This documentation is for a legacy ScanImage version. The current documentation is ScanImage 2019.
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The ALIGNMENT CONTROLS panel is used for various image alignment purposes including some of the following common tasks:

  • Physical alignment of parallel scanning paths
  • Calibration of resonant image aspect ratio at various zoom levels
  • Registration between X galvo and resonant mirror for RGG scanners
  • Generating affine transformation matrices for fine parallel scanner alignment
  • Day to day sample alignment

Main Panel

Shows the alignment image window. Uncheck this when alignment is not in use to avoid performance impact during imaging.

Specify which image channel to use as a video stream.
Pause the video stream at current image.
Select color of video stream.
Apply scaling factor and offset to reference image overlaid on video stream.
If reference image and video stream were captured from different scanners, use the entered scaling and offsets to generate scanner transforms for fine alignment.
Reset fine scanner transforms to default that assumes perfect alignment using angular ranges from MDF settings.

Reference Image Panel

Copies the image from the selected video stream into the reference image buffer
Loads reference image from a saved file
Saves current reference image to file
Adjusts alpha blending level between reference image and video stream
Sets color of reference image