OPTIMIZED METHOD FOR LID BIOSENSOR RESONANCE DETECTION

• US 20110238382A1
• Filed: 06/02/2011
• Published: 09/29/2011
• Est. Priority Date: 03/10/2006
• Status: Active Grant

• Current Assignee: Garrett A. Piech, Jacques Gollier, Michael B. Webb, Qi Wu
• Original Assignee: Garrett A. Piech, Jacques Gollier, Michael B. Webb, Qi Wu
• Inventors: Gollier, Jacques, Piech, Garrett A., Webb, Michael B., Wu, Qi
• Granted Patent: US 8,510,082 B2
• Time in Patent Office: Days
• US Class Current: 702/191
• CPC Class Codes: G01J 3/02 Details
• CPC Class Codes: G01J 3/0218 using optical fibers
• CPC Class Codes: G01J 3/1895 using fiber Bragg gratings or gratings integrated in a waveguide
• CPC Class Codes: G01J 3/28 Investigating the spectrum using colour filters G01J3/51
• CPC Class Codes: G01J 3/2803 using photoelectric array detector
• CPC Class Codes: G01N 21/7743 the reagent-coated grating coupling light in or out of the waveguide

Abstract

An optical interrogation system is described herein that can interrogate a label-independent-detection (LID) biosensor and monitor a biological event on top of the biosensor without suffering from problematical parasitic reflections and/or problematical pixelation effects.

Claims

1. An optical interrogation system comprising:

a launch system that emits an optical beam towards a biosensor;

a receive system that collects an optical beam from the biosensor and then outputs a signal which corresponds to the collected optical beam; and

the receive system includes a spectrometer which has a misaligned entrance spectrometer slit or fiber.

2. An optical interrogation system comprising:

a launch system that emits an optical beam towards a biosensor;

a receive system that collects an optical beam from the biosensor and then outputs a signal which is representative of the collected optical beam; and

a processor that reduces pixelation oscillations in an optical resonance of the signal by oversampling at least a portion of the optical resonance, smoothing the optical resonance and calculating a resonance location or centroid that is based on the smoothed-oversampled optical resonance.

3. The optical interrogation system of claim 2, wherein said processor oversamples and then smoothes the optical resonance or said processor smoothes and then oversamples the optical resonance.

4. The optical interrogation system of claim 2, wherein said centroid has a threshold that can be raised due to the oversampling of the optical resonance such that the threshold effectively excludes background noise and excludes pixelation oscillations which are not desired in the smoothed-oversampled optical resonance.

5. The optical interrogation system of claim 2, wherein said oversampled optical resonance is smoothed by:

a low pass filter;

an interpolation process.

a cubic spline interpolation process.

6. The optical interrogation system of claim 2, wherein said optical resonance is oversampled and smoothed by:

calculating a Fourier transform of the optical resonance;

multiplying the Fourier transform by a filter function;

adding zeros on a left and a right of the filtered function; and

calculating an inverse Fourier transform to obtain the smoothed-oversampled optical resonance.

7. The optical interrogation system of claim 2, wherein said optical resonance is oversampled and smoothed by:

oversampling the optical resonance in the signal to resemble a stairstep function; and

convolving the oversampled optical resonance by a low pass filter.

8. A method for interrogating a biosensor, said method comprising the steps of:

emitting an optical beam towards a biosensor;

collecting an optical beam from the biosensor

generating a signal which corresponds to the collected optical; and

reducing oscillations in an optical resonance of the signal caused by a problematical pixelation effect by;

oversampling at least a portion of the optical resonance;

smoothing the optical resonance; and

calculating a resonance location or centroid that is based on the smoothed-oversampled optical resonance.

9. The method of claim 8, wherein said oversampling step and said smoothing step are interchangeable in sequence.

10. The method of claim 8, wherein said centroid has a threshold that can be raised due to the oversampling of the optical resonance such that the threshold effectively excludes background noise and excludes pixelation oscillations which are not desired in the smoothed-oversampled optical resonance.

11. The method of claim 8, wherein said oversampled optical resonance is smoothed by:

a low pass filter;

an interpolation process.

a cubic spline interpolation process.

12. The method of claim 8, wherein said oversampling step and smoothing step are performed by:

calculating a Fourier transform of the optical resonance;

multiplying the Fourier transform by a filter function;

adding zeros on a left and a right of the filtered function; and

calculating an inverse Fourier transform to obtain the smoothed-oversampled optical resonance.

13. The method of claim 8, wherein said oversampling step and smoothing step are performed by:

oversampling the optical resonance to resemble a stairstep function; and

convolving the oversampled optical resonance by a low pass filter.

14. The method of claim 8, wherein the entire optical resonance within the signal is oversampled and smoothed.

15. The method of claim 8, wherein a portion of the optical resonance within the signal that is located near a threshold in the centroid is oversampled and smoothed.

16. An optical interrogation system comprising:

a launch system that emits an optical beam towards a biosensor;

a receive system that collects an optical beam from the biosensor and then outputs a signal which corresponds to the collected optical beam; and

a processor that applies a low pass filter to the signal, wherein the low pass filter has a low pass filter width wide enough to suppress detrimental effects of parasitic fringes located on each side of an optical resonance represented within the signal by applying the low pass filter to the signal, wherein the parasitic fringes are generated at least by presence of linearly polarized parasitic reflections, and wherein the linearly polarized parasitic reflections are caused by the optical beam which passes through a substrate of the biosensor and is then reflected from a top surface of the biosensor.

17. The optical interrogation system of claim 16, wherein the low pass filter has a filter width of 500 pm.

18. The optical interrogation system of claim 16, further comprising an optical isolator located between the biosensor and both a lensed fiber of the launch system and a lensed fiber of the receive system, wherein the optical isolator filters out parasitic reflections caused by a part of the optical beam reflected from a face of the substrate of the biosensor.

19. A method for interrogating a biosensor, said method comprising the steps of:

emitting an optical beam towards the biosensor;

collecting an optical beam from the biosensor;

generating a signal which corresponds to the collected optical beam; and

applying a low pass filter to the signal, wherein the low pass filter has a low pass filter width wide enough to suppress detrimental effects of parasitic fringes located on each side of an optical resonance represented within the signal by applying the low pass filter to the signal, wherein the parasitic fringes are generated at least by presence of linearly polarized parasitic reflections, and wherein the linearly polarized parasitic reflections are caused by the optical beam which passes through a substrate of the biosensor and is then reflected from a top surface of the biosensor.

20. The method of claim 19, wherein said low pass filter is represented as follows:

Y′

=Gy

where;

y is the signal;

represents a convolution product;

G is a filter function; and

Y′

is a filtered signal.

21. The method of claim 19, wherein said low pass filter is represented as follows:

Y1=G*FFT(y); and

Y′

=FFT<sup>−

1</sup>(Y1)

where;

y is the signal;

G is a filter function;

FFT is a Fourier transform;

FFT<sup>−

1</sup> is an inverse Fourier transform; and

Y′

is a filtered signal.

22. The method of claim 19, wherein the low pass filter has a filter width of 500 pm.

23. The method of claim 19, further comprising a step of inserting an optical isolator between the biosensor and both a lensed fiber of a launch system and a lensed fiber of a receive system, wherein the optical isolator filters out the parasitic reflections caused by a part of the optical beam reflected from a face of the substrate of the biosensor.