Stack Controls

 Stack Controls

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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

Stack mode

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

Slow Stack

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Control

Descripti on

Actuator

Actuator that moves the focus. Options are

  1. motor

  2. fastZ

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.

Fast Stack

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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

Uniform

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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

Bounded

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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

Arbitrary

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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