A high-throughput fluorescence imaging system with sample heating capability includes an image sensor wafer with a plurality of image sensors for fluorescence imaging a plurality of samples disposed in a respective plurality of fluidic channels on the image sensor wafer. The high-throughput fluorescence imaging system further includes a heating module, thermally coupled with the image sensor wafer, for heating the samples. A method for high-throughput assay processing includes modulating temperature of a plurality of samples disposed in a respective plurality of fluidic channels on an image sensor wafer 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 capturing a plurality of fluorescence images of the samples, using a respective plurality of image sensors of the image sensor wafer, to detect one or more components of the plurality of samples.