US20010031502A1 - Biochip detection system - Google Patents

Abstract

A biochip detection system detects and locates samples that are labeled with multiple fluorescent tags and are located on a biochip. This biochip detection system includes a charge coupled device (CCD) sensor, a broad spectrum light source, a lens, a light source filter, and a sensor filter. The CCD sensor comprises two dimensional CCD arrays to simultaneously detect light waves from at least a substantial portion of the biochip. The broad spectrum light source is optically coupled to the CCD sensor and is configured to be utilized with a variety of different fluorescent tags which have differing excitation wavelengths.

The lens and the CCD sensor are optimized and matched to each other such that the sensor operates at or below the diffraction rating of the lens. Further, the resolution of the CCD sensor is matched to the samples on the biochip such that the CCD sensor oversamples each of the samples a sufficient number of times. Additionally, the lens is configured to frame at least a substantial portion of the biochip.

The biochip detection system is optimized to provide a higher dynamic range, increased sensitivity, and faster throughput compared to system utilizing laser scanners. Further, the biochip detection system is capable of utilizing a same broad spectrum light source to excite samples labeled with a variety of fluorescent tags.

Description

FIELD OF THE INVENTION
• The invention relates to the field of detectors for analysis of biological samples located on biochips. More particularly, the invention relates to the field of detectors that analyze samples labeled with a tag while utilizing a charge coupled device sensor.[0001]
BACKGROUND OF THE INVENTION
• Detection devices that detect and locate samples contained on a biochip via laser light sources and laser scanners are well known in the art. These detection devices require that the samples be labeled by a fluorescent tag. Typically, these detection devices rely on laser light sources to excite the samples that are labeled by a fluorescent tag and causes biologically active samples to output emitted light waves. The laser source is scanned to serially excite each sample on the biochip to detect any emitted light waves from the samples that are biologically active.[0002]
• Unfortunately, these detection devices utilizing either the laser light source or the laser scanner suffer from various drawbacks. First, laser scanners utilized to detect the emitted light waves from the exited samples on the biochip typically require wait times upwards of five minutes for sufficient resolution. Because laser scanners operate as a serial scanning device by sequentially detecting one sample at a time on the surface of the biochip, laser scanners are inherently inefficient at detecting the emitted light waves from an array of samples.[0003]
• Further, laser light sources utilized within the detection devices inherently only emit coherent light waves which span over an extremely narrow range of wavelengths. Fluorescent tags are generally responsive to a single frequency of light or light from a narrow frequency band. Thus, the use of the laser light sources severely limits the flexibility of those detection devices because only one type of fluorescent tag can be used. To use other tags, additional laser sources must be used. Further, to evaluate a biochip that has been treated with multiple tags, the prior art's long duration scan cycle must be performed for each one of the required laser sources.[0004]
• For example, if samples on a biochip were labeled with two different fluorescent tags and the different tags required light waves with substantially different excitation wavelengths, analyzing these samples would require the user to change laser light sources the analysis of all the samples were completed. Additionally, to be able to handle samples labeled with different fluorescent tags with differing excitation wavelengths, the user is required to have access to a variety of laser light sources. Since laser light sources are costly and specialized items, there are substantial costs and inconveniences associated with utilizing these prior detection devices.[0005]
• Therefore, it is desirable to have an ability to detect and locate samples labeled with multiple tags contained on a biochip, without the need for a laser light source. It is also desirable have an ability to detect and locate samples labeled with a tag contained on a biochip, without the need for a serial scanning device.[0006]
SUMMARY OF THE INVENTION
• The invention is a biochip detection system for detecting and locating samples that are labeled with multiple tags and are located on a biochip. This biochip detection system includes a charge coupled device (CCD) sensor, a broad spectrum light source, a lens, a light source filter, and a sensor filter. The CCD sensor comprises two dimensional CCD arrays to simultaneously detect light waves from at least a substantial portion of the biochip. The broad spectrum light source is optically coupled to the CCD sensor and is configured to be utilized with a variety of different fluorescent tags which have differing excitation wavelengths.[0007]
