(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)
`
`(19) World Intellectual Property Organization
`International Bureau
`
`I lllll llllllll II llllll lllll llll I II Ill lllll lllll 111111111111111111111111111111111
`
`(43) International Publication Date
`24 January 2002 (24.01.2002)
`
`PCT
`
`(10) International Publication Number
`WO 02/06796 A2
`
`(51) International Patent Classification7:
`BOlL 3/00
`
`GOIN 21/64,
`
`(21) International Application Number: PCT/USOl/41350
`
`(22) International Filing Date:
`
`13 July 2001 (13.07.2001)
`
`(25) Filing Language:
`
`(26) Publication Language:
`
`(30) Priority Data:
`09/617,549
`
`English
`
`English
`
`14 July 2000 (14.07.2000) US
`
`(71) Applicant: APPLERA CORPORATION [US/US]; 850
`Lincoln Centre Drive, Foster City, CA 94404 (US).
`
`(72) Inventors: OLDHAM, Mark, F.; 16500 Soda Springs
`Road, Los Gatos, CA 95033 (US). YOUNG, Eugene, F.;
`802 Balboa Lane, Foster City, CA 94404 (US).
`
`(81) Designated States (national): AE, AG, AL, AM, AT, AU,
`AZ, BA, BB, BG, BR, BY, BZ, CA, CH, CN, CO, CR, CU,
`CZ, DE, DK, DM, DZ, EC, EE, ES, Fl, GB, GD, GE, GH,
`GM, HR, HU, ID, IL, IN, IS, JP, KE, KG, KP, KR, KZ, LC,
`LK, LR, LS, LT, LU, LV, MA, MD, MG, MK, MN, MW,
`MX, MZ, NO, NZ, PL, PT, RO, RU, SD, SE, SG, SI, SK,
`SL, TJ, TM, TR, TT, TZ, UA, UG, UZ, VN, YU, ZA, ZW.
`
`(84) Designated States (regional): ARIPO patent (GH, GM,
`KE, LS, MW, MZ, SD, SL, SZ, TZ, UG, ZW), Eurasian
`patent (AM, AZ, BY, KG, KZ, MD, RU, TJ, TM), European
`patent (AT, BE, CH, CY, DE, DK, ES, Fl, FR, GB, GR, IE,
`IT, LU, MC, NL, PT, SE, TR), OAPI patent (BF, BJ, CF,
`CG, CI, CM, GA, GN, GW, ML, MR, NE, SN, TD, TG).
`
`Published:
`without international search report and to be republished
`upon receipt of that report
`
`(74) Agents: GARRETT, Arthur, S. et al.; Finnegan, Hen(cid:173)
`derson, Farabow, Garrett & Dunner, L.L.P., 1300 I Street,
`N.W., Washington, DC 20005-3315 (US).
`
`For two-letter codes and other abbreviations, refer to the "Guid(cid:173)
`ance Notes on Codes and Abbreviations" appearing at the begin(cid:173)
`ning of each regular issue of the PCT Gazette.
`
`iiiiiiii
`
`iiiiiiii
`
`!!!!!!!!
`
`iiiiiiii
`
`----iiiiiiii
`!!!!!!!! -iiiiiiii
`!!!!!!!! -
`!!!!!!!! -iiiiiiii
`iiiiiiii ----
`
`M
`<~~~~~~~~~~~~~~~~~~-
`\0 (54) Title: SCANNING SYSTEM AND METHOD FOR SCANNING A PLURALITY OF SAMPLES
`
`°" ~ (57) Abstract: A system for detecting fluorescence emitted from a plurality of samples in a sample tray is provided. The system
`
`Q generally includes a plurality of lenses positioned in a linear arrangement, a linear actuator configured to translate the plurality of
`-..... lenses, an excitation light source for generating an excitation light, an excitation light direction mechanism for directing the excitation
`~ light to a single lens of the plurality of lenses at a time so that a single sample holder aligned with the lens is illuminated at a time,
`and an optical detection system for analyzing light from the sample holders. In certain embodiments, the optical detection system
`0 includes a light dispersing element configured to spectrally disperse the light from the sample holder being illuminated, and a lens
`> element configured to receive light from the light dispersing element and direct the light onto a light detection device. A method of
`~ scanning a sample tray having a plurality of samples positioned in sample holders to detect fluorescence is also provided.
