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Stack Controls

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

Stack geometry definition

Stack DefintionDescription
UniformStack is defined by number of slices and slice distance
BoundedStack is defined by top position, bottom position and slice distance
ArbitraryStack is defined by a vector of arbitrary zs

Stack mode

ModeDescription
SlowAfter each slice, the acquisition halts, the actuator moves the focus, and then continues the acquisition
FastThe acquisition is continuous, the actuator sweeps through all slices of the stack

 

 

 

 

Stack Controls

 

 

 

 

 

 

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

 

 

 

Slow Stack

ControlDescription
Actuator

Actuator that moves the focus. Options are

1) motor
2) fastZ

Return HomeReturn to initial position afer the stack acquisition is completed
Close Shutter btwn SlicesClose shutter between slices to limit exposure of the sample while actuator moves.

Fast Stack

ControlDescription
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 HomeReturn 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 RateVolume Rate [Hz]
Test WaveformShow the FastZ Tuning Window

Uniform

ControlDescription
Frames per Slice

Number of frames acquired per slice

Number of SlicesNumber of slices in stack
Number of VolumesNumber of times the stack is acquired
Step Size (um)Distance between slices
Centered StackCenter stack around current z position

 

 

Bounded 

ControlDescription
Frames Per Slice

Number of frames acquired per slice

Number of SlicesNumber of slices in stack
Number of VolumesNumber of times the stack is acquired.
Step Size (um)Distance between slices (auto calculated)
Set/Clear StartSet / Clear the stack start position
Set/Clear EndSet / Clear the stack end position
Use start end powersUse the stack start and end powers

Arbitrary

ControlDescription
Frames Per Slice

Number of frames acquired per slice

Number of SlicesNumber of slices in stack (auto calculated)
Number of VolumesNumber of times the stack is acquired
Arbitrary Zs \[um\]Vector defining zs
Copy from ROI groupCopy zs vector from ROI refinition