A method for high-throughput assay processing includes (a) modulating temperature of a plurality of samples disposed in a respective plurality of fluidic channels on an image sensor wafer, including a plurality of image sensors, by heating the image sensor wafer using a heating module thermally coupled with the image sensor wafer, to control reaction dynamics in the samples, and (b) capturing a plurality of fluorescence images of the samples, using the plurality of image sensors, to detect one or more components of the plurality of samples. A method for manufacturing a high-throughput fluorescence imaging system with sample heating capability includes (a) bonding a fluidic wafer, including a plurality of recesses, to an image sensor wafer including a plurality of image sensors, and (b) bonding a heating module, including a heater for generating heat, to the image sensor wafer to thermally couple the heater and the image sensor wafer.