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 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 , 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 ; 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 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 , 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 ; 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. <EOS>