• The light source filter is optically coupled between the light source and the biochip and is configured to only substantially allow light waves that have an excitation wavelength corresponding to a particular fluorescent tag to reach the biochip. The light source filter prevents light waves that have similar wavelengths to an emission wavelength of the particular fluorescent tag from reaching the biochip or the CCD sensor. The sensor filter is optically coupled between the biochip and the CCD sensor and is configured to only substantially allow light waves that have the emission wavelength corresponding to the fluorescent tag to reach the CCD sensor. The sensor filter prevents extraneous light waves from giving the CCD sensor false signals.[0008]
• The lens and the CCD sensor are optimized and matched to each other such that the sensor operates at or below the diffraction rating of the lens. Further, the resolution of the CCD sensor is matched to the samples on the biochip such that the CCD sensor oversamples each of the samples a sufficient number of times. Additionally, the lens is configured to frame at least a substantial portion of the biochip.[0009]
• The biochip detection system is optimized to provide a higher dynamic range, increased sensitivity, and faster throughput compared to system utilizing laser scanners. Further, the biochip detection system is capable of utilizing a same broad spectrum light source to excite samples labeled with a variety of fluorescent tags.[0010]
BRIEF DESCRIPTION OF THE DRAWINGS
• FIG. 1 illustrates a schematic side view of internal elements of the preferred embodiment of the present invention.[0011]
• FIG. 2 illustrates a schematic side view of the preferred embodiment configured to analyze two sets of samples on a single biochip with each set of samples labeled with a different fluorescent tag.[0012]
• FIG. 3 illustrates a schematic side view of the preferred embodiment configured to analyze a plurality of samples on a single biochip with the plurality of samples labeled with multiple fluorescent tags.[0013]
• FIG. 4 is a graph that illustrates a relationship between a light intensity versus a wavelength of an excitation light of a particular fluorescent tag, an emitted light of this particular fluorescent tag, and the source light as utilized in the present invention.[0014]
• FIG. 5 illustrates a top view of an external housing of an alternate embodiment.[0015]
• FIG. 6 illustrates a side view of the external housing of the alternate embodiment.[0016]
• FIG. 7 illustrates a perspective view of the external housing of the alternate embodiment.[0017]
• FIG. 8 illustrates a side view of a camera housing of the preferred embodiment.[0018]
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
• FIG. 1 illustrates a side view of the preferred embodiment of the present invention. This preferred embodiment is a[0019]biochip detection system100 as shown in FIG. 1. Thebiochip detection system100 preferably includes alens120, asensor filter130, a charge coupled device (CCD)sensor140, alight source150, and alight source filter160. Preferably, thebiochip detection system100 is configured to detect and locatesamples110 within abiochip170. Thesamples110 and thebiochip170 are shown for exemplary purposes only and are not intended to be part of the present invention. For the purposes of this specification, thebiochip170 is configured to have an array ofsamples110 arranged in a predetermined number of rows and columns on top of a substrate. Further, thesamples110 contained within thebiochip170 are capable of including DNA or other biological material. For thebiochip detection system100 to properly operate, thesamples110 are labeled with a tag. Thebiochip170 in the preferred embodiment is configured to holdsamples110 which are labeled with multiple tags. However, it will be apparent to those skilled in the art to utilizesamples110 only labeled by one tag on thebiochip170. Thesamples110 in the preferred embodiment are labeled with a fluorescent tag. However, it will be apparent to those skilled in the art to substitute this fluorescent tag with a chemiluminescent tag, colormetric tag, or the like. The process of labeling samples with a tag is well known in the art.
• The[0020]biochip detection system100 detects and locates which ones of the plurality ofsamples110 are fluorescently labeled within thebiochip170. Thebiochip detection system100 operates by exciting thesamples110 labeled by a fluorescent tag with light waves having an excitation wavelength thereby generatingsamples110 that emit light waves having an emitted wavelength. Next, theCCD sensor140 simultaneously detects the light waves having the emitted wavelength from at least a portion of thebiochip170. Specific elements and procedures of thebiochip detection system100 are described in detail below.
