Generally, the software will notify you if your chip is not aligned correctly. The electrode images can additionally give you some information about the alignment. If each excitation light spot fully illuminates one of the two electrodes, the alignment is good. If a larger part of the excitation light spot illuminates an area next to the electrodes, the alignment is not good. See also the exemplary images below.
Bad alignment:
Good alignment:
Category:
Instrument and Chip Handling