ScanImage 2016 : Slow Stacks


A ScanImage Slow Stack acquisition is composed of multiple sub-acquisitions termed Slices, each identical but obtained at one of a set of evenly spaced axial (Z) positions of the motor.

  • Slow Stack acquisitions require that a stage and motor controller is configured for motion in the axial (Z) direction (typically along the microscope objective) is available and is defined in the Machine Data File.
  • A Slow Stack acquisition is fundamentally configured by three parameters on the Motor Controls window.
    • # Slices
    • Z Step/Slice
    • Return Home After Each Repeat
  • A Slow Stack acquisition can be started anytime # Slices > 1, by selecting GRAB (or LOOP) on the Main Controls panel:
    • Beginning acquisition immediately, starting from the current axial (Z) position
    • If a Start Position is defined in the Motor Controls Window, acquisition begins after moving first to the defined Start position on that panel
  • Each Slice can consist of a single Frame or a set of frames, if # Frames > 1 (set on the Main Controls panel.)

A saved slow stack is a TIF file with each slice consecutively stored in the file, from first to last. If there are multiple frames/slice, then all frames for a given slice are written first before writing the next slice's frames.

Defining Image Stack Endpoints Interactively

Please refer to the Motor Controls Window reference for instructions on how to set the Slow Stack Start/End positions interactively.