• The[0021]CCD sensor140 is preferably configured to include a two dimensional array of charge coupled devices. Preferably by having theCCD sensor140 as a two dimensional sensor, thebiochip detection system100 is capable of simultaneously imaging either an entire area or a portion of the biochip170 (depending on the size of the biochip170) for light waves emitted by thesamples110. By simultaneously imaging all thebiochip170, theCCD sensor140 allows thebiochip detection system100 to complete the detection process in most cases well under one minute and in some cases in twenty-five seconds. In an alternate embodiment, theCCD sensor140 comprises cooled charge coupled devices. By having the charge coupled devices within theCCD sensor140 cooled, background noise is reduced and signal clarity is maximized. In this preferred embodiment, theCCD sensor140 is manufactured by Sony Corporation having the model number ICX 038DLA. It will be apparent to those skilled in the art to utilize adifferent CCD sensor140.
• The[0022]light source150 is preferably a broad spectrum bulb that is configured to output light waves over a wide range of wavelengths. Preferably, thelight source150 is optically coupled to thebiochip170. Because thelight source150 generates light waves over a wide range of wavelengths, thelight source150 is capable of forming light waves to excite samples labeled with a wide variety of fluorescent tags. In this preferred embodiment, thelight source150 is manufactured by General Electric Corporation having themodel number 150 Watt EKE. It will be apparent to those skilled in the art to select a different light source.
• The[0023]lens120 is preferably a compound lens that includes multiple lens elements. Thelens120 is located in an optical path between thebiochip170 and theCCD sensor140. Preferably, thelens120 transmits light waves emitted from thesamples110 to theCCD sensor140. Thelens120 is capable of adjusting and optimizing a magnification parameter such that a desired portion of thebiochip170 is captured by theCCD sensor140 with an appropriate field of view. Preferably, thelens120 is configured such that theCCD sensor140 operates at or below the diffraction limit of thelens120. In this preferred embodiment, thelens120 is manufactured by Fujinon having a focal length of 25 millimeters and f-stop of 1:0.85. It will be apparent to those skilled in the art that thelens120 can be substituted for a different lens or multiple lenses.
• Preferably, the[0024]light source filter160 is optically coupled between thelight source150 and thebiochip170. Thelight source filter160 is preferably configured to substantially only allow light waves generated by thelight source150 with a predetermined excitation wavelength to reach thebiochip170. The predetermined excitation wavelength corresponds to a particular wavelength that excites one of thesamples110 that is labeled with a particular fluorescent tag. The predetermined excitation wavelength depends on the sample in conjunction with the fluorescent tag. In other words, thelight source filter160 substantially blocks all light waves from thelight source150 with wavelengths other than the predetermined excitation wavelength from reaching thebiochip170. By blocking substantially all light waves that have wavelengths other than the predetermined excitation wavelength, thelight source filter160 prevents erroneous light waves generated by thelight source150 from giving theCCD sensor140 erroneous signals.
• Preferably, the[0025]sensor filter130 is optically coupled between theCCD sensor140 and thebiochip170. As shown in FIG. 1, thesensor filter130 is preferably between theCCD sensor140 and thelens120. By placing thesensor filter130 between thelens120 and theCCD sensor140, the chances of distorting the light waves for detection by theCCD sensor140 is minimized. Nevertheless, it will be apparent to those skilled in the art that thesensor filter130 also can be configured between thelens120 and thebiochip170. Thesensor filter130 is preferably configured to substantially only allow light waves that are emitted from a sample labeled with a particular fluorescent tag that has a predetermined emitted wavelength to reach theCCD sensor140. The predetermined emitted wavelength occurs during excitation of this sample and depends on the sample in conjunction with the particular fluorescent tag. Preferably, thesensor filter130 is optimized to parameters of thelight source150 and prevents extraneous light waves from reaching theCCD sensor140 thereby increasing the accuracy and sensitivity of thebiochip detection system100. It will be apparent to those of ordinary skill in the art that the filter selection is made to correspond with the fluorescent tags and also the sample type.
• The[0026]biochip detection system100 is capable of efficiently detecting and locatingsamples110 on thebiochip170. TheCCD sensor140 and thelens120 are preferably optimized relative to each other and also to thesamples110 on thebiochip170. In particular, theCCD sensor140 preferably has a transmission resolution to oversample each of thesamples110 by eight to nine times. For example, theCCD sensor140 is preferably configured to have each of thesamples110 be optically detected by eight to nine pixels. Additionally, thelens120 is preferably optimized to allow theCCD sensor140 to operate at or below the diffraction limit of thelens120.
