A system comprising a multi-lane microfluidic cartridge and a diagnostic apparatus for amplifying and carrying out diagnostic analyses on nucleotides from biological samples, wherein: the multi-lane microfluidic cartridge is a disposable multi-lane microfluidic cartridge containing 12 sample lanes in parallel, the multi-lane microfluidic cartridge including first, second and third layers that together define a plurality of microfluidic networks, each of the multiple sample lanes having a microfluidic network, each network having a PCR reactor configured to carry out PCR on a sample having one or more nucleotides, the multi-lane microfluidic cartridge further comprising a window arranged above the PCR reactor that permits optical detection of fluorescence by the diagnostic apparatus when a detector of the diagnostic apparatus is situated above the window; and the diagnostic apparatus comprising: a reusable instrument platform to actuate on-cartridge operations, detect and analyze the products of PCR amplification in each of the lanes separately; a heater substrate, the microfluidic cartridge being disposed on top of and in contact with the heater substrate for heating each PCR reactor through a series of cycles to carry out amplification of nucleotides in the sample; and, a detection system for monitoring fluorescence from biochemical reactions comprising an optical detector for multiplexed detection positioned above the multi-lane microfluidic cartridge when the multi-lane microfluidic cartridge is disposed on top of the heater substrate, the detection system configured to mate with the multi-lane microfluidic cartridge, the optical detector comprising a plurality of independently controllable detector units, each detector unit comprising a light source that selectively emits light in an absorption band of a fluorescent dye and a light detector that selectively detects light in an emission band of the fluorescent dye, wherein the fluorescent dye corresponds to fluorescent nucleotide probe or a fragment thereof, the optical detector configured to detect fluorescence from each lane of the multi-lane microfluidic cartridge. the multi-lane microfluidic cartridge is a disposable multi-lane microfluidic cartridge containing 12 sample lanes in parallel, the multi-lane microfluidic cartridge including first, second and third layers that together define a plurality of microfluidic networks, each of the multiple sample lanes having a microfluidic network, each network having a PCR reactor configured to carry out PCR on a sample having one or more nucleotides, the multi-lane microfluidic cartridge further comprising a window arranged above the PCR reactor that permits optical detection of fluorescence by the diagnostic apparatus when a detector of the diagnostic apparatus is situated above the window; and the diagnostic apparatus comprising: a reusable instrument platform to actuate on-cartridge operations, detect and analyze the products of PCR amplification in each of the lanes separately; a heater substrate, the microfluidic cartridge being disposed on top of and in contact with the heater substrate for heating each PCR reactor through a series of cycles to carry out amplification of nucleotides in the sample; and, a detection system for monitoring fluorescence from biochemical reactions comprising an optical detector for multiplexed detection positioned above the multi-lane microfluidic cartridge when the multi-lane microfluidic cartridge is disposed on top of the heater substrate, the detection system configured to mate with the multi-lane microfluidic cartridge, the optical detector comprising a plurality of independently controllable detector units, each detector unit comprising a light source that selectively emits light in an absorption band of a fluorescent dye and a light detector that selectively detects light in an emission band of the fluorescent dye, wherein the fluorescent dye corresponds to fluorescent nucleotide probe or a fragment thereof, the optical detector configured to detect fluorescence from each lane of the multi-lane microfluidic cartridge. a reusable instrument platform to actuate on-cartridge operations, detect and analyze the products of PCR amplification in each of the lanes separately; a heater substrate, the microfluidic cartridge being disposed on top of and in contact with the heater substrate for heating each PCR reactor through a series of cycles to carry out amplification of nucleotides in the sample; and, a detection system for monitoring fluorescence from biochemical reactions comprising an optical detector for multiplexed detection positioned above the multi-lane microfluidic cartridge when the multi-lane microfluidic cartridge is disposed on top of the heater substrate, the detection system configured to mate with the multi-lane microfluidic cartridge, the optical detector comprising a plurality of independently controllable detector units, each detector unit comprising a light source that selectively emits light in an absorption band of a fluorescent dye and a light detector that selectively detects light in an emission band of the fluorescent dye, wherein the fluorescent dye corresponds to fluorescent nucleotide probe or a fragment thereof, the optical detector configured to detect fluorescence from each lane of the multi-lane microfluidic cartridge.