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`SCANNING SYSTEM AND METHOD FOR
`
`SCANNING A PLURALITY OF SAMPLES
`
`BACKGROUND OF THE INVENTION
`
`Field of the Invention
`This invention relates to systems and methods for scanning a sample tray
`
`5
`
`with a plurality of samples. The invention further relates to detection systems for
`
`detecting fluorescence from a plurality of samples in a sample tray.
`
`Background
`Biological testing involving analyzing the chemical composition of nucleic
`
`10
`
`acid samples in order to determine the nucleotide sequence of the sample has
`
`become increasingly popular. Currently, experiments in chemistry and biology
`
`typically involve evaluating large numbers of samples using techniques such as
`
`detection of fluorescence emitted from a sample in conjunction with a
`polymerase chain reaction (PCR). These experiments, as well as other
`
`15
`
`techniques such as sequencing of nucleic acid samples, are typically time
`
`consuming and labor intensive. Therefore, it is desirable that a large number of
`
`samples can be analyzed quickly and accurately. With large scale projects such
`
`as the Human Genome Project, it is desirable to increase throughput of nucleic
`
`acid sequencing and polymerase chain reactions.
`
`20
`
`Existing systems are typically not well-adapted for real-time detection of
`a plurality of samples in an efficient manner. Existing systems typically include
`
`a separate detector for each sample well and are not compatible for large-scale
`
`testing using fluorescent detection. Therefore, there is a need for an efficient
`
`method and system for real-time detection of a plurality of sample wells of a
`sample well tray.
`
`25
`
`SUMMARY OF THE INVENTION
`
`The advantages and purposes of the invention will be set forth in part in
`
`the description which follows, and in part will be obvious from the description, or
`'
`may be learned by practice of the invention. The advantages and purposes of
`
`1
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`the invention will be realized and attained by the elements and combinations
`
`particularly pointed out in the appended claims.
`
`To attain the advantages and in accordance with the purposes of the
`
`invention, as embodied and broadly described herein, the invention includes a
`
`5
`
`scanning system for detecting fluorescence emitted from a plurality of samples
`in a sample tray. According to certain embodiments of the invention, the optical
`system generally includes a plurality of lenses positioned in a linear
`
`arrangement, an excitation light source for generating an excitation light, an
`excitation light direction mechanism for directing the excitation light to a single
`
`10
`
`lens of the plurality of lenses at a time so that a single sample holder aligned
`
`with the lens is illuminated at a time, and an optical detection system for
`analyzing light from the sample holders. The plurality of lenses and sample tray
`are configured so that relative motion may be imparted between the plurality of
`lenses and the sample well tray so that the plurality of lenses may linearly
`
`translate in a second direction perpendicular to a first direction of the linear row
`of sample holders. Preferably, the excitation light source directs the excitation
`light to each of the sample holders of a row of sample holders in a sequential
`manner as the plurality of lenses linearly translates in the second direction. A
`sample in the sample holder may generate light, e.g. fluoresce, upon
`illumination. In certain embodiments, the optical detection system includes a
`
`light dispersing element configured to spectrally disperse the light from the
`sample holder being illuminated, and a lens element configured to receive light
`
`from the light dispersing element and direct the light onto a light detection
`device. In certain embodiments, the sample holders are sample wells.
`
`In another aspect of the present invention, the invention is directed toward
`a detection system for detecting fluorescence from a plurality of sample holders
`in a sample tray. In certain embodiments, the detection system includes a single
`
`excitation source for generating an excitation light, a lens housing comprising a
`
`plurality of lenses positioned in a linear row, each lens configured to direct the
`excitation light source to an aligned sample holder, and a single detection device
`for analyzing light from the plurality of sample holders. The linear row of lenses
`is arranged to be angularly offset relative to an adjacent row of sample holders.