• In operation, the[0027]biochip detection system100 is preferably configured to analyze thebiochip170. Thesamples110 are contained within thebiochip170 and are labeled with a multiple fluorescent tags. Thebiochip detection system100 initiates operation by activating thelight source150. The light waves emitted from thelight source150 are represented with alight wave180 in FIG. 1. Next, thelight wave180 preferably passes through thelight source filter160. As thelight wave180 passes through the filter, some wavelengths of thelight wave180 are blocked. A resultant light wave after passage through thelight source filter160 is represented as alight wave190 as shown in FIG. 1. Preferably, thelight wave190 only substantially includes light waves with a predetermined excitation wavelength which correspondingly excites thesamples110 which are labeled with the particular fluorescent tag.
• As the[0028]samples110 are excited by the predetermined excitation wavelength in thelight wave190, thesamples110 produce light waves which are represented by alight wave200 as shown in FIG. 1. Thelight wave200 preferably includes light waves with a predetermined emission wavelength which are produced by thesamples110. Thelight wave200 then passes through thelens120. Some extraneous light waves with the predetermined excitation wavelength also pass through thelens120 as shown by thelight wave190. Next, thesensor filter130 preferably blocks out substantially all light waves with wavelengths other than the predetermined emission wavelength; thesensor filter130 substantially only allows light waves represented by thelight wave200 to reach theCCD sensor140. By substantially allowing only light waves having the predetermined emission wavelength to reach theCCD sensor140, theCCD sensor140 is capable of accurately detecting and locating thesamples110 on thebiochip170. As a result, theCCD sensor140 is prevented from erroneously detecting stray light waves.
• The[0029]biochip detection system100 is capable of accommodating a variety of fluorescent tags without switching thelight source150, thelens120, or theCCD sensor140. To utilize multiple fluorescent tags with thebiochip detection system100, only thelight source filter160 and theemission filter130 are preferably changed. By merely changing thelight source filter160 and thesensor filter130, thebiochip detection system100 is capable of detecting and locating the samples labeled by this new fluorescent tag. Preferably, thelight source filter160 is changed such that substantially only light waves with an excitation wavelength corresponding to a new fluorescent tag reach the samples labeled by this new fluorescent tag. Further, thesensor filter130 is preferably changed such that substantially only light waves with an emission wavelength corresponding to the new fluorescent tag reach theCCD sensor140.
• FIG. 2 illustrates the[0030]biochip detection system100 configured to analyze abiochip210 having two sets of samples with each set of samples labeled by a different fluorescent tag. The configuration of thebiochip detection system100 which includes thelight source150, thelens120, the sensor filters130 and130′, the light source filters160 and160′, and theCCD sensor140 is similar to thebiochip detection system100 in FIG. 1. The sensor filters130 and130′ are used interchangeably, one each for detecting the presence of different fluorescent tags. The light source filters160 and160′ are used interchangeably to illuminate thebiochip210 with different wavelengths of light. It will be apparent to those skilled in the art that additional filters can be utilized. Thebiochip210 contains a first set ofsamples220 which is labeled by a first fluorescent tag, and a second set ofsamples230 which is labeled by a second fluorescent tag. First, thebiochip detection system100 is configured to locate and detect the first set ofsamples220. For proper configuration to detect and locate the first set ofsamples220, the sourcelight filter160 preferably substantially only allows light waves with an excitation wavelength corresponding to the first fluorescent tag to reach thebiochip210. Further, thesensor filter130 preferably substantially only allows light waves with an emission wavelength corresponding to the first fluorescent tag to reach theCCD sensor140.
• After the[0031]biochip detection system100 is finished detecting and locating the first set ofsamples220, thesystem100 is configured to detect and locate the second set ofsamples230. For proper configuration to detect and locate the second set ofsamples230, the sourcelight filter160′ preferably substantially only allows light waves with an excitation wavelength corresponding to the second fluorescent tag to reach thebiochip210. Further, thesensor filter130′ preferably substantially only allows light waves with an emission wavelength corresponding to the second fluorescent tag to reach theCCD sensor140. The filter can be manually changed. For systems used to routinely tests samples labeled with several known fluorescent tags, the filters can be automatically interchanged, for example, using a so-called “jukebox”. Although the first set ofsamples220 and the second set ofsamples230 are described as being labeled with a fluorescent tag, it will be apparent to those skilled in the art to substitute a fluorescent tag with a chemiluminescent tag, colormetric tag, and the like.
