documents the contract every imaging system honors. This page covers what each concrete subclass adds - the properties you need once you know which scanner you are actually driving.

Class	scannerType	Hardware
ResScan	varies	Resonant plus galvo, on National Instruments hardware.
LinScan	'GG'	Galvo-galvo, on National Instruments hardware.
RggScan	varies	Resonant-galvo-galvo on the vDAQ. Switches between resonant, linear and stage scanning modes.
SlmScan	'SLM'	Spatial light modulator, usually paired with a linear scanner.

class(hSI.hScan2D)
hSI.hScan2D.scannerType
hSI.hScan2D.hasResonantMirror
hSI.hScan2D.hasXGalvo

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RggScan

The vDAQ scanner, and the one most current systems use. Its distinguishing feature is scanMode: one physical scanner is driven as a resonant, a linear or a stage scanning system, and ScanImage caches the mode-specific settings so switching between them does not lose your configuration.

Property	Description
scanMode	'resonant', 'linear' or 'stage'. Setting it asserts that the scanner can do it: 'resonant' requires hasResonantMirror, 'linear' requires hasXGalvo, and 'stage' requires the XY motors to be Zaber devices that support streamed moves - selecting it sets isStreamScanning.
scanModePropCache	The per-mode cache. Leaving a mode stores that mode’s properties; returning to it restores them. Linear mode caches sampleRate, pixelBinFactor, fillFractionSpatial, bidirectional, stripingEnable, tfSinusoidalX and linePhase; resonant and stage modes cache the same list with uniformSampling in place of sampleRate and linePhase.
sampleRate	Digitizer rate. Settable only in linear mode; in resonant mode it is fixed by the hardware.
sampleRateCtl, desiredSampleRateCtl	Control (mirror output) sample rate, actual and requested.
sampleRateFdbk	Feedback recording rate.
pixelBinFactor	Samples per pixel, applied in linear mode or when uniformSampling is on.
uniformSampling	When true, every pixel is formed from the same number of samples, so the resonant scanner’s non-uniform velocity across the field is not corrected.
mask	The resonant scan mask - samples binned per pixel along a line.
keepResonantScannerOn	Leave the resonant scanner running between acquisitions, avoiding settle time and temperature drift.
linePhaseMode	How line phase is estimated when it has not been measured at the current amplitude. Default 'Nearest Neighbor'.
xActuatorLag_ms, yActuatorLag_ms	Per-axis actuator lag compensation.
stripingPeriod	Display striping period, in seconds.
recordScannerFeedback	Record galvo position feedback to disk.
acquisitionEngineIdx	Which vDAQ acquisition engine to use.
logAverageDisableDivide	Skip the divide when averaging logged frames.
channelOffsets	Dark counts subtracted per channel.
isStreamScanning	True when the Y galvo is currently acting as a motor.
hVCAM	Attached VCAM, if configured.
lineScanSamplesPerFrame, lineScanFdbkSamplesPerFrame, lineScanNumFdbkChannels	Read-only sample counts for arbitrary line scanning.

RggScan also implements scanimage.components.scan2d.interfaces.SignalConditioning, which is where the laser-trigger and signal-conditioning settings live.

See also

Stage Scanning for scanMode = 'stage'.

hSI.hScan2D.scanMode = 'linear';       % settings for resonant mode are cached
hSI.hScan2D.sampleRate = 1.25e6;       % now settable
hSI.hScan2D.scanMode = 'resonant';     % resonant settings come back

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ResScan

The National Instruments resonant scanner.

Property	Description
scanMode	'resonant'.
sampleRate	Read-only; fixed by the digitizer.
pixelBinFactor	Default 50. Applies when uniformSampling is true.
uniformSampling	As for RggScan.
maskDisableAveraging	Per-channel: disable sample averaging within a pixel.
keepResonantScannerOn, linePhaseMode	As for RggScan.
channelsInvert	Invert the sign of the acquired channels.
externalSampleClock, externalSampleClockRate	Clock the digitizer externally. Default rate 80 MHz.
auxTriggersEnable	Enable the auxiliary trigger inputs.
laserTriggerPort	Terminal carrying the laser trigger.
laserTriggerSampleMaskEnable, laserTriggerSampleWindow, laserTriggerDebounceTicks	Laser-gated sampling, for low repetition rate sources.
xActuatorLag_ms, yActuatorLag_ms	Actuator lag compensation.

See also

Acquisition Gating for low rep rate Lasers for the laser trigger settings in context.

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LinScan

The National Instruments galvo-galvo scanner. hasXGalvo is true and hasResonantMirror is false.

