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.


If using multiple objectives, ensure that the currently applied coordinate system data file is the one associated with the currently installed objective.


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. There is also backlash compensation which can be applied from the SI Motors configuration page.

Manual Shift method

If you are imaging with poor signal-to-noise ratio, then the automated image correlation may provide detected motion estimates with great variance. This could make it very difficult or impossible to set alignment points at proper locations. To combat this, ScanImage 2023.0.0 provides a manual shift method to allow the user to overlay live and reference images before adding alignment points.


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

hSI.hMotors.hCSMicron          % contains a 2D affine matrix (3x3) containing just the scaling from optical degrees to microns
hSI.hMotors.hCSAlignment       % contains a 2D affind matrix (3x3) containing shear and rotation without scaling.