An analysis system, comprising: a housing comprising a chamber sized and configured to receive at least one microfluidic device; at least one microfluidic device comprising a plurality of fluid channels, each with a plurality of sets of microwells positioned along a length dimension associated with a direction between a sample input port and a second opposing port; an optic system coupled to the housing in optical communication with the at least one microfluidic device, wherein the optic system comprises a camera with a field of view that covers only a sub-set of microwells of the microfluidic device with the sub-set residing in at least two adjacent fluid channels of the microfluidic device; a controller coupled to the optic system, wherein the controller comprises at least one processor; a heat source coupled to the optic system and thermally coupled to the at least one microfluidic device held in the housing; a sub-array selection module comprising computer program code in communication with the controller, wherein the sub-array selection module is configured to select a sub-set of sets of microwells of at least one fluid channel of the microfluidic device for imaging by the optic system after a reaction step (e.g., one thermocycle) during an assay; and a signal analysis module integrated in and/or coupled to the controller, wherein the signal analysis module is configured to obtain an analog signal for each microwell in the selected sub-set of the sets of microwells, and wherein the analog signal provides PCR data as amplitude changes with cycles of the assay and the concentration of target molecules for a reaction associated with a defined bead type is determined by the analog signal, and wherein the signal analysis module is further configured to obtain a digital PCR signal(s) of the sets of microwells. a housing comprising a chamber sized and configured to receive at least one microfluidic device; at least one microfluidic device comprising a plurality of fluid channels, each with a plurality of sets of microwells positioned along a length dimension associated with a direction between a sample input port and a second opposing port; an optic system coupled to the housing in optical communication with the at least one microfluidic device, wherein the optic system comprises a camera with a field of view that covers only a sub-set of microwells of the microfluidic device with the sub-set residing in at least two adjacent fluid channels of the microfluidic device; a controller coupled to the optic system, wherein the controller comprises at least one processor; a heat source coupled to the optic system and thermally coupled to the at least one microfluidic device held in the housing; a sub-array selection module comprising computer program code in communication with the controller, wherein the sub-array selection module is configured to select a sub-set of sets of microwells of at least one fluid channel of the microfluidic device for imaging by the optic system after a reaction step (e.g., one thermocycle) during an assay; and a signal analysis module integrated in and/or coupled to the controller, wherein the signal analysis module is configured to obtain an analog signal for each microwell in the selected sub-set of the sets of microwells, and wherein the analog signal provides PCR data as amplitude changes with cycles of the assay and the concentration of target molecules for a reaction associated with a defined bead type is determined by the analog signal, and wherein the signal analysis module is further configured to obtain a digital PCR signal(s) of the sets of microwells. wherein the signal analysis module is configured to obtain an analog signal for each microwell in the selected sub-set of the sets of microwells, and wherein the analog signal provides PCR data as amplitude changes with cycles of the assay and the concentration of target molecules for a reaction associated with a defined bead type is determined by the analog signal, and wherein the signal analysis module is further configured to obtain a digital PCR signal(s) of the sets of microwells.