Property	Description
scanMode	'linear'.
sampleRate	Digitizer and mirror control rate. Default 1.25 MHz, and settable.
sampleRateCtl	XY galvo control task rate.
pixelBinFactor	Default 4.
recordScannerFeedback	For line scanning, record galvo position feedback to disk.
sampleRateFdbk	Feedback recording rate. Default 50 kHz.
maskDisableAveraging	Disable sample averaging within a pixel.
stripingMaxRate, maxDisplayRate	Display rate limits, in Hz.
startTriggerTermOut, lineClockTermOut, pixelClockTermOut	Terminals the clocks and start trigger are exported on.
laserTriggerPort, laserTriggerSampleMaskEnable, laserTriggerSampleWindow, laserTriggerDebounceTicks	Laser-gated sampling.
hDAQAcq, hDAQAux	The acquisition and auxiliary DAQ boards.

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SlmScan

SLM-based scanning. It reports hasXGalvo and hasResonantMirror as false, and pairs with a linear scanner for beam positioning.

Property	Description
scanMode	'slm'.
wavelength	Excitation wavelength in meters. Default 635 nm.
isPointHolography	Point holography mode.
galvoReferenceAngleXY	XY reference angle of the paired galvos - the zero point for the SLM.
slmRefreshRate	Rate at which the SLM is repointed between samples. Clamped to the device’s maxRefreshRate.
sampleRate	Read-only digitizer rate. Note this is not the SLM repointing rate; that is slmRefreshRate.
pixelDwellTime	Data-scope acquisition window per SLM pixel. On the laser-gated path the number of pulses averaged per pixel is roughly pixelDwellTime * laserRepRate.
imagingDepth	Z of the plane the SLM scans, in reference-space microns - the SLM defocus from the objective focal plane. Independent of parkPosition_um.
parkPosition_um	Park position, in microns.
zeroOrderBlockMask	256 x 256 single mask blocking the zero order beam. 0 unblocked, 1 blocked.
applyDiffractionEfficiencyToPower	Scale per-pixel beam power by 1/diffractionEfficiency to flatten excitation across the field, clamped to each beam’s power limit.
wavefrontCorrectionNominal, wavefrontCorrectionNominalWavelength_um	Wavefront correction for the current wavelength, and the wavelength it was measured at.
lut	The SLM lookup table.
acquisitionEngineIdx	vDAQ acquisition engine index.

Warning

applyDiffractionEfficiencyToPower must be false while acquiring data for a diffraction efficiency calibration - otherwise the calibration measures its own correction.

See also

SLM Optogenetics, and the SLM branch of the coordinate system tree in ScanImage Coordinate System Instances.

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DataScope

hSI.hScan2D.hDataScope gives access to raw digitizer samples, below the image formation layer. It is the tool for checking what the PMT signal actually looks like - pulse shapes, baseline, saturation - rather than what the image looks like after binning.

Property	Description
trigger	One of triggerAvailable: 'none', 'frame', 'slice', 'line'.
triggerLineNumber, triggerSliceNumber	Which line or slice to trigger on.
triggerHoldOffTime	Delay after the trigger, in seconds.
channel	Channel to acquire.
acquireAllChannels	Medium-speed mode only. Return [nSamples x numChannels] for every physical channel instead of just channel.
applyChannelSign	When false, samples come back raw, without the per-channel invert sign.
inputRange	Input range, in volts.
acquisitionTime	Seconds to acquire. Default 0.1.
desiredSampleRate	Requested rate; empty uses the digitizer rate.
includeDigital, includeSyncTrigger	Include the digital lines and the sync trigger in the returned data.
callbackFcn	Called with each acquisition. Defaults to @(src,evt)plot(evt.data).
errorCallbackFcn	Called on error.
active	Read-only. True while acquiring.
channelsAvailable, digitizerSampleRate, digitizerActualSampleRate, currentDataRate	Read-only capability and rate information.

Method	Description
hDataScope.start(options)	Start a triggered acquisition.
hDataScope.startContinuousAcquisition()	Start a free-running acquisition.
hDataScope.acquire(callback)	Acquire once and hand the data to callback.
hDataScope.abort()	Stop.
info = hDataScope.mouseHoverInfo2Pix(mouseHoverInfo)	Translate a display hover position into a pixel, so the scope can be pointed at what the cursor is over.

hDS = hSI.hScan2D.hDataScope;

hDS.channel         = 1;
hDS.trigger         = 'line';
hDS.acquisitionTime = 1e-3;
hDS.callbackFcn     = @(src,evt) plot(evt.data);

hSI.startFocus();
hDS.start();
% ...
hDS.abort();

Note

The data scope is available on vDAQ-based scanners. hDataScope is empty on imaging systems that do not provide one, so check before using it.