Abstract:
An apparatus and method for imaging biochip spots in which a linearly spaced array of micro-lenses has a set of optical fibers which are associated with each micro-lens to receive and transmit the image magnified by the micro-lens. The micro-lenses are spaced to that of the biochip spots so that the microlens array can be positioned over a selected group of biochip spots, one for each micro-lens. The microlens array can be translated to be over selected groups of biochip spots. A detector and user devise such as a computer and a screen are used to record and view the collected images.

Description:
FIELD OF THE INVENTION  
         [0001]    The invention relates to imaging of biochip spots.  
         BACKGROUND OF THE INVENTION  
         [0002]    One method of observing and imaging biochip spots is through the use of confocal microscopes. These devices are large and expensive.  
         SUMMARY OF THE INVENTION  
         [0003]    The apparatus has a micro-lens and optical fiber array in which a plurality of micro-lenses are linearly spaced apart an amount equal to the spacing of spots on a biochip so that they can be simultaneously focused on the respective spots to enlarge the spot image. An optical fiber is terminated and fixed above each of the micro-lenses to transmit the image. A scanner will translate the array to successively adjacent groups of spots in the biochip (x direction) or if desired, along the axis of the array to an adjacent set of spots in the same line (y direction) or both. The transmitted images are sent over the optical fibers to a detector and then to a user device which may be a display screen, data processor, or other device. Confocal effect can be achieved with certain optical fiber diameters. 
       
    
    
     BRIEF DESCRIPTION OF DRAWINGS  
       [0004]    [0004]FIG. 1 shows the apparatus with an enlargement of a portion showing the micro-lens optic fiber array in place over a biochip.  
         [0005]    [0005]FIG. 2 shows a test bench set up for testing the concept of the invention.  
         [0006]    [0006]FIG. 3 shows a micro-lens construction according to the invention.  
     
    
     DETAILED DESCRIPTION  
       [0007]    As seen in FIG. 1, a micro-lens optic fiber array  10  has a plurality of micro-lenses  12  linearly arranged and spaced apart a distance equal to the spacing of the spots  14  of a biochip  16 .  
         [0008]    Mounted above the micro-lenses  12  are optical fibers  18 , one for each micro-lens  12  positioned to receive the focused image transmitted through the micro-lens  12 .  
         [0009]    The micro-lenses  12  can be separate lenses, or as seen in FIG. 1, can be constructed as a multi-lens unit  20  having a spaced apart plurality of micro-lenses  12 , linearly arranged and spaced to be in position over a set of linearly spaced apart spots  14  on a biochip.  
         [0010]    A connector structure  22  is shown which terminates the optical fibers  18  so as to be securely and accurately placed to receive the magnified image transmitted through the micro-lenses  12 . Structure  24  is a scanning apparatus, which enables moving the array  10  from a position over one set of spots  14 A of a biochip  16 , to another set of spots,  14 B. The scanner can move orthogonally to the linear axis of the array  10  so as to be positioned over successively adjacent sets of spots, or it can be moved to any selected set of spots along the scanning path orthogonal to the linear axis of the array.  
         [0011]    The scanner  24  can also be set up to move the array axially, so that, in case of a biochip that has a line of spots greater in number than the array, it can be translated along the line, that is, in the direction of the axis of the array of lenses.  
         [0012]    Scanning of the array  10  by the scanning structure can be conveniently designated as being x direction scanning, in the direction shown by the arrows x-x parallel to the axis of the micro-lens array  10  and y direction scanning in the direction shown by the arrows y-y orthogonally to the axis of the micro-lens array.  
         [0013]    It is preferable that the array  10  have the same number of micro-lenses and optic fiber positions as there are spots in the x direction so that only y direction scanning is necessary. Of course, as few as a single micro lens along with a single optical fiber could be implemented, which then can be translated in the x and y direction by a scanning device that moves one spot at a time, or to any selected spot on the biochip. But such an apparatus would sacrifice the advantage of having a plurality of linearly spaced micro-lenses to image an equal number of biochip spots simultaneously. Also, whatever the selected number of micro-lenses  10  in the x direction, a plurality of parallel adjacent rows of micro-lenses could be placed in a single micro-lens array.  
         [0014]    The apparatus also has a light source  26  which is arranged to illuminate the biochip spots which are under the micro-lenses and is preferably fixed to the array  10 . It can be fixed to the array  10  to move with it so as to selectively illuminate the biochips being imaged by the array.  
         [0015]    The optical fibers  18  extend to and terminate at a detector  28  whose output is connected to either or both a recording instrument, or as shown in FIG. 1, a display screen  34  or both. In use, a biochip  16  is placed in the scanner  24  and the array  10  positioned over a selected set of spots  14 . Usually the procedure will start on one side of the biochip  16  and then proceed sequentially to adjacent sets of spots  14  across the biochip  16 . The apparatus can be constructed so that either the biochip  16  is moved under the array  10 , or the array is moved over the biochip  16 .  
         [0016]    The microlens array of FIG. 1 may be used to test the high density biochips such as DNA chips with arrays of spots containing thousands of specific DNA binding sites. The array device is configured according to the chip configuration. An exemplary microlens array is based on the most common chip configuration, which is 100 microns by 100 microns per site and 200 microns between the centers of each site. In such an array device, using a 100-microlens linear array, 10,000 sites can be rapidly scanned in one direction of translation of the 100-microlens linear array. Based on the chip format, the proper size for the optical fibers is selected. The fibers are coupled to the microlens array as described above, each fiber having a corresponding microlens.  
         [0017]    The microlens array will provide the necessary spot size and resolution. The spot size on the chip is determined by two factors; the numerical operative (NA) of the objective microlens and the fiber core diameter. In an exemplary system the laser beam will be collimated with a fiber coupling lens. Assuming the effective focal length (EFL) of the fiber coupling lens is F 1 , and the EFL of the objective lens is F 2 , then the magnification of the microlens is M=F 2  /F 1 . The estimated spot size for the fiber probe can be calculated by the following formula:  
         Spot size=(fiber core diameter)× M +(Gaussian Beam Dispersion)  
         [0018]    where the Gaussian Beam Dispersion is calculated as FWHM (full-width half maximum) of the laser beam diameter. The core size of the optical fiber arranges from 3.5 microns (single mode) to 100 microns (multimode), although up to 150 microns diameter will work.  
         [0019]    Table 1 shows combinations of different objective lens sizes and their corresponding spot size for a fiber whose core diameter is 5 microns, for example, with a 0.9 NA 1× lens, the diffraction limited spot size=1.22×λ/NA=6.9 microns. In this case the FWHM is 3.5 microns. The total estimated spot size for the fiber probe is 5 microns+3.5 microns=8.5 microns. As the table shows, the range of the spot sizes can be from 8.5 microns to 48 microns based on a fiber core diameter of 5 microns and reasonable lens choices. By carefully choosing F 1  and F 2 , the spot size of the probe can be controlled so that it matches the size of biochemical spots on the biochip.  
         [0020]    Table 1. The estimated spot size of a confocal fiber probe using a 5 micron core fiber.  
                                                                                                     EFL   CA   WD   Mag.   Est. Spot Size           NA   (μm)   (μm)   (μm)   (x)   (μm)                                        0.50   100   120   55   1.0   8.5           0.55   136   170   48   1.4   10.3           0.62   201   205   78   2.0   13.6           0.41   225   266   119   2.3   14.8           0.40   312   293   172   3.1   19.1                      
 
