Stack Controls¶

Stack Controls

The ‘Enable Stack’ checkbox in the main controls window activates stack acquisition for Grab or Loop acquisitions

The Stack Controls window allows to define stack acquisition. ScanImage supports multiple modes of defining and executing stacks:

Stack geometry definition¶

Stack Defintion	Description
Uniform	Stack is defined by number of slices and slice distance
Bounded	Stack is defined by top position, bottom position and slice distance
Arbitrary	Stack is defined by a vector of arbitrary zs

Mode	Description
Slow	After each slice, the acquisition halts, the actuator moves the focus, and then continues the acquisition
Fast	The acquisition is continuous, the actuator sweeps through all slices of the stack

Control

Descripti on

Actuator

Actuator that moves the focus. Options are

Return Home

Return to initial position afer the stack acquisition is completed

Close Shutter btwn Slices

Close shutter between slices to limit exposure of the sample while actuator moves.

Control	Descripti on
Waveform	Waveform shape to drive the FastZ actuator. Options: 1) sawtooth ( unavailable for arbitrary zs stacks OR if Frames per Slice > 1) 2) step (ensure the fastZ actuator can settle in time)
Return Home	Return to initial position afer the stack acquisition is completed
Flyback Time (ms)	Flyback time granted to
#Discard Frames	(not settable) number of flyback frames, calculated based on flyback time
Actuator Lag (ms)	lead time applied to FastZ drive waveform to compensate for actuator lag
Volume Rate	Volume Rate [Hz]
Test Waveform	Show the FastZ Tuning Wi ndow

Control	Descripti on
Frames per Slice	Number of frames acquired per slice
Number of Slices	Number of slices in stack
Number of Volumes	Number of times the stack is acquired
Step Size (um)	Distance between slices
Centered Stack	Center stack around current z position

Control	Descripti on
Frames Per Slice	Number of frames acquired per slice
Number of Slices	Number of slices in stack
Number of Volumes	Number of times the stack is acquired.
Step Size (um)	Distance between slices (auto calculated)
Set/Clear Start	Set / Clear the stack start position
Set/Clear End	Set / Clear the stack end position
Use start end powers	Use the stack start and end powers

Control	Descripti on
Frames Per Slice	Number of frames acquired per slice
Number of Slices	Number of slices in stack (auto calculated)
Number of Volumes	Number of times the stack is acquired
Arbitrary Zs \[um]	Vector defining zs
Copy from ROI group	Copy zs vector from ROI refinition