`
`15
`
`20
`
`25
`
`30
`
`2
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`In yet another aspect of the present invention, the invention includes a
`
`method of scanning a sample tray having a plurality of samples positioned in
`
`sample holders to detect fluorescence. The method includes generating an
`
`excitation light with an excitation light source, directing the excitation light to a
`
`5
`
`first lens of a row of lenses, the row of lenses being angularly offset relative to
`
`an adjacent row of sample holders, illuminating a sample in a first sample holder
`
`of the row of sample holders positioned adjacent the row of lenses with the
`
`excitation light to generate an emission light, optically detecting the optical
`
`characteristics of the emission light, directing the excitation light to a second lens
`
`10
`
`positioned adjacent the first lens of the row of lenses, illuminating a sample in
`
`a second sample holder of the row of sample holders to generate an emission
`
`light, and optically detecting the optical characteristics of the emission light from
`
`the second sample holder. Throughout the above method of scanning, relative
`
`motion is imparted between the row of lenses and the sample tray so that the
`
`15
`
`row of lenses is linearly translated in a direction perpendicular to the row of
`
`sample wells.
`
`It is to be understood that both the foregoing general description and the
`
`following detailed description are exemplary and explanatory only and are not
`
`restrictive of the invention, as claimed.
`
`20
`
`25
`
`BRIEF DESCRIPTION OF THE DRAWINGS
`
`The accompanying drawings, which are incorporated in and constitute a
`
`part of this specification, illustrate several embodiments of the invention and
`
`together with the description, serve to explain principles of the invention. In the
`
`drawings,
`
`Fig. 1 is a front schematic view of a system for scanning a plurality of
`
`sample wells and measuring the fluorescence of the samples therein according
`
`to certain embodiments of the present invention;
`
`Fig. 2 is a side schematic view of the system of Fig. 1;
`
`Fig. 3 is a close up side schematic view of a portion of an optical system;
`
`30
`
`Fig. 4 is a close up front schematic view of a portion of an optical system;
`
`3
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`Fig. 5 is a side view of a system according to certain embodiments of the
`
`present invention;
`Fig. 6 is a top view of the system of Fig. 5; and
`Figs. 7 A-7F illustrate a method of scanning the sample wells in a sample
`
`5
`
`well tray according to the present invention.
`
`DESCRIPTION OF PREFERRED EMBODIMENTS
`
`Reference will now be made in detail to several preferred embodiments
`of the invention, examples of which are illustrated in the accompanying
`drawings. Wherever possible, the same reference numbers will be used
`throughout the drawings to refer to the same or like parts.
`According to certain embodiments, the present invention provides a
`
`scanning system for detecting fluorescence emitted from a plurality of samples
`in a sample tray. According to certain embodiments of the invention, the optical
`system generally includes a plurality of lenses positioned in a linear
`arrangement, an excitation light source for generating an excitation light, an
`excitation light direction mechanism for directing the excitation light to a single
`lens of the plurality of lenses at a time so that a single sample well aligned with
`
`the well lens is illuminated at a time, and an optical detection system for
`analyzing light from the sample holders. Preferably, the excitation light source
`
`directs the excitation light to each of the sample holders of a row of sample
`holders in a sequential manner as the plurality of lenses linearly translates in a
`first direction relative to the sample tray, the sample holder generating light upon
`illumination. Either the plurality of lenses or the sample tray may be translated
`
`so that a relative motion is imparted between the plurality of lenses and the
`sample tray.
`
`The present invention further provides methods of scanning a sample well
`tray, which has a plurality of samples positioned in sample holders, to detect
`
`fluorescence. The method includes generating an excitation light with an
`excitation light source, and directing the excitation light to a first lens of a row of
`
`lenses, the row of lenses being angularly offset relative to an adjacent row of
`sample holders. The method further includes illuminating a sample in a first
`
`1 O
`
`15
`
`20
`
`25
`
`30
`
`4
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`sample holder of the row of sample holders positioned adjacent the row of
`lenses with the excitation light to generate an emission light, and optically
`detecting the spectral characteristics of the emission light. Preferably, the
`method includes directing the excitation light to a second lens positioned
`
`5
`
`adjacent the first lens of the row of lenses, illuminating a sample in a second
`
`10
`
`15
`
`20
`
`25
`
`sample holder of the row of sample holders to generate an emission light, and
`
`optically detecting the spectral characteristics of the emission light from the
`
`second sample holder. In certain embodiments, the row of lenses is linearly
`translated in a direction substantially perpendicular to the row of sample holders
`throughout the above methods.