• FIG. 3 illustrates the[0032]biochip detection system100 configured to analyze abiochip700 having a plurality ofsamples710 wherein each of the plurality ofsamples710 are preferably labeled by multiple fluorescent tags. The configuration of thebiochip detection system100 which includes thelight source150, thelens120, the sensor filters130 and130′, the light source filters160 and160′, and theCCD sensor140 remain identical to thebiochip detection system100 in FIG. 2. The sensor filters130 and130′ are used interchangeably, one each for detecting the presence of different fluorescent tags. The light source filters160 and160′ are used interchangeably to illuminate thebiochip700 with different wavelengths of light. It will be apparent to those skilled in the art that additional filters can be utilized. The plurality ofsamples710 are represented as being labeled by a firstfluorescent tag720 and a secondfluorescent tag730. It will be apparent to those with ordinary skill in the art to label the plurality ofsamples710 with any number of tags.
• First, the[0033]biochip detection system100 is configured to locate and detect the plurality ofsamples710 that are labeled with the firstfluorescent tag720. For proper configuration to detect and locate the plurality ofsamples710 that are labeled with the firstfluorescent tag720, the sourcelight filter160 preferably substantially only allows light waves with an excitation wavelength corresponding to the first fluorescent tag to reach thebiochip700. Further, thesensor filter130 preferably substantially only allows light waves with an emission wavelength corresponding to the firstfluorescent tag720 to reach theCCD sensor140.
• After the[0034]biochip detection system100 is finished detecting and locating the plurality ofsamples710 that are labeled with the firstfluorescent tag720, thesystem100 is configured to detect and locate the plurality ofsamples710 that are labeled with thesecond fluorescent tag730. For proper configuration to detect and locate the plurality ofsamples710 that are labeled with thesecond fluorescent tag730, the sourcelight filter160′ preferably substantially only allows light waves with an excitation wavelength corresponding to thesecond fluorescent tag730 to reach thebiochip700. Further, thesensor filter130′ preferably substantially only allows light waves with an emission wavelength corresponding to thesecond fluorescent tag730 to reach theCCD sensor140. The filter can be manually changed. For systems used to routinely tests samples labeled with several known fluorescent tags, the filters can be automatically interchanged, for example, using a so-called “jukebox”. Although the plurality ofsamples710 are described as being labeled with multiple fluorescent tags, it will be apparent to those skilled in the art to substitute multiple fluorescent tags with multiple chemiluminescent tags, colormetric tags, and the like.
• FIG. 4 illustrates a graph representing intensity of light along the vertical axis and wavelength along the horizontal axis. A[0035]curve300 is representative of the light output from the light source150 (FIGS. 1, 2, and3). As observed from thecurve300, thelight source150 outputs light waves preferably at an uniform intensity over a range of wavelengths. Acurve310 is centered around λ_Excitedand represents a desired light intensity and wavelength to strike a sample labeled with a particular fluorescent tag in order to excite this sample. Acurve320 is centered around λ_Emittedand represents an emitted light intensity and wavelength from this sample while this sample is excited by light waves represented by thecurve310.
• The[0036]curves300,310, and320 illustrate the functions of thelight source filter160 and thesensor filter130 as illustrated in FIGS. 1, 2, and3 and as described above. For example, while in operation, thelight source150 preferably outputs light waves represented by thecurve300. Preferably, thelight source filter160 substantially only allows light waves that have wavelengths centered around the λ_Excitedto reach the sample labeled by this particular fluorescent tag. Consequently, these light waves that have wavelengths centered around the λ_Excitedexcite the sample and are represented by thecurve310. While excited, this sample preferably emits light waves that have wavelengths centered around the λ_Emitted. Preferably, thesensor filter130 substantially only allows light waves that have wavelengths centered around the λ_Emitted(which are represented by the curve320) to reach theCCD sensor140.
• By having the source[0037]light filter160 prevent light waves that have wavelengths centered around the λ_Emittedfrom striking this sample, the sourcelight filter160 prevents erroneous light waves from passing through thesensor filter130 and striking theCCD sensor140. Further, by having thesensor filter130 prevent light waves that have wavelengths centered around the λ_Excitedfrom passing through thebiochip170 and then striking theCCD sensor140, thesensor filter130 prevents erroneous readings from theCCD sensor140. As a result of the sourcelight filter160 and thesensor filter130, fewer or no stray, erroneous light waves strike theCCD sensor140.
