(12) United States Patent
`Perov et al.
`
`I lllll llllllll Ill lllll lllll lllll lllll lllll 111111111111111111111111111111111
`US006329661Bl
`US 6,329,661 Bl
`Dec. 11, 2001
`
`(10) Patent No.:
`(45) Date of Patent:
`
`(54) BIOCHIP SCANNER DEVICE
`
`(75)
`
`Inventors: Alexander Perov, Troitsk (RU);
`Alexander I. Belgovskiy, Mayfield
`Heights, OH (US); Andrei D.
`Mirzabekov, Darien, IL (US)
`
`(73) Assignee: The University of Chicago, Chicago,
`IL (US)
`
`( *) Notice:
`
`Subject to any disclaimer, the term of this
`patent is extended or adjusted under 35
`U.S.C. 154(b) by 0 days.
`
`(21) Appl. No.: 09/515,814
`
`(22)
`
`Filed:
`
`Feb.29,2000
`
`(51)
`(52)
`(58)
`
`(56)
`
`Int. Cl.7 ..................................................... GOlN 21/64
`U.S. Cl. ...................................... 250/461.2; 250/459.1
`Field of Search .............................. 250/461.2, 461.1,
`250/459.1
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`4,006,360 * 2/1977 Mueller ............................. 250/461.2
`5,061,075 * 10/1991 Alfano et al. ........................ 356/417
`5,108,179 * 4/1992 Myers .................................. 356/344
`5,418,371 * 5/1995 Aslund et al. .................... 250/458.1
`5,459,325
`10/1995 Hueton et al. .
`5,528,050
`6/1996 Miller et al. .
`5,631,734
`5/1997 Stern et al. .
`5,713,364 * 2/1998 DeBaryshe et al. ................. 128/644
`5,874,219 * 2/1999 Rava et al. ............................... 435/6
`
`6,071, 748 * 6/2000 Modlin et al. ....................... 436/174
`6,104,945 * 8/2000 Modell et al. ....................... 600/473
`6,134,002 * 10/2000 Stimpson et al. .................... 356/326
`6,215,894 * 4/2001 Zeleny et al. ........................ 382/133
`
`OTHER PUBLICATIONS
`
`DNA analysis and diagnostics on oligonucleotide microhips,
`by Yershov, G. et al, Proc. Natl. Acad. Sci. USA, vol. 93, pp.
`4913-4918, May 1996.
`* cited by examiner
`
`Primary Examiner---Constantine Hannaher
`Assistant Examiner-Albert Gagliardi
`(74) Attorney, Agent, or Firm-Joan Pennington
`
`(57)
`
`ABSTRACT
`
`A biochip scanner device used to detect and acquire fluo(cid:173)
`rescence signal data from biological microchips or biochips
`and method of use are provided. The biochip scanner device
`includes a laser for emitting a laser beam. A modulator, such
`as an optical chopper modulates the laser beam. A scanning
`head receives the modulated laser beam and a scanning
`mechanics coupled to the scanning head moves the scanning
`head relative to the biochip. An optical fiber delivers the
`modulated laser beam to the scanning head. The scanning
`head collects the fluorescence light from the biochip,
`launches it into the same optical fiber, which delivers the
`fluorescence into a photodetector, such as a photodiode. The
`biochip scanner device is used in a row scanning method to
`scan selected rows of the biochip with the laser beam size
`matching the size of the immobilization site.