         [0021]    [0021]FIG. 2 is a test bench set-up  30  used to confirm confocal operation of the microlens array. This set-up  30  has a battery back and driver which are not shown. A sensor head assembly  32  contains the micro-lens and optical fiber assembly  34  which is shown in detail in FIG. 3. A fiber sensor base plate  36  supports the set-up and has a test specimen area  38 . Optical fiber  40  extends from the sensor head assembly  32  to one end of a fused fiber coupler  42 . Exiting the fused fiber coupler  42  are optical fibers  44  and  46 . Optical fiber  46  goes to a laser  48  and the optical fiber  44  goes to a filter detector  50 . The laser  42  is a compact diode laser (635 nm, 30 mW) pigtailed to the single mode fiber  44  to provide light source for illumination which was operated with a 9 VDC battery. The output beam of the fiber is collimated. The lens in the sensor head assembly  32  is an aspheric microlens (numerical aperture (NA)=0.62, effective focal length (EFL)=2 mm, CT=2.0 mm from Geltech of Florida to generate a minimal spot size of 10 microns. The bifurcated fiber delivered light to the sample  52  and directed the fluorescence light back to a compact PMT/high gain amplifier and color filter  50 . The combination of the optical fiber “pinhole” and the high NA microlens offers a sharp, high contrast fluorescence image.  
         [0022]    [0022]FIG. 3 shows schematically, detail of the sensor head assembly  32 , having aligned micro-lenses  54  and  56 , bifurcated optical fiber  40  terminating at and optically aligned with the micro-lens  54 . The bifurcated optical fiber  40  goes via branch  46  to the laser fiber coupler  48  and the other branch  44  to a filter detector  50 .  
         [0023]    An operational test of the test bench set-up  30  as described above was conducted. The fiber used was a 3.5 micron core single mode fiber. The test specimen was a CY5 dye on a glass slide. The specimen was diluted with water to a solution concentration of 1 mg/ml. The spot was about 2 mm in diameter. The laser diode and the PMT were turned on. The PMT was calibrated. The background signal was measured. The sample was placed under the lens. An increase in signal was observed. Confocal effect was observed. In the test, the z axis (vertical distance to the spot) was adjusted, up and down, in increments of {fraction (1/2)} mm. The signal was observed to diminish when adjusted off the calibration point for which the confocal effect was observed. The optical signal is collected by the PMT, converted to voltage and read through a voltmeter.  
         [0024]    Numerous modifications and alterations can be made to the apparatus and processes of the invention without departing from its scope as defined in the following claims and it is intended that the claims cover such modifications and alterations as may permissibly fall within their scope and equivalents thereof.