• FIG. 5 illustrates an external top view of an alternate embodiment of the[0038]biochip detection system100. Amain housing400 is configured to hold thebiochip170 and thelight source150. Themain housing400 is also configured to be light proof. By being light proof, themain housing400 prevents extraneous light waves from giving theCCD sensor140 erroneous signals. At least one articulatingmirror410 is utilized within themain housing400 for appropriately directing light waves from thelight source150 to thebiochip170. Acamera housing420 is utilized to hold theCCD sensor140 and coupled to themain housing400.
• FIG. 6 illustrates an external side view of the alternate embodiment of the[0039]biochip detection system100. Themain housing400 includes adrawer440 which allows a user to change thebiochip170, adjust thelight source filter160, and/or adjust thelight source150. Thedrawer440 includes appropriate seals to engage themain housing400 such that themain housing400 remains light proof. Afilter box480 is coupled to themain housing400. Thefilter box480 is configured to securely hold thesensor filter130 and has anopening450 to accept thesensor filter130. Thecamera housing420 is mounted to thefilter box480 via acamera mounting bracket430. Preferably, alight shield510 is mounted between thecamera housing420 and thefilter box480 to prevent stray light waves from entering either thecamera housing420, themain housing400, or thefilter box480.
• FIG. 7 illustrates an external perspective view of the alternate embodiment of the[0040]biochip detection system100. For the sake of clarity, thecamera housing420, thecamera mounting bracket430, and thelight shield510 are omitted from FIG. 6. Afiber optic port490 is provided in themain housing400. Thefiber optic port490 allows thebiochip detection system100 to interface with an external light source which is capable of transmitting light via a fiber optic cable connected to the external light and thefiber optic port490. Thefilter box480 has alight channel530 for allowing light to pass through thefilter box480 from themain housing400 to thecamera housing420. Further, thefilter box480 also has anopening505 to accept aball plunger500. Afilter holder460 is configured to hold at least onesensor filter130 and has a plurality ofnotches520. Thefilter holder460 is configured to slide through theopening450 in thefilter box480. Theball plunger500 is configured to engage one of the plurality ofnotches520 to appropriately position thefilter holder460 relative to thefilter box480.
• A preferred embodiment of the external housing is similar to the alternate embodiment as shown in FIGS. 5, 6, and[0041]7. A main difference between the alternate embodiment and the preferred embodiment is that the preferred embodiment does not utilize thefilter box480 and thefilter holder460 as shown in FIGS. 5, 6, and7. Instead, the preferred embodiment of the external housing preferably couples thecamera mount bracket430 directly to themain housing400. Further, thecamera housing420 as shown in FIGS. 5 and 6 is modified and replaced in the preferred embodiment by acamera housing600. Thecamera housing600 is illustrated in FIG. 8. Unlike the alternate embodiment of the camera housing420 (FIGS. 5 and 6), thecamera housing600 preferably contains afilter wheel610 which holds at least onesensor filter130. Preferably, thefilter wheel610 optically couples thesensor filter130 between thelens120 and theCCD sensor140. Further, thefilter wheel610 is preferably configured to change positions thus allowingdifferent sensor filters130 to be optically coupled between thelens120 and theCCD sensor140.
• The present invention has been described in terms of specific embodiments incorporating details to facilitate the understanding of the principles of construction and operation of the invention. Such reference herein to specific embodiments and details thereof is not intended to limit the scope of the claims appended hereto. It will be apparent to those skilled in the art that modifications can be made in the embodiments chosen for illustration without departing from the spirit and scope of the invention.[0042]
• Specifically, it will be apparent to one of ordinary skill in the art that the device of the present invention could be implemented in several different ways and the apparatus disclosed above is only illustrative of the preferred embodiment of the invention and is in no way a limitation. For example, it would be within the scope of the invention to vary the dimensions disclosed herein. In addition, it will be apparent that the various aspects of the above-described invention can be utilized singly or in combination with one or more of the other aspects of the invention described herein. In addition, the various elements of the present invention could be substituted with other elements.[0043]