`In other embodiments, the row of sample
`
`holders is linearly translated relative to the row of lenses.
`
`In certain
`
`embodiments, the sample holders are sample wells.
`
`According to certain embodiments shown in Figs. 1-7, the scanning
`system 10 for detecting fluorescence includes a plurality of well lenses 12
`positioned in a well lens housing 14, an excitation light source 16, an excitation
`light direction mechanism 18 for directing the excitation light to a single well lens
`at a time, and an optical detection system 20 for analyzing light from the sample
`wells 22 of the sample well tray 24 or other sample holding device.
`In accordance with certain embodiments of the present invention, the
`scanning system includes a plurality of lenses, hereinafter referred to as well
`lenses, positioned in a linear arrangement. As embodied herein and shown in
`Figs. 1-5, the plurality of well lens 12 are positioned within a well lens housing
`
`14. In certain preferred embodiments, the well housing contains a single row of
`
`well lenses 12 arranged so that the well lenses are equally spaced from each
`other, as shown in Fig. 2. The well lenses 12 are arranged in a linear manner
`
`within the well housing. The well lens are arranged so that each of the well
`lenses will align with a corresponding column of sample wells in a sequential
`manner as the well lens housing is linearly translated relative to an adjacent
`
`sample well tray. Throughout the scanning of the sample well tray, the well lens
`
`30
`
`housing moves at a substantially uniform speed relative to the sample well tray
`
`in a plane parallel to the top surface of the sample well tray. For example, the
`well lens housing 14 in Fig. 2 moves in a first direction (into the page in Fig. 2)
`
`5
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`as the well lens housing 14 linearly translates in a plane parallel to the top
`surface of sample well tray 24. In other embodiments, the sample well tray is
`
`linearly translated relative to a stationary well lens housing.
`The well lens housing is preferably positioned adjacent a sample well tray
`with a plurality of sample wells to be scanned. As shown in Fig. 2, the well lens
`housing is preferably positioned adjacent a stationary sample well tray 24 with
`
`a plurality of sample wells 22. In certain embodiments, the sample well tray 24
`has a number of columns equal to the number of well lenses in the well lens
`housing. In the example shown, the sample well tray is 384-well tray. In a 384-
`well sample well tray, the wells are arranged in a sixteen by twenty-four array
`
`with sixteen columns and twenty-four rows. The scanning device is also
`preferably configured for use with 96-well sample trays, in addition to microcard
`
`sample trays.
`Examples of sample well trays suitable for use in the apparatus of the
`present invention are described in PCT Application No. W0#00/25922 to Moring
`et aL, which is assigned to the assignee of the present invention, the contents
`
`of which are hereby incorporated by reference herein for any purpose.
`Examples of microcard sample trays suitable for use in the apparatus of the
`
`present invention are described in PCT Application No. W0#97/36681 to
`Woudenberg et al., which is assigned to the assigne~ of the present invention,
`the contents of which are hereby incorporated by reference herein for any
`purpose. Sample well trays having any number of sample wells and sample well
`
`sizes may also be used. According to certain embodiments, the volume of the
`sample wells may vary anywhere from 0.01 µI to thousands of microliters (µI),
`with a volume between 5 to 500 µI being typical. The scanning system may be
`used for a variety of applications, such as, but not limited to, fluorescent PCR(cid:173)
`based detection.
`
`Likewise, although certain preferred embodiments employ trays with
`
`sample wells, the present invention is suitable for use with sample trays that do
`
`not include wells. The tray may include any type of sample holder that can
`maintain a sample in a fixed position on a tray. In certain embodiments, the
`sample trays may have a flat surface on which a sample of biological material
`
`6
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`is placed. The flat surface on which the sample is placed may be similar to a
`
`microscope slide for a sample.