`
`20 Claims, 5 Drawing Sheets
`
`LASER
`102
`
`(HeNe
`LASER
`2mW@
`594 nm)
`
`CONTROLLED(cid:173)
`TEMPERATURE TABLE 124
`
`HOST
`COMPUTER
`140
`
`POSITIONER 116
`
`ICROCHIP 122
`
`THERMO FISHER EX. 1018
`
`

`
`U.S. Patent
`
`Dec. 11, 2001
`
`Sheet 1 of 5
`
`US 6,329,661 Bl
`
`CHOPPER
`...------------DRIVER 107
`
`POSITION ER
`136
`
`LASER
`102
`
`(He Ne
`LASER
`2mW@
`594 nm)
`
`IRIS
`DIAPHRAGM
`130
`
`EMISSION
`FILTER 128
`
`LOCK-IN
`AMPLIFIER
`138
`
`ADC
`CARD
`142
`HOST
`COMPUTER
`140
`
`LENS 132
`
`100
`
`MIRROR 10
`
`MIRROR 108
`
`CHOPPER
`106
`
`POSITIONER 116
`
`OPTICAL FIBER 112
`SCANNING HEAD 118
`SCANNING MECHANICS
`126 - - -
`____ LL-l......--LENS 120
`r-...,__---l-t...,... __ __,..J...1-----' LENS --.u ...
`121
`
`ICROCHIP 122
`
`CONTROLLED(cid:173)
`TEMPERATURE TABLE 124
`
`FIG. 1
`
`THERMO FISHER EX. 1018
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`

`
`U.S. Patent
`
`Dec. 11, 2001
`
`Sheet 2 of 5
`
`US 6,329,661 Bl
`
`/
`GEL PADS 200
`\
`
`8
`
`I
`FOCUSED LASER
`BEAM 204
`
`FIG. 2
`
`I
`
`BEAM TRAJEC TORY
`202
`
`D
`
`THERMO FISHER EX. 1018
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`

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`U.S. Patent
`
`Dec. 11, 2001
`
`Sheet 3 of 5
`
`US 6,329,661 Bl
`
`OPTICAL FIBER 112
`
`~
`SCANNING HEAD 120
`
`t======I--- DEPTH OF
`FOCUS304
`....__,_......._........_......._ ......... _._......._........_......._----1
`FIELD OF
`VIEW 302
`
`CONTROLLED(cid:173)
`TEMPERATURE TABLE 124
`
`FIG. 3
`
`THERMO FISHER EX. 1018
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`

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`U.S. Patent
`
`Dec. 11, 2001
`
`Sheet 4 of 5
`
`US 6,329,661 Bl
`
`FIG. 4A
`
`BEGIN 401
`
`X SCAN AMPLITUDE 402
`
`USER INPUT 403
`
`SCAN VELOCITY 404
`
`Y INCREMENT 405
`
`NUMBER N OF ROWS TO SCAN 406 - - - -
`
`XY START POINT 407
`
`BRING SCANNING HEAD TO START
`POINT 408
`
`CLEAR COUNTERS OF SCANNED ROWS
`409
`
`INITIATE X SCAN IN
`....------.. "-" DIRECTION 411
`
`YES
`
`INITIATE X SCAN IN
`"+" DIRECTION 412
`
`THERMO FISHER EX. 1018
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`

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`U.S. Patent
`
`Dec. 11, 2001
`
`Sheet 5 of 5
`
`US 6,329,661 Bl
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`ON "START" TRIGGER PULSE FROM
`MOTION CONTROLLER INITIATE
`DATA ACQUISITION 413
`
`ON "FINISH" TRIGGER PULSE FROM
`MOTION CONTROLLER STOP DATA
`ACQUISITION 414
`
`DISPLAY SIGNAL INTENSITY
`PROFILE 415
`
`INCREMENT Y COORDINATE OF
`SCANNING HEAD BY Y INCREMENT
`416
`
`INCREASE S BY 1
`417
`
`YES
`
`NO
`
`END 420
`
`FIG. 48
`
`THERMO FISHER EX. 1018
`
`

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`US 6,329,661 Bl
`
`1
`BIOCHIP SCANNER DEVICE
`
`RELATED APPLICATION
`
`A related U.S. patent application Ser. No. 09/515,290
`entitled "A PORTABLE BIOCHIP SCANNER DEVICE",
`by Alexander Perov, Alexei Sharonov and Andrei D. Mirza(cid:173)
`bekov is being filed on the same day as the present patent
`application.
`
`CONTRACTUAL ORIGIN OF THE INVENTION
`
`The United States Government has rights in this invention
`pursuant to Contract No. W-31-109-ENG-38 between the
`United States Department of Energy (DOE) and the Uni(cid:173)
`versity of Chicago representing Argonne National Labora(cid:173)
`tory.
