ANALYTICAL INSTRUMENT SYSTEMS

1 . A detection system, comprising:

an excitation light source;

a reaction vessel comprising an array of capture probe sites disposed thereon, the array producing one or more fluorescent signals in response to the excitation light;

an image sensor;

an optical train for transmitting excitation light from the excitation light source to the array, and fluorescent signals from the array to the image sensor;

one or more thermal control elements disposed in thermal communication with the reaction vessel; and

a processor operably coupled to the one or more thermal control elements, for subjecting contents of the reaction vessel to a thermal cycling profile.

2 . The system of claim 1 , wherein the optical train includes a focusing lens for focusing the fluorescent signals onto the image sensor, and an optical path length adjustment component between the focusing lens and the image sensor.

3 . The system of claim 2 , wherein the optical path length adjustment component comprises a rotatable variable thickness disk.

4 . The system of claim 3 , wherein the rotatable variable thickness disk comprises a transparent material selected from glass, quartz, fused silica, and a transparent polymer.

5 . The system of claim 4 , wherein the transparent polymer is selected from polymethylmethacrylate, poly(carbonate), poly(styrene), poly(ethersulfone), poly(aliphatic ether), halogenated poly(aliphatic ether), poly(aryl ether), halogenated poly(aryl ether), poly(amide), poly(imide), poly(ester)poly(acrylate), poly(methacrylate), poly(olefin), halogenated poly(olefin), poly(cyclic olefin), halogenated poly(cyclic olefin), and poly(vinyl alcohol).

6 . The system of claim 1 , wherein at least one thermal control element is a thermoelectric element disposed in an optical path between the excitation light source and the array, the thermal control element having an optical aperture disposed therein, for transmitting the excitation light to the array, the optical aperture comprising a transparent thermally conductive material.

7 . The system of claim 6 , wherein the transparent thermally conductive material comprises a thermal conductivity of at least 1 W/mK, preferably greater than 5 W/mK, and more preferably, greater than 10 W/mK, and in some cases greater than 100 W/mK or even 500 W/mK

8 . The system of claim 6 , wherein the transparent thermally conductive material comprises a material selected from glass, sapphire, diamond, crystalline quartz, MgAl2O4 and ALON.

9 . The system of claim 6 , wherein when the reaction vessel is positioned in thermal communication with the thermal control element having the aperture disposed therethrough, a gap of from about 1 to about 50 microns thick is provided between the optically transparent, thermally conductive material and the reaction vessel.

10 . The system of claim 1 , wherein the one or more thermal control elements can create different temperature regions within the reaction vessel and thus apply a differential temperature across at least a portion of the reaction vessel.

11 . The system of claim 10 , wherein the processor includes programming to apply different temperatures to the different temperature regions of the thermal control element.

12 . The system of claim 10 , wherein the thermal control elements can cause thermal mixing of one or more components within the reaction vessel.

13 . A method of detecting an nucleic acid amplification product, comprising:

amplifying a target nucleic acid in a reaction mixture in the presence of a nucleic acid array;

in a hybridization step, cooling the reaction mixture to a hybridization temperature to permit hybridization of the amplification product to the array;

subjecting the reaction mixture to convective mixing before or during the hybridization step; and,

detecting amplification product that hybridizes to the array.