ScanImage 2016 : Configuration Controls


Imaging System

Active Imaging System

Select a scanning system to use for imaging from the systems that have been configured in the Machine Data File

AlignmentOpens the ALIGNMENT CONTROLS panel that can be used to align parallel scanning systems

Acquisition Parameters

Keep resonant scanner on

When selected, the resonant scanner is kept on even when not actively imaging


This option is only available if the currently selected imaging system is a resonant scanner. Using this option can help avoid drift over time in the resonant frequency which can lead to drifting phase.

Bidirectional Scan

Enables two way scanning (ie data is acquired when the X scan mirror is traveling in both directions). Bidirectional scanning will increase the frame rate, while unidirectional scanning can produce higher quality images by avoiding the interlace effect from the phase being slightly incorrect.


Even when using unidirectional scanning it is important to have the scan phase properly adjusted to avoid image distortion. Use bidirectional scanning first to get the phase correct then switch over to unidirectional scanning.

Pixels Per Line

Imaging resolution in the fast scan mirror (X) dimension. Only applies in non multiple-ROI imaging

Lines Per Frame

Imaging resolution in the slow scan mirror (Y) dimension. Only applies in non multiple-ROI imaging


Apply square pixelation constraint: if selected, the values of Pixels/Line and Lines/Frame are constrained to be equal, e.g 512x512, 256x256, etc.

(info) The Lines/Frame control is disabled (slaved to Pixels/Line) when this option is enabled

Square Pix

Apply square pixel constraint: if selected, the value of Scan Angle Multiplier Slow on the Main Controls is constrained to match the fraction (Lines/Frame)/(Pixels/Line).

(info) Without this constraint, individual pixels may have rectangular aspect ratio.

Frame Rate (Measure)

Rate in which frames are acquired.


For resonant scanning the frame rate is affected by the resonant mirror scanning frequency. This can be measured using the "measure" button.

Scan Phase AdjustmentAdjusts the timing between acquisition of forward and reverse lines for bidirectional scanning. If bidirectional scanning is on the Auto Adjust button can be used to find the correct scan phase by image analysis
Pixel Dwell Time/ Line Rate/
Line Period
Display/control for scanning rate. For resonant scanning this is a display only, as the scanner rate is fixed. For linear scanning, this value can be changed. The scanning rate is set by a combination of the sampling rate and pixel bin factor.

Advanced Timing Controls Panel 

Fill Fraction (Temporal/Spatial)

Sets the fraction of the scanned area in the fast mirror (X) dimension where image acquisition occurs


For resonant scanning since the velocity profile of the resonant mirror is sinusoidal, the temporal and spacial fill fractions are different. For linear scanning they are the same.

Pixel Time (Mean)Mean acquisition time, in ns, for each pixel.
Pixel Time (Max/Min)

Ratio of pixel dwell time at outer pixel (max) to center pixel (min) of each scanned line

Resonant Scanning: Ratio is positive, as dwell time for sinusoidal scan trajectory is greater towards the field edges compared to the center

Linear Scanning: Ratio is always one (1) - the pixel dwell time is uniform across the scanned line

Line PeriodTime interval between the start of each line in the frame
Pixel Bin Factor

The numer of ADC samples that are averaged into one pixel.


For resonant scanning, due to the sinusoidal scan trajectory each pixel is slightly different; this field is non editable and will just show NaN

 Sampling Rate

 Sets the rate that ADC samples are collected


For resonant scanning, this is set by the FPGA and cannot be changed. If synchronization with an external clock is enabled, this will show the actual clock rate

 Frame FlybackThe time to allow for the slow scan mirror (Y) to travel from the end position back to the start position at the end of a frame
 Frame FlytoFor multiple ROI imaging, the time to allow for the scanner to transition from the end position of one ROI to the start position of another 

Line Scan Controls

Scan Type

If the currently selected scanning system is a linear scanner, this control appears to switch between traditional frame scanning and arbitrary line scanning.

Monitor Scanner FeedbackWhen enabled, displays (and records to disk if data logging is on) the actual scanner path during arbitrary line scanning
Calibrate Feedback SensorsCalibrated the position feedback sensor for line scanning. This must be done once for position feedback to work


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