`
`FIELD OF THE INVENTION
`
`The present invention relates to a biochip scanner device
`used to detect and acquire fluorescence signal data from
`biological microchips (biochips) and method of use.
`
`DESCRIPTION OF THE RELATED ART
`
`2
`(biochips) and method of use are provided. The biochip
`scanner device includes a laser for emitting a laser beam. A
`modulator, such as an optical chopper modulates the laser
`beam. A scanning head receives the modulated laser beam
`5 and a scanning mechanics coupled to the scanning head
`moves the scanning head relative to the biochip.
`In accordance with features of the invention, an optical
`fiber delivers the modulated laser light to the scanning head.
`The scanning head serves for both focusing the excitation
`10 laser light onto the biochip and collecting the emitted
`fluorescence which is then delivered to a photodiode via the
`same optical fiber. The biochip scanner device is used in a
`row scanning method to scan selected rows of the biochip
`with the laser beam size matching the size of the immobi-
`15 lization sites.
`
`BRIEF DESCRIPTION OF THE DRAWINGS
`
`The present invention together with the above and other
`20 objects and advantages may best be understood from the
`following detailed description of the preferred embodiments
`of the invention illustrated in the drawings, wherein:
`FIG. 1 is a schematic and block diagram illustrating a
`biochip scanner device in accordance with the preferred
`25 embodiment;
`FIG. 2 is a diagram illustrating a method of scanning with
`the biochip scanner device in accordance with the preferred
`embodiment;
`FIG. 3 is a diagram illustrating a field of view and depth
`30 of focus of a scanning head of the biochip scanner device in
`accordance with the preferred embodiment; and
`FIGS. 4Aand 4B together provide a flow chart illustrating
`a Row Scanning (RS) method of the preferred embodiment.
`
`At the present time, biochips, after being incubated with
`a sample solution containing fluorescently labeled target
`molecules are assayed using either a microscope equipped
`with a charge coupled device (CCD) camera or a laser
`scanner. Regardless of the technique of fluorescence mea(cid:173)
`surement used, all known biochip analyzers are high(cid:173)
`resolution imaging instruments. This means that their output
`data is essentially a digital image of the chip composed of
`approximately lOOON elementary data points, where N
`represents the number of biochip immobilization sites. As a
`biochip user is typically interested in relative fluorescence 35
`intensities of the immobilization sites, an image as the
`output data format is highly redundant and requires further
`processing before the data can be analyzed. This may
`include signal integration over the immobilization sites,
`background subtraction, and normalization. The image pro- 40
`cessing is especially difficult in the case of analyzers based
`on wide-field microscopes, in which both the sensitivity and
`the image background are inherently non-uniform.
`Due to the restraints on allowable working distance of the
`objective lens, currently available imaging biochip analyzers
`cannot be readily used with biochips mounted in an optical
`flow cell. This feature would be very desirable in order to
`facilitate the use of an experimental setup designed for
`multiple biochip use. Further high-resolution imaging
`requires the use of sophisticated electronic and optical
`components, which increase the instrument's complexity
`and cost.
`A need exists for an improved mechanism to detect and
`acquire fluorescence signal data from biological microchips
`(biochips).
`
`DETAILED DESCRIPTION OF THE
`PREFERRED EMBODIMENTS
`
`Having reference now to the drawings, in FIG. 1, there is
`shown a biochip scanner device in accordance with the
`preferred embodiment generally designated by the reference
`character 100. Biochip scanner device 100 is used to detect
`and acquire fluorescence signal data from biological micro(cid:173)
`chips (biochips), such as oligonucleotide biochips.
`In accordance with features of the invention, biochip
`45 scanner device 100 provides advantages over conventional
`fluorescence microscope equipped with a CCD camera.
