Optics Collection and Detection System and Method

Abstract

Optics collection and detection systems are provided for measuring optical signals from an array of optical sources over time. Methods of using the optics collection and detection systems are also described.

1 - 37 . (canceled) 
     
     
         38 . An integrated device for analysis of fluorescent species, comprising:
 an array of reaction cells;   at least one illumination waveguide disposed beneath the array of reaction cells extending across a plurality of reaction cells in the array of reaction cells and illuminating the plurality of reaction cells from below so that fluorescent species in the plurality of reaction cells emit fluorescent light;   optical filters disposed below the at least one illumination waveguide and selectively passing the fluorescent light emitted from the plurality of reaction cells; and   detectors disposed below the optical filters and detecting the fluorescent light passed through the optical filters;   wherein each reaction cell in the plurality of reaction cells is optically coupled to one or more detectors;   wherein the device is integrated such that the fluorescent light emitted from the fluorescent species in the plurality of reaction cells is transmitted to the detectors without passing through air or free space.   
     
     
         39 . The device of  claim 38 , wherein for each respective cell in the plurality of reaction cells, each of the one or more detectors is associated with a different optical filter that selectively passes a different wavelength range of the fluorescent light emitted from the respective reaction cell. 
     
     
         40 . The device of  claim 38 , wherein the optical filters comprise dichroic filters, photon band gap (PBG) filters, and Bragg gratings. 
     
     
         41 . The device of  claim 38 , wherein the optical filters are band pass filters. 
     
     
         42 . The device of  claim 38 , wherein each reaction cell is coupled to two detectors. 
     
     
         43 . The device of  claim 38 , wherein each reaction cell is coupled to two, three, or four detectors. 
     
     
         44 . The device of  claim 38 , wherein each reaction cell is coupled to one detector. 
     
     
         45 . The device of  claim 38 , further comprising a layer below the illumination waveguide that selectively rejects illumination light from the at least one illumination waveguide. 
     
     
         46 . The device of  claim 38 , further comprising attenuators between the detectors. 
     
     
         47 . The device of  claim 46 , wherein the attenuators are metal attenuators. 
     
     
         48 . The device of  claim 38 , wherein the reaction cells are contained within a top layer, and the top layer further comprises a series of dielectric posts between the reaction cells, the dielectric posts providing lateral confinement of the illumination light from the at least one illumination waveguide. 
     
     
         49 . The device of  claim 38 , wherein the reaction cells comprise nanoscale apertures.