In this paper we present an alignment methodology for a non-linear laser scanning fluorescence microscopic imaging
system integrated with a MEMS deformable mirror that is used to compensate microscope aberrations and improve
sample image quality. The procedure uses an accurate open-loop control mechanism of the MEMS DM, a high
resolution CMOS camera and a compact Shack-Hartmann wavefront sensor. The success of the indirect AO control
method used by the microscope to compensate aberrations requires careful alignment of the optical system, specifically
the DM conjugate planes in the scanning laser optical path. Considerations of this procedure are presented here, in
addition to an assessment of the final accuracy of the alignment task is presented, by verifying the pupil conjugation and
wavefront response. This method can also serve as a regular check-up of the system's performance and trouble-shoot for
system misalignment.
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