`
`In this type of sample tray, a liquid may be
`
`dropped onto the tray at a plurality of positions, and then a film or cover
`
`positioned on the top surface of the tray over the samples. Alternately, a sample
`
`5
`
`tray may include a porous material such as a frit on the top surface, instead of
`
`sample wells, for holding samples of biological material. Therefore, although the
`
`description refers to sample well trays throughout, it should be understood that
`
`the present invention is also suitable for sample trays that do not have sample
`
`wells.
`
`10
`
`For purposes of illustration only, the sample well tray described is a 384-
`
`well tray arranged in the sixteen by twenty-four array shown in Fig. 7 A. For a
`
`384-well sample tray with a conventional sixteen by twenty-four array, it is
`
`desirable to have sixteen well lenses in the well lens housing. Each well lens
`corresponds to a particular column of the sample well tray 24. For example, as
`
`15
`
`shown in Fig. 7 A, the first well lens of the row of well lenses corresponds to the
`
`first column of the sample well tray. Likewise, the second well lens of the row
`
`of well lenses corresponds to the second column of the sample well tray, and so
`
`forth.
`
`In accordance with certain embodiments of the present invention, the row
`
`20
`
`of well lenses are configured to be offset at an acute angle relative to a linear
`
`row of sample wells arranged in a first direction in a sample well tray. As
`
`embodied herein and shown in Fig. 7A, the well lens housing 14 (and row of well
`
`lenses 12) is arranged on a centerline 30 that passes through the center of each
`of the well lenses. The centerline 30 of the row of well lenses 12 is arranged to
`
`be offset at a predetermined angle 9 relative to a centerline 32 passing through
`the first row of sample wells as shown in Fig. 7A. In certain embodiments, the
`
`angular offset 9 between the row of well lenses and the row of sample wells
`
`allows the scanning system to operate by the desired method.
`
`In view of the arrangement of the well lens housing and well lenses
`
`relative to the sample well tray, an excitation light can pass through the first well
`lens when the well lens is aligned with the first sample well (column 1) of the first
`
`row of the sample well tray, as shown in Fig. 7 A. The first sample well is thereby
`
`25
`
`30
`
`7
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`illuminated, generating an emission light that is analyzed by an optical system.
`
`As the well lens housing continues to translate at a substantially uniform speed
`
`in the x-axis direction to the position shown in Fig. 78, an excitation light is
`
`passed through a second well lens when the second well lens is aligned with the
`
`5
`
`second sample well of the first row as shown in Fig. 78. An excitation light
`
`direction mechanism according to certain embodiments of the present invention
`
`directs the excitation light from one well lens to another in a sequential manner.
`
`The excitation light should be directed to the respective well lens at the time at
`
`which the well lens is substantially aligned with an adjacent sample well. This
`
`10
`
`process continues so that all of the sample wells in the first row are scanned,
`
`and then continues to the next row, thereby scanning all of the sample wells in
`the second row. This process continues until all of the sample wells are
`
`scanned.
`
`In certain embodiments, the angle 8 between the row of sample wells and
`
`15
`
`the row of well lenses is selected as a function of the number of sample wells
`
`and the spacing between adjacent sample wells. In the configuration shown in
`
`Fig. 7A, the angle 8 is selected to be between one and three degrees, preferably
`approximately two degrees. In certain embodiments, this is a suitable angle for
`
`a sample well tray having spacing of 4.5 mm and sixteen sample wells in each
`
`20
`
`row.
`
`In certain embodiments, the angle is selected so that an entire row is
`
`scanned before any of the well lenses are aligned with the next row to be
`
`scanned. The value for the angle 8 can vary for each specific design and is not
`
`limited by the range described above. For example, in a 96-well format with one
`
`particular design, the angle 8 is selected to be approximately four degrees.
