ScanImage 2018 : Alignment Controls




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

Show Alignment Window

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

Video Stream Source ChannelSpecify which image channel to use as a video stream.
Pause VideoPause the video stream at current image.
ColorSelect color of video stream.
Offset, Scale, Rotation, ShearApply offset, scaling factor, rotation, and shear to the video stream.
Generate Ref to Scanner Transforms

Generate an alignment relationship for the currently active scanner from the scanner used to create the reference image using the offsets, scaling, rotation, and shear.

Reset AlignmentReset scanner alignment relationships for all scanners to default that assumes perfect alignment using angular ranges from MDF settings.
Create Alignment ROICreate an ROI that can be imaged by all scanners and enter multiple ROI mode in order to perform alignment

Reference Image Panel

Copy ChannelCopies the image from the selected channel video stream into the reference image buffer
Load from fileLoads reference image from a saved file
Save to fileSaves current reference image to file
AlphaAdjusts alpha blending level between reference image and video stream
ColorSets color of reference image


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