`Biochip scanner device 100 provides much lower and con(cid:173)
`siderably more uniform background. The detector field of
`view is limited to the focal spot of the laser beam on a
`50 microchip surface; as a result, the detector is substantially
`insensitive to all out-of-focus light. Biochip scanner device
`100 provides essentially uniform and reproducible excita(cid:173)
`tion and fluorescence-collection conditions. For each gel
`pad, the fluorescence is excited and detected under the same
`55 conditions; the same detector, the same optical path and the
`same excitation intensity. Biochip scanner device 100 uses
`a single-element photodetector that is significantly less
`expensive than a scientific-grade CCD camera. Biochip
`scanner device 100 employs a laser, such as a HeNe,
`60 diode-pumped solid state, and diode laser, that tend to be
`more reliable and consume significantly less power than
`microscopes using high-pressure arc lamps. Biochip scanner
`device 100 provides an improved data acquisition rate.
`Biochip scanner device 100 can be used to scan only the chip
`65 rows with the beam matching the size of the immobilization
`site instead of running a high-resolution scan of the entire
`chip surface. Biochip scanner device 100 allows real-time
`
`SUMMARY OF THE INVENTION
`
`A principal object of the present invention is to provide a
`biochip scanner device used to detect and acquire fluores(cid:173)
`cence signal data from biological microchips (biochips) and
`method of use. Other important objects of the present
`invention are to provide such method and biochip scanner
`device substantially without negative effect; and that over(cid:173)
`come some disadvantages of prior art arrangements.
`In brief, a biochip scanner device used to detect and
`acquire fluorescence signal data from biological microchips
`
`THERMO FISHER EX. 1018
`
`

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`US 6,329,661 Bl
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`3
`data processing with the integral signal intensities being
`available for comparison and storage at the same rate as the
`rate of the chip being scanned.
`Biochip scanner device 100 includes a laser 102 emitting
`a wavelength matching the excitation band maximum of a
`particular flurophore. In one embodiment, laser 102 is a 2
`mW He-Ne laser emitting at 594 nm, which falls close to
`the absorption maximum of the popular fluorescent label,
`"Texas Red". For example, a He-Ne laser model 05 LYR
`173 sold by Melles Griot of Irvine, Calif. can be used for
`laser 102. It should be understood that other lasers could be
`used for laser 102. The sensitivity of biochip scanner device
`100 can be improved by using a red or infrared diode laser
`102 as the excitation source. A red or infrared diode laser is
`more compact and more reliable than a He-Ne laser.
`The laser beam is directed by a first mirror 104 and then
`is modulated by an optical chopper 106. A chopper driver
`107 drives the optical chopper 106. In particular, this can be
`a chopper set at a frequency of 4.3 kHz. It should be
`understood that other techniques could be used to achieve
`intensity modulation of the excitation laser light. For
`example, in the case of a diode laser, the light intensity can
`be modulated by driving the laser with a periodic train of
`current pulses with a period corresponding to the desired
`modulation frequency. A mirror 108 and lens 110 then focus
`the laser beam into an optical fiber 112 supported by a fiber
`holder 114 and an X-Y-Z theta-phi positioner 116. The
`optical fiber delivers the laser beam, excitation light to a
`miniature scanning head 118. Scanning head 118 contains a
`first lens 120 and a second objective lens 121. The scanning
`head 118 is moved relative to a microchip 122.
`Examples parts that can be used to form the biochip
`scanner device 100 are provided in the following; however,
`it should be understood that various other components could
`be used. A mirror part number 05D510BD.1 sold by New(cid:173)
`port of Irvine, Calif. can be used for mirror 104. Chopper
`106 and chopper driver 107 can be implemented with an
`optical chopper model 3501 sold by New Focus of Santa
`Clara, Calif. A mirror part number BRP-5-A sold by New(cid:173)
`port of Irvine, Calif. can be used for mirror 108. A lens part
`number PAC070 sold by Newport of Irvine, Calif. can be
`used for lens 110. A lens part number PAC510 sold by
`Newport of Irvine, Calif. can be used for the first lens 120
`of the scanning head 118. A lens part number 350340B-OO
`sold by Geltech of Orlando, Fla. can be used for the
`objective lens 121 of the scanning head 118. The fiber optic
`X-Y-Z theta-phi positioner 116 can be implemented with a
`part number M-FPR2-Cl sold by Newport of Irvine, Calif.
