Alignment between Stage and Scanner

A relation between distances in pixels to distances in stage units (ordinarily microns) can be made with a scanner to stage alignment. This process is semi-automated and takes advantage of ScanImage’s Motion Correction framework. After a successful calibration, ScanImage® can perform measurements in stage units, move the stage to defined positions, and perform motion correction.


A minimum of three calibration points is required for a successful alignment. More points can be added to generate a more precise alignment.


Stages can have play in their gears. During calibration it is advantageous to always finish a move from the same direction to minimize the effect of backlash.


The scanner-stage alignment affects the transforms to reference space, including the following properties:

hSI.hScan2D.scannerToRefTransform            % contains a 2D affine matrix (3x3) to go from scanner space to reference space