ScanImage 2019 : Glossary

Created by Lawrence Niu on May 07, 2019

 

  • Acquisition: A finite set of acquired frames (at one or more axial slices) collected 
     
  • Acquisition Mode: ScanImage supports three acquisition modes termed FOCUS, GRAB, and LOOP. FOCUS is  GRAB is a single acquisition and a LOOP consists of multiple acquisitions.
     
  • Beams:  Term for output DAQ channels used to control laser power modulation devices, which set laser power and blank laser illumination during non-imaging portions of line/frame/acquisition mode. 
     
  • Channels: Term for input DAQ channels connected 
     
  • Configuration (CFG): The large (nearly complete) set of ScanImage setting values which users can modify to control operation of a subsequently started ScanImage acquisition mode. Can be saved & loaded to/from CFG files. 

  • FastZ: Colloquial term for control of volume imaging, the collection of live multi-frame (movie) acquisitions spanning multiple axial planes. Volume imaging devices are typically fast axial scanners allowing rapid sweeps or steps of axial position without interrupting lateral scanning. FastZ devices are distinguished from plain stage controllers which can be used . FastZ devices can (and usually do) double as stage controllers as well. 

  • Imaging System: The type of scanner set that is used to form an image. Currently two types are supported - Resonant (resonant-galvo RG scanner set) and Linear (galvo-galvo GG scanner set).
     
  • Machine Data File: An M file script parsed on ScanImage startup to specify rig-specific settings, such as the hardware present and connection channels. This must be user created & edited prior to first ScanImage operation.
     
  • ROI: A three-dimensional set of ScanFields at various planes which form a bounding volume of interest to be imaged in Multi-ROI imaging mode. 
     
  • ScanField: Term for the set of scanner zoom, angular shift, rotation, and aspect ratio settings which determined the scanned area relative to the full scanner field-of-view at the current stage controller position.
     
  • Stage/Motor Controller: Device supporting controlled positioning of the sample, relative to the scanner's field-of-view, in the X, Y, and/or Z dimensions. Adjustments of position in the Z dimension allow three-dimensional stack acquisitions where one or more image frames is collected at two or more axial slices. 
     
  • User Settings (USR): A select set of ScanImage setting values that are changed infrequently during operation; plus the default location/visibility of ScanImage GUI windows. Can be saved & loaded to/from USR files. Loaded on ScanImage startup, after the Machine Data File.