`An optional fiber patchcord part number F-MCC-T-OPT-10-
`10 sold by Newport of Irvine, Calif. can be used.
`A controlled-temperature table 124 supports the micro(cid:173)
`chip 122. Scanning mechanics 126 is coupled to the scan(cid:173)
`ning head 118 to move the scanning head 118 in both X and
`Y directions, under computer control, to perform scanning of
`the biochip 122. A manual stage allows adjustments of the
`scanning head position in the Z direction perpendicular to
`the focal plane. Scanning head 118 includes for example, an
`objective lens 121 with a 3 mm working distance and
`acceptance angle of approximately 77°, focusing the exci(cid:173)
`tation light onto the spot that is roughly equivalent to a gel
`pad in size, so as to excite most of the label in an immobi(cid:173)
`lization site simultaneously.
`A novel feature of the biochip scanner device 100 is that
`the objective lens 121 used for both focusing the excitation
`beam and collecting the fluorescent signal is located in a
`miniature remote scanning head 118 linked to the rest of the
`
`4
`optical path elements by the optical fiber 112. Accordingly,
`the fiber 112 is used for transmitting both the excitation
`beam and the fluorescence signal to and from the scanning
`head, respectively. This feature considerably simplifies the
`5 scanner design, because other optical path elements can be
`stationary. The fluorescence light emerging from the fiber
`112 at the fiber holder 114 has a divergence much greater
`than that of the original laser beam. As a result, the diameter
`of the fluorescence beam after the collimating lens 110 is
`about 3 cm, which means that the small deflection mirror
`10 108 used for coupling the excitation beam into the fiber 112
`will block only a small fraction of the fluorescence flux.
`After passing through the lens 110, the fluorescence beam
`passes through an emission interference filter 128 and an iris
`diaphragm 130. The emission interference filter 128 is a
`15 filter that rejects all light except fluorescent light. A second
`lens 132 is used to focus the filtered light onto a silicon
`photodiode 134 that is equipped with a low-noise pre(cid:173)
`amplifier and supported by a positioner 136. The output of
`the photodiode pre-amplifier is further amplified and
`20 demodulated by a lock-in amplifier 138. The lock-in ampli(cid:173)
`fier 138 is phase-locked to the chopper driver reference
`signal, to provide improved signal-to-noise ratio. The output
`of the lock-in amplifier 138 is a DC voltage that is propor(cid:173)
`tional to the intensity of the fluorescence signal. The output
`25 of the lock-in amplifier 138 is digitized by an analog-to(cid:173)
`digital converter (ADC) card 142 and then processed by a
`host computer 140.
`The same lens part number PAC070 sold by Newport of
`Irvine, Calif. as used for lens 110 can be used for lens 132.
`30 A filter part number 645RDF72 sold by Omega Optical of
`Brattleboro, Vt. can be used for emission filter 128. Iris
`diaphragm 130 can be implemented with a part number
`M-ID-1.5 sold by Newport of Irvine, Calif. A photoreceiver
`model 2001 sold by New Focus of Santa Clara, Calif. can be
`35 used for PIN photodiode 134. A lock-in amplifier model
`5105 sold by EG&G Instruments of Princeton, N.J. can be
`used for lock-in amplifier 138. The ADC card 142 can be
`implemented with a data acquisition card number PCI-MI0-
`16XE-50 sold by National Instruments of Austin, Tex. The
`40 scanning mechanics 126 can be implemented with X-Y
`scanning stage sold by Newport of Irvine, Calif.
