Nucleic acid amplification and detection devices, systems and methods

A method of monitoring nucleic acid amplification in a plurality of amplification reaction vessels, the method comprising:

• a) scanning the plurality of amplification reaction vessels with a traveling optics detection unit having an excitation component and a plurality of optics block apertures, wherein the spacing between amplification reaction vessels is unequal to the spacing between the optics block apertures and only one of the plurality of optics block apertures optically aligns with one of the plurality of amplification reaction vessels;
• b) receiving a scan signal from the optics detection unit comprising background noise and emission peaks;
• c) determining emission peaks within the background noise according to a plurality of reaction vessel windows;
• d) measuring an intensity value for each reaction vessel window to monitor the amplification in each reaction vessel of the plurality.