`
`25
`
`In accordance with certain embodiments of the present invention, the
`
`well lens housing may be translated relative to a stationary sample well tray by
`
`a linear actuator or other device. Alternately, the well lens housing may be
`
`stationary and the sample well tray translated relative to the stationary well lens
`
`housing. The operation and principles of the present invention typically are
`identical with either configuration. For purposes of illustration only, the present
`
`30
`
`description will be directed toward the embodiments with a well lens housing
`
`being translated relative to a stationary sample well tray. In embodiments with
`
`8
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`a stationary sample well tray, the well lens housing is typically linearly translated
`
`in a plane substantially parallel to the top of the sample well tray. As shown for
`
`example in Fig. 2, the well lens housing 14 may be translated in a first direction
`
`(into the page in Fig. 2) relative to the sample well tray 24. In certain preferred
`
`5
`
`embodiments, the well lens housing 14 is translated at a substantially uniform
`
`speed relative to the stationary sample well tray 24. As shown in Figs. 7A-7F,
`
`the sample well tray translates along the sample well tray so that all twenty-four
`
`sample well rows may be scanned. According to certain embodiments of the
`
`present invention, the well lens housing translates at a uniform speed so that the
`
`10
`
`scanning device does not undergo the accelerations associated with stopping
`
`and starting during an intermittent motion. Therefore, the well lens housing does
`
`not dwell over each individual sample well, but instead moves at a substantially
`
`constant speed. Preferably, the well lens housing moves at a sufficiently slow
`
`speed that the optical system is able to obtain an accurate analysis of each
`
`15
`
`sample well. In certain examples where the angle 9 is 2 degrees, the well lens
`
`housing is translated at a predetermined speed so that the well lens is aligned
`
`with the corresponding sample well for approximately 5 milliseconds. The
`
`alignment time is determined by 9, which may be selected as desired to achieve
`
`optimal results. In certain embodiments where the sample concentration is low,
`
`20
`
`the alignment time may be as much as 20 milliseconds. In certain embodiments
`
`where maximum sample throughput and speed are desired, the alignment time
`may be as low as 1 millisecond.
`
`The well lens housing 14 and scanning system 10 may be translated by
`
`any suitable type of linear actuator, such as a motor driven carriage assembly.
`
`25
`
`Alternately, as mentioned above, the sample well tray may be translated relative
`
`to a stationary well lens housing. In certain embodiments in which the well lens
`
`housing 14 translates relative to a stationary sample well tray, the well lens
`
`housing 14 may be positioned on a scanning carriage with a screw actuator for
`
`linearly translating the scanning carriage. The screw actuator is typically rotated
`
`30
`
`by a motor or other device, and the scanning carriage may slide on one or more
`
`guide rods. Other types of linear actuators may also be suitable with the present
`
`invention.
`
`9
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`5
`
`10
`
`15
`
`20
`
`25
`
`In certain embodiments, the plurality of lenses may be joined together into
`
`In certain alternate embodiments, a single lens, such as a
`an integral lens.
`cylindrical lens, may be used instead of a plurality of well lenses. In such an
`arrangement, the single lens would be positioned at approximately the same
`location as the plurality of well lenses described above. The excitation light will
`be allowed to pass through the cylindrical lens to the sample well tray, and the
`
`excitation light will pass back through toward the optical detection system. The
`
`use of a single lens has an advantage of requiring less-precise timing for the
`excitation light to strike the respective sample well. However, in certain
`embodiments, a single lens may suffer from reduced optical quality compared
`to the multiple well lens configuration shown in the figures.
`
`In accordance with certain embodiments of the present invention, the
`
`scanning system 10 includes an excitation light source 16 that generates an
`excitation light to illuminate the samples in the sample wells, as shown in Figs.
`1. One or several excitation sources may be provided. In certain embodiments,
`excitation is provided to the sample by an Argon ion laser. Other types of
`conventional light sources may also be used. The excitation source is typically
`
`selected to emit excitation light at one or several wavelengths or wavelength
`ranges. In certain examples, a laser having a wavelength of 488 nm is used for
`generating the excitation light. The excitation light from excitation light source
`16 may be directed to the well lenses by any suitable manner.
`In certain
`embodiments, the excitation light is directed to the well lenses by using one or
`
`mirrors to reflect the excitation light at the desired well lens. After the excitation
`
`light passes through the well lens into an aligned sample well, the sample in the
`
`sample well is illuminated, thereby emitting an emission light. The emission light
`can then be detected by an optical system. The excitation light is then directed
`to another well lens so that a second sample well may be illuminated.