`FIG. 2 illustrates a method of scanning with the biochip
`scanner device 100 in accordance with the preferred
`embodiment. An innovative method called Row Scanning
`45 (RS) is used with the biochip scanner device 100. In the RS
`method, a row of a biochip is scanned with a beam of a size
`that matches the immobilization site. An advantage of the
`RS method of the preferred embodiment where the length of
`time to accumulate the data is a consideration is that the RS
`50 method allows for real-time data processing, so that the
`integral signal intensities can be available for comparison
`and storage at the same rate that the chip 122 is being
`scanned. On the other hand, a reduction in scanning velocity
`can allow the sensitivity and dynamic range of the biochip
`55 scanner device 100 to be comparable with that of more
`expensive, conventional systems. Using the RS method
`provides a flexible and reliable way to relax hardware
`characteristics such as bandwidth, analog-to-digital conver(cid:173)
`sion rate, optical resolution, and scanning mechanics
`60 parameters, depending upon the constraint of a particular
`user's needs, without sacrificing sensitivity and dynamic
`range of the biochip scanner device 100.
`FIG. 3 illustrates a field of view 302 and a depth of focus
`304 with the scanning head 118 of the biochip scanner
`65 device 100 in accordance with the preferred embodiment.
`Referring also to FIG. 2, the laser beam size substantially
`matches the gel pads 200 or immobilization site.
`
`THERMO FISHER EX. 1018
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`US 6,329,661 Bl
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`10
`
`25
`
`5
`FIGS. 4A and 4B together provide a flow chart illustrating
`the Row Scanning (RS) method of the preferred embodi(cid:173)
`ment starting at a block 401. The area to be scanned is
`limited to essentially the rows of the biochip array. Each row
`is scanned in a single pass of the laser beam while the laser 5
`beam size is matched to the immobilization site. At the same
`rate of the chip being scanned, the amplitudes of the
`fluorescence peaks are recorded. As a result, the amplitudes
`of the fluorescence peaks recorded give the integral signal
`intensities, which are most relevant to biochip applications.
`Since the scanner implementing the RS technique generates
`data that requires minimum, if any off-line processing, it is
`inherently suitable for high-rate data acquisition, which, in
`the same time, can be realized at slower scanning speeds. Or
`on the other hand, the reduction in scanning speed allows the
`sensitivity and dynamic range of the inexpensive biochip
`scanner device 100 to be comparable with that of more
`expensive, conventional systems.
`An X scan amplitude as indicated in a block 402 is
`received from a user input at block 403. Other received user
`inputs include scan velocity, Y increment, number N of rows
`to scan and XY start point, respectively indicated at blocks
`404, 405, 406, and 407. The scanning head 118 is brought to
`the start point as indicated in a block 408. Then counter S is
`cleared of scanned rows as indicated in a block 409. Check-
`ing whether S is even is performed as indicated in a decision
`block 410. When not even, the X scan is initiated in the"-"
`direction as indicated in a block 411. Otherwise, when even
`the X scan is initiated in the "+" direction as indicated in a
`block 412. Continuing with FIG. 2B following entry point B,
`on a start trigger pulse from the motion controller, data
`acquisition is initiated as indicated in a block 413. On a
`finish trigger pulse from the motion controller, data acqui(cid:173)
`sition is stopped as indicated in a block 414. The signal
`intensity profile is displayed as indicated in a block 415. The 35
`Y coordinate of the scanning head is incremented by the Y
`increment as indicated in a block 416. S is increased by 1 as
`indicated in a block 416. Next Xis compared to the number
`of rows to scan, S<N-1, as indicated in a decision block 418.
`When S is less than N-1, then the sequential operations
`return to decision block 410 in FIG. 4A. Otherwise, the
`sequential operations end as indicated in a block 420.
`A practical evaluation of the biochip scanner device 100
`of the preferred embodiment has shown that compact pho(cid:173)
`todiodes 134 and low-power lasers 102 can provide the 45
`performance characteristics necessary for reliable detection
`of fluorescence at the level of 100,000 fluorescent
`molecules/gel pad. This sensitivity could be further
`improved by using a red and/or an infrared diode laser 102
`as an excitation source. Assuming a 100 µm gel pad size, a 50
`200 µm space between adjacent gel pads, biochip scanner
`device 100 can provide an effective acquisition rate of about
`29 immobilization sites per second. This is an improvement
`over conventional systems.