Claims (19)

What is claimed is:

1. An apparatus configured for analyzing a sample, the apparatus comprising:

a. a sensor configured for detecting emitted light from the sample;

b. a light source optically coupled to the sensor configured to illuminate the sample with an excitation light having a first wavelength; and

c. a matched filter optically coupled between the sample and the sensor for allowing substantially only the emitted light having a second wavelength to pass therethrough and strike the sensor.

2. The apparatus according to

claim 1

wherein the sensor is a charge coupled device.

3. The apparatus according to

claim 1

wherein the sensor is a two dimensional charge coupled device.

4. The apparatus according to

claim 1

wherein the light source is a coherent light source such as a laser.

5. The apparatus according to

claim 1

wherein the light source is a broad spectrum light source and the apparatus further comprising a secondary filter located between the broad spectrum light source and the sample such that substantially only the excitation light with the first wavelength reaches the sample.

6. The apparatus according to

claim 1

further comprising a lens optically coupled between the sample and the sensor for focussing the emitted light.

7. An apparatus configured for analyzing a biochip containing a tag labeled sample, the apparatus comprising

a. a two dimensional CCD sensor for detecting emitted light from the tag labeled sample on the biochip; and

b. a lens optically coupled between the two dimensional CCD sensor and the biochip and configured to transmit the emitted light to the two dimensional CCD sensor wherein the lens is configured to be within two inches of the tag labeled sample.

8. The apparatus according to

claim 7

further comprising a light source to illuminate the tag labeled sample.

9. The apparatus according to

claim 8

wherein the light source is a broad spectrum light source.

