With premium ScanImage® you can use affine transformations to align the scan fields of separate scanners. You can also align the scanner to the stage so that you will be able to measure distances in stage units.


When using the photostimulation with a single scan path microscope, alignment is not necessary. If you are using a resonant-galvo-galvo scanhead however, it is important to have accurate settings for scan mirror angular ranges if you intend to use images collected in resonant mode to identify ROIs to stimulate. Details on how to do this can be found in the scanner configuration pages

Alignment between Multiple Scanners

When using a dual scan path microscope for photostimulation it is often desirable to image and identify cells for stimulation with one scan path, then stimulate the cells using the other scan path. For this targeting to be accurate, alignment between the scanners is critical.

This same process can be applied between a scanner and a camera.


Alignment between Stage and Scanner

Similar to the Scanner Alignment, ScanImage® can align the stage (motors) to the laser scanners. 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 and can move the stage to defined positions.


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 motor alignment is stored in the following properties:

hSI.hMotors.motorToRefTransform            % contains a relative (3x3) matrix
hSI.hMotors.motorToRefTransformAbsolute    % contains the absolute (3x3) matrix that takes the current motor position into account