`While the present invention has been described with 55
`reference to the details of the embodiments of the invention
`shown in the drawing, these details are not intended to limit
`the scope of the invention as claimed in the appended
`claims.
`What is claimed is:
`1. A biochip scanner device, said biochip scanner device
`for quantifying a plurality of linear arrays of substantially
`separated, dimensionally uniform fluorescent targets, said
`arrays located at known positions on a plain support of a
`biochip; said biochip scanner device comprising:
`a laser for emitting a laser beam of excitation radiation;
`a modulator for modulating said laser beam;
`
`6
`a scanning head for receiving said modulated laser beam;
`said scanning head for focusing said laser beam of
`excitation radiation into a focal spot; said focal spot
`having a selected size substantially equal to a size of
`said substantially separated, dimensionally uniform
`fluorescent targets; and
`a scanning mechanics coupled to said scanning head for
`moving said scanning head relative to the biochip for
`directing said laser beam focal spot for sequentially
`illuminating said fluorescent targets one at a time; said
`laser beam focal spot causing substantially entire exci-
`tation of each said illuminated fluorescent target; and
`for sequentially collecting fluorescence of each said
`illuminated fluorescent target.
`2. A biochip scanner device as recited in claim 1 wherein
`15 said scanning head includes an objective lens for focusing
`said modulated laser beam into said focal spot.
`3. A biochip scanner device as recited in claim 2 wherein
`said scanning head for sequentially collecting fluorescence
`of each said illuminated fluorescent target has a field of view
`20 substantially equal to size of said fluorescent target.
`4. A biochip scanner device as recited in claim 1 includes
`an optical fiber delivering said modulated laser beam to said
`scanning head and collecting said fluorescence from said
`scanning head for each said illuminated fluorescent target.
`5. A biochip scanner device as recited in claim 1 includes
`an emission interference filter coupled to said scanning head
`for receiving and filtering said fluorescence from each said
`illuminated fluorescent target.
`6. A biochip scanner device as recited in claim 1 includes
`30 a photodiode for detecting said fluorescence from each said
`illuminated fluorescent target.
`7. A biochip scanner device as recited in claim 1 includes
`a single-element photodetector for detecting said fluores(cid:173)
`cence from each said illuminated fluorescent target.
`8. A biochip scanner device as recited in claim 7 wherein
`said single-element photodetector includes a preamplifier
`and further includes a lock-in amplifier coupled to said
`photodetector, said lock-in amplifier for amplifying a pho(cid:173)
`todetector signal at a modulating frequency of said modu-
`40 lator.
`9. A biochip scanner device as recited in claim 8 wherein
`said lock-in amplifier provides a DC signal proportional to
`an intensity of said fluorescence; and includes an analog(cid:173)
`to-digital converter (ADC) for digitizing said DC signal; and
`a computer for processing said digitized DC signal.
`10. A biochip scanner device as recited in claim 1 wherein
`said laser includes a low-power He-Ne laser and wherein
`said modulator includes an optical chopper.
`11. A biochip scanner device as recited in claim 1 wherein
`said laser includes one of a red or infrared diode laser and
`wherein said modulator includes a current driver providing
`a periodic train of current pulses with a period correspond(cid:173)
`ing to a desired modulation frequency.
`12. A method of using a biochip scanner device, said
`biochip scanner device for quantifying a plurality of linear
`arrays of substantially separated, dimensionally uniform
`fluorescent targets, said arrays located at known positions on
`a plain support of a biochip; said method comprising the
`steps of:
`defining a number of linear segments for scanning; at least
`some of said segments passing along a number of said
`linear arrays of fluorescent targets;
`focusing a laser beam of excitation radiation into a focal
`spot; said laser beam focal spot substantially matching
`a size of said fluorescent targets; and
`sequentially scanning each of said defined linear seg(cid:173)
`ments; directing said laser beam focal spot and sequen-
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`tially illuminating predefined ones of said fluorescent
`targets one at a time within each of said defined linear
`segments; said laser beam focal spot causing substan(cid:173)
`tially entire excitation of each said illuminated fluores-
`cent target;
`sequentially collecting fluorescence of each said illumi(cid:173)
`nated fluorescent target and quantifying an intensity of
`said collected fluorescence of each said illuminated
`fluorescent target; and
`recording said fluorescence intensity of each said illumi- 10
`nated fluorescent target.
