An apparatus for performing a microassay in a microassay cartridge inserted into a docking bay of a host instrument, the apparatus comprising the instrument, which is adapted for removably receiving the microassay cartridge wherein said instrument comprises: a) a supporting baseplate; b) the docking bay for receiving the microassay cartridge, wherein said docking bay is mounted on said baseplate; c) a pneumatic control manifold disposed within said baseplate, said manifold having disposed thereon a pneumatic interface port array within said docking bay; d) attached to said baseplate within said docking bay, a heater assembly comprising at least one heating member (341, 342, 343, 344) with spring mount and with superior surface dimensioned for interfacing with an undersurface of said microassay cartridge; and, e) a first fan for convectively dissipating heat from a cooling member disposed on said heating member (341, 342, 343, 344), wherein said docking bay comprises a clamping mechanism configured to reposition the microassay cartridge within the docking bay from first position above the pneumatic interface port array to a second position wherein said microassay cartridge is operatively engaged with said pneumatic interface port array, and further wherein said spring mount is configured to press an undersurface of the microfluidic cartridge in said second position against said superior surface of said heating member (341, 342, 343, 344); f) a detector head for fluorescence scanning of the microassay cartridge; the apparatus is characterized in that the host instrument further comprises a second fan for convectively cooling a sample well disposed in said microassay cartridge, wherein the second fan is constituted by a blower mounted on an external wall of an instrument chassis of the host instrument, and a baffled duct connected to the second fan and directed onto a nose of the microassay cartridge on which nose the sample well is provided, wherein said second fan is configured for performing a thermal annealing function by cooling said sample well while the sample is fluorescently monitored. a) a supporting baseplate; b) the docking bay for receiving the microassay cartridge, wherein said docking bay is mounted on said baseplate; c) a pneumatic control manifold disposed within said baseplate, said manifold having disposed thereon a pneumatic interface port array within said docking bay; d) attached to said baseplate within said docking bay, a heater assembly comprising at least one heating member (341, 342, 343, 344) with spring mount and with superior surface dimensioned for interfacing with an undersurface of said microassay cartridge; and, e) a first fan for convectively dissipating heat from a cooling member disposed on said heating member (341, 342, 343, 344), wherein said docking bay comprises a clamping mechanism configured to reposition the microassay cartridge within the docking bay from first position above the pneumatic interface port array to a second position wherein said microassay cartridge is operatively engaged with said pneumatic interface port array, and further wherein said spring mount is configured to press an undersurface of the microfluidic cartridge in said second position against said superior surface of said heating member (341, 342, 343, 344); f) a detector head for fluorescence scanning of the microassay cartridge; the apparatus is characterized in that the host instrument further comprises a second fan for convectively cooling a sample well disposed in said microassay cartridge, wherein the second fan is constituted by a blower mounted on an external wall of an instrument chassis of the host instrument, and a baffled duct connected to the second fan and directed onto a nose of the microassay cartridge on which nose the sample well is provided, wherein said second fan is configured for performing a thermal annealing function by cooling said sample well while the sample is fluorescently monitored.