Systems and methods for biological analysis

1. A case for containing a plurality of biological samples, the case comprising:

a base;

a substrate attached to the base, the substrate comprising a plurality of reaction regions configured to receive one or more biological samples; and

a cover comprising an inner surface, the cover configured to be attached to the base; and

wherein the inner surface includes a central area and a recessed area disposed about the central area, the central area configured to cover the reaction regions, the recessed area being offset from the central area in a direction normal to the inner surface;

wherein during use the base, the central area, and the recessed area together provide a cavity containing the substrate;

wherein the recessed area comprises a trough disposed along a perimeter of the central area, the trough comprising a bottom surface that is offset from the central area in a direction normal to the inner surface; and

wherein the bottom surface has a depth that varies along the perimeter.

2. The case of claim 1 , wherein the central area is transparent to provide optical access to the plurality of reaction regions.

3. The case of claim 1 , wherein the substrate comprises a first surface and an opposing second surface, and the plurality of reaction regions comprises a plurality of through-holes disposed between the surfaces, the through-holes configured to receive one or more biological samples.

4. The case of claim 3 , further comprising a fluid, wherein the cover is attached to the base and the fluid is in contact with the first surface, the second surfaces, and an inner surface of the cover.

5. The case of claim 1 , wherein the recessed area is configured to receive gas from the central area that is released by a fluid in the cavity when the cover is attached to the base.

6. The case of claim 1 , wherein the base comprises a plurality of support pads disposed about a periphery of a bottom surface of the base, wherein support pads maintain the substrate over the bottom surface of the base.

7. The case of claim 6 , wherein the substrate is maintained by a contact force between the substrate and one or more of the support pads.

8. The case of claim 6 , wherein support pads comprise a first group of support pads and a second group of support pads distinct from the first group of support pads, wherein the substrate is held by a contact force between the substrate and the first group of the support pads and a spacing between the substrate and the bottom surface is maintained by the second group of support pads.

9. The case of claim 5 , wherein the received gas comprises a plurality of air bubbles.

10. The case of claim 1 , wherein the recessed area comprises a rim disposed about the trough, the rim being offset below the central area in a direction normal to the inner surface, the trough being offset below the rim in a direction normal to the inner surface.

11. An instrument for biological analysis, comprising:

a carrier configured to be received within the instrument and to contain a plurality of cases according to claim 1 ;

an electromagnetic radiation source configured to produce one or more excitation beams;

an excitation optical system configured to direct the one or more excitation beams to the biological samples;

an optical sensor configured to receive an emission from the biological samples in response to the one or more excitation beams; and

an emission optical system configured to direct the emission from at least some of the biological samples to the optical sensor.

12. The instrument according to claim 11 , further comprising a second carrier that is not configured to receive a case according to claim 1 .

13. The instrument according to claim 12 , wherein the second carrier is configured to receive a microtiter plate containing 384 sample wells.

14. A case for containing a plurality of biological samples, the case comprising:

a base;

a substrate attached to the base, the substrate comprising a plurality of reaction regions configured to receive one or more biological samples; and

a cover comprising an inner surface, the cover configured to be attached to the base; and

wherein the inner surface includes a central area and a recessed area disposed about the central area, the central area configured to cover the reaction regions, the recessed area being offset from the central area in a direction normal to the inner surface;

wherein during use the base, the central area, and the recessed area together provide a cavity containing the substrate;

wherein the recessed area comprises a trough disposed along a perimeter of the central area, the trough comprising a bottom that is offset from the central area in a direction normal to the inner surface;

wherein the trough comprises a first portion having a first width and a second portion having a second width that is greater than the first width; and

wherein the first portion has a first depth and the second portion has a second depth that is greater than the first depth.

15. The case of claim 14 , wherein the recessed area comprises a rim disposed about the trough, the rim being offset below the central area in a direction normal to the inner surface, the trough being offset below the rim in a direction normal to the inner surface.