We have constructed a Holographic Scanning Microscopy (HSM) setup, which employs an optical design and a scanning unit of a commercial confocal laser scanning microscope. This arrangement helps to construct the HSM easier, but the scanning unit gives additional phase distortions modifying an object wave and introducing phase shift. We offer a way to dispose such distortions changing the way of recording holograms and reconstruction algorithm. Analyzing recorded holograms we conclude, that we need to record a hologram of flat mirror first, which would contain required information about phase distortions, and use it for reconstruction. Finally reconstruction algorithm becomes like to “coded” reference wave reconstruction algorithm. Proposed algorithm was successfully implemented and tested in MatLab.
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