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.

Alignment Source

Specify which image channel to use as a video stream.

Pause Video

Pause the video stream at current image.


Select color of video stream.

Offset, Scale, Rotation,Shear

Apply offset, scaling factor, rotation, and shear to the video stream.

Save Scanner Alignment Transform

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 Alignment

Reset scanner alignment relationships for all scanners to default that assumes perfect alignment using angular ranges from MDF settings.

Create Alignment ROI

Create an ROI that can be imaged by all scanners and enter multiple ROI mode in order to perform alignment

Reference Image Panel

Copy Channel

Copies the image from the selected channel video stream into the reference image buffer

Load from file

Loads reference image from a saved file

Save to file

Saves current reference image to file


Adjusts alpha blending level between reference image and video stream


Sets color of reference image