10. The apparatus according to

claim 8

further comprising a light source filter configured to be optically coupled between the light source and the tag labeled sample wherein the light source filter is configured to only substantially allow light waves having an excitation wavelength corresponding to the tag labeled sample to reach the tag labeled sample.

11. The apparatus according to

claim 7

further comprising a sensor filter optically coupled between the two dimensional CCD sensor and the lens wherein the sensor filter is configured to only substantially allow light waves emitted from the tag labeled sample to reach the CCD sensor.

12. A system configured to detect and locate fluorescently labeled samples on a biochip, the biochip having a plurality of samples, the system comprising:

a. a light source configured to simultaneously illuminate all the fluorescently labeled samples;

b. a two dimensional CCD sensor optically coupled to the light source and configured for concurrently detecting and locating emitted light from the fluorescently labeled samples on the biochip; and

c. a lens optically coupled between the light source and the two dimensional CCD sensor and configured to appropriately magnify the biochip onto the two dimensional CCD sensor.

13. A system configured to detect and locate a first set of samples labeled by a first fluorescent tag and a second set of samples labeled by a second fluorescent tag, the system comprising:

a. a light source configured to simultaneously illuminate all the flourescently labeled samples;

b. a two dimensional CCD sensor optically coupled to the light source and configured for concurrently detecting and locating a first emitted light from the first set of samples and a second emitted light from the second set of samples;

c. a lens optically coupled between the light source and the two dimensional CCD sensor and configured to transmit the first emitted light and the second emitted light to the two dimensional CCD sensor;

d. a first light source filter selectively and optically coupled to the light source and configured for substantially only transmitting a first illuminating light to the first set of samples to excite the first set of samples;

e. a first sensor filter selectively and optically coupled to the two dimensional CCD sensor and configured for substantially only transmitting the first emitted light to the two dimensional CCD sensor;

f. a second light source filter selectively and optically coupled to the light source and configured for substantially only transmitting a second illuminating light to the second set of samples to excite the second set of samples; and

g. a second sensor filter selectively and optically coupled to the two dimensional CCD sensor and configured for substantially only transmitting the second emitted light to the two dimensional CCD sensor.

14. A method of detecting and locating a first sample labeled by a first fluorescent tag and a second sample labeled by a second fluorescent tag wherein the first sample and the second sample are on a biochip, the method comprising the following steps:

a. selectively exciting the first sample by substantially directing only light having a first excitation wavelength for exciting the first fluorescent tag from a broad spectrum light source to the first sample;

b. selectively detecting the first sample during the step of exciting the first sample by substantially directing only light having a first emission wavelength emitted by and from the first sample to a two dimensional CCD sensor;

c. selectively exciting the second sample by substantially directing only light having a second excitation wavelength for exciting the second fluorescent tag from the broad spectrum light source to the second sample; and

d. selectively detecting the second sample during the step of exciting the second sample by substantially directing only light having a second emission wavelength emitted by and from the second sample to the two dimensional CCD sensor.

15. A method of detecting and locating a sample labeled with a fluorescent tag, the method comprising the following steps:

a. illuminating the sample with a light source;

b. focussing an emitted light from the sample via a lens wherein the lens is located at a distance that is less than 6.0 inches from the sample; and

c. detecting the emitted light from the sample via a CCD sensor.

16. The method according to

claim 15

further comprising inserting a light source filter adjacent to the light source wherein the light source filter is configured to substantially block light waves that have wavelengths outside an excitation wavelength range of the fluorescent tag from reaching the sample.

17. The method according to

claim 15

further comprising inserting a sensor filter adjacent to the CCD sensor wherein the sensor filter is configured to substantially block light waves that have wavelengths outside an emission wavelength range of the fluorescent tag from reaching the CCD sensor.

18. The method according to

claim 15

wherein the CCD sensor comprises a two dimensional array of charge coupled devices.

19. The method according to

claim 15

wherein the light source is a broad spectrum light source.

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