ScanImage 2018 : Fast Z Controls

Sawtooth waveform, uniform slices (left); Step/settle waveform, arbitrary z planes (right)

Main Controls

EnableIf enabled, Fast Z Image Stack(s) are acquired on GRAB and LOOP acquisitions where #Slices > 1 for frame scanning. This also enables 3D scans for arbitrary line scanning.
Scan TypeSpecifies whether a sawtooth or stepped Z waveform should be used for Z control.
Volumes to CollectSpecifies number of FastZ Image Stacks to scan during each GRAB or LOOP Repeat. For Volume Imaging acquisitions, ScanImage collects a total of #Volumes x #Slices frames for each GRAB or LOOP Repeat.
Return Home

If enabled, FastZ motor controller returns to its Home position – the initial axial position when a GRAB or LOOP was initiated – following the GRAB acquisition or each LOOP Repeat. This ensures subsequent acquisitions or Repeats traverse the same axial positions.

 For LOOP acquisitions, this option should typically be enabled. If not enabled, successive Repeats will image progressively further along the axial direction specified, which is typically not desired.
# SlicesSpecifies number of slices (i.e. frames) to acquire during each volume period.

Specifies axial distance traversed between each successive slice (frame) during a volume period in microns


Either a positive or negative value can be specified, so motion may proceed in either axial direction

Centered Stack

If enabled, axial position at start of image stack acquisition is taken as the center of the stack. Actuator is moved backwards by half the total span implied by #Slices and Step/Slice prior to the start of the stack acquisition.


If Centered Stack is enabled and #Slices is even, then none of the frames within each volume period will be centered on the starting axial position at time of GRAB/LOOP initiation.

Specify ZsControl only appears when stepped waveform is selected. Allows manually entering desired Z planes with arbitrary spacing to image.
Z SeriesControl only appears when manual selection of Z planes is enabled. Allows entry of a space-separated or comma-separated list of z planes to image.

The #SlicesStep/SliceReturn Home, and Centered Stack controls are all linked to same controls on the MOTOR CONTROLS interface.

Volume Timing Controls

Volume Period Adjustment

Specifies amount by which to reduce length of Z actuator waveform. Value should always be negative.


For volume imaging, in order to avoid missing triggers, the duration of axial command waveform must be set slightly shorter than (N * FP) where N is #Slices and FP is the frame period. When resonant scanning, the frame period varies slightly from frame to frame due to jitter in the resonant mirror frequency. The Frame Period Adjustment is used to determine how much to shorten the axial command waveform period relative to (N * FP) in order to avoid missing triggers if the frame periods are shorter than expected.


If frame trigger adjustment is too small, frame triggers will be missed and axial waveform will become desynchronized with each volume's image slices (frames). You might notice image appears to be occasionally shifting through Z planes.

Flyback Time (ms)

Time to allow for Z actuator to travel back from end position of the volume to the start position. This has a slightly different effect between sawtooth and step/settle modes:

  • Sawtooth: If this value is greater than zero, flyback frames will be added to the volume. These are frames that are discarded by the image acquisition to allow time for flyback of the Z actuator. The number of flyback frames will be calculated to give the desired flyback time.
  • Step/Settle: This value will be used as the ammount of time to wait between slices for the actuator to settle. 

Use the actuator tuning window to help find an appropriate value for this setting

Actuator Lag (ms)

Specifies the lag in the Z actuator response. This value advances the Z actuator waveform to compensate for the lag.


Use the actuator tuning window to help find an appropriate value for this setting

# Discard Frames

Displays the number of flyback frames that will be added to the volume. This is controlled by the flyback time set above.


This value will only be nonzero if FastZ is enabled, number of slices > 1, number of volumes > 1, and flyback time > 0.

Actuator Tuning...Launches the FastZ Actuator Tuning window.


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