`13. A method as recited in claim 12 includes the step of
`digitizing said fluorescence intensity utilizing an analog-to(cid:173)
`digital converter; and processing said digitized DC signal
`utilizing a computer.
`14. A method as recited in claim 13 wherein the step of
`sequentially collecting fluorescence of each said illuminated
`fluorescent target and quantifying an intensity of fluores(cid:173)
`cence of each said illuminated fluorescent target includes the
`steps of coupling said collected fluorescence of each said 20
`illuminated fluorescent target to a photodiode and amplify(cid:173)
`ing a photodiode signal with a lock-in amplifier at a modu(cid:173)
`lating frequency of a modulator for quantifying said inten(cid:173)
`sity of fluorescence of each said illuminated fluorescent
`target.
`15. A method as recited in claim 12 wherein the step of
`sequentially scanning each of said defined linear segments
`includes the step of providing a scanning head coupled to an
`optical fiber for receiving a modulated laser beam; utilizing
`said scanning head for focusing a laser beam of excitation 30
`radiation into a focal spot, said laser beam focal spot
`substantially matching a size of said fluorescent targets;
`directing said laser beam focal spot and sequentially illu(cid:173)
`minating predefined ones of said fluorescent targets one at a
`time within each of said defined linear segments; said laser 35
`beam focal spot causing substantially entire excitation of
`each said illuminated fluorescent target; and said scanning
`head for transmitting said collected fluorescence peaks to
`said optical fiber.
`16. A biochip scanner device, said biochip scanner device 40
`for quantifying a plurality of linear arrays of substantially
`separated, dimensionally uniform fluorescent targets, said
`arrays located at known positions on a plain support of a
`biochip; said biochip scanner device comprising:
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`a laser for emitting a laser beam of excitation radiation;
`a modulator for modulating said laser beam;
`a scanning head for receiving said modulated laser beam;
`said scanning head for focusing said laser beam of
`excitation radiation into a focal spot; said focal spot
`having a selected size substantially equal to a size of
`each said substantially separated, dimensionally uni(cid:173)
`form fluorescent targets;
`a scanning mechanics coupled to said scanning head for
`moving said scanning head relative to the biochip for
`directing said laser beam focal spot for sequentially
`illuminating said fluorescent targets one at a time; said
`laser beam focal spot causing substantially entire exci(cid:173)
`tation of each said illuminated fluorescent target; and
`for sequentially collecting fluorescence of each said
`illuminated fluorescent target;
`a photodetector for detecting said collected fluorescence
`of each said illuminated fluorescent target from the
`biochip; and
`an optical fiber for delivering said modulated laser beam
`to said scanning head and said optical fiber for deliv(cid:173)
`ering said collected fluorescence of each said illumi(cid:173)
`nated fluorescent target to said photodetector.
`17. A biochip scanner device as recited in claim 16 further
`includes an emission interference filter coupled to said
`optical fiber for filtering said collected fluorescence of each
`said illuminated fluorescent target.
`18. A biochip scanner device as recited in claim 16
`wherein said modulator includes an optical chopper and
`wherein said photodetector includes a photodiode and a
`lock-in amplifier for amplifying a photodiode signal at a
`modulating frequency of said optical chopper.
`19. A biochip scanner device as recited in claim 18
`wherein said lock-in amplifier provides a DC signal propor(cid:173)
`tional to an intensity of said collected fluorescence of each
`said illuminated fluorescent target.
`20. A biochip scanner device as recited in claim 16
`wherein said scanning head includes an objective lens for
`focusing said modulated laser beam of excitation radiation
`into a focal spot and for collecting said fluorescence of each
`said illuminated fluorescent target.
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`THERMO FISHER EX. 1018