`
`In accordance with certain embodiments of the present invention, the
`
`scanning system 10 includes an excitation light direction mechanism 18 for
`
`30
`
`directing the excitation light to a single well lens 12 at a time. According to
`
`certain embodiments shown in Figs. 1-6, the excitation light direction mechanism
`18 includes a stationary mirror 40, a rotating mirror 42, a motor 44 for rotating
`
`10
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`the rotating mirror 42, and a beam splitter 46. The excitation light direction
`mechanism is configured so that the excitation light may be intermittently
`directed at each of the well lenses 12 in a sequential manner. As shown in Figs.
`1 and Fig. 5, the stationary mirror 40 reflects the excitation light from the laser
`
`5
`
`16 to the rotating mirror 42. In certain embodiments, the excitation light passes
`
`10
`
`15
`
`20
`
`25
`
`30
`
`through an aperture 48 in the mirror housing 50 as it travels between the laser
`
`16 and the stationary mirror 40, as shown in Fig. 5. The stationary mirror 40
`may be mounted to the mirror housing 50 in any suitable manner and at any
`suitable angle. In certain embodiments, the stationary mirror is mounted on the
`mirror housing by an adjustable mount 41. In other embodiments, the stationary
`
`mirror may be eliminated and the laser 16 may be positioned so that it directs the
`
`excitation light directly onto the rotating mirror 42.
`According to certain embodiments shown in Figs. 1-5, the rotating mirror
`42 is positioned at an angle to the rotational axis 52 of a scan motor 44. The
`scan motor rotates the rotating mirror about the rotational axis 42. The scan
`
`motor 44 is mounted to a bottom of the mirror housing 50 in any suitable
`
`manner. The rotating mirror is attached to an output shaft 54 of the scan motor
`
`44 by any suitable manner. In the example shown in Fig. 5, the rotating mirror
`42 is positioned on a sleeve 56 that is rotatably fixed to the output shaft 54 of the
`scan motor. As shown in Fig. 1, the surface of the rotating mirror may be
`positioned at an angle of forty-five degrees to the rotational axis 52 of the scan
`.motor 44. With the surface of the rotating mirror 42 arranged at a forty-five
`
`degree angle, the excitation light beam reflects at an angle of ninety degrees to
`the rotational axis 52, as shown by beam 60 in Fig. 1. The excitation light beam
`
`60 will maintain the ninety degree angle relative to the incoming beam for every
`rotational position of the rotating mirror. However, as the rotating mirror is
`
`rotated about the rotational axis 52, the reflected excitation beam 60 will move
`about the rotational axis 52.
`
`In certain embodiment, the present invention is configured so that the
`
`scan motor rotates to sixteen discrete angular positions, so that each discrete
`angular position corresponds to a particular well lens. In particular, the motor is
`a stepper motor that has a limited range of rotation. For example, in one
`
`11
`
`THERMO FISHER EX. 1011
`
`

`
`WO 02/06796
`
`PCT/USOl/41350
`
`embodiment, a fifteen degree range of rotation will cause the excitation light to
`
`travel from the first to the sixteenth well lens in a given row. The rotating mirror
`
`42 starts at a first angular position corresponding to the first lens, pauses at this
`
`position for a predetermined length of time so that the sample well aligned with
`
`5
`
`the first well lens may be scanned, and then rotates to a second angular position
`
`for a predetermined period, and so forth until the excitation light has been
`
`directed at all sixteen well lenses. After the sixteenth well lens, the motor rotates
`
`the mirror back to the first position corresponding to the first well lens. In certain
`
`embodiments, the timing of the rotation of the scan motor is coordinated with the
`
`1 O
`
`speed of translation of the well housing so that the excitation light passes
`
`through the correct well lens at the desired time. In other words, the excitation
`
`light is directed at the first well position when the first well lens is properly
`
`positioned above the first sample well, and the excitation light is directed at the
`
`second well position when the second well lens is properly positioned above the
`
`15
`
`second sample well, and so forth.
`
`According to certain embodiments, the scanning system includes a beam
`
`splitter 46 that not only reflects the reflected excitation light 60 to the well lens,
`
`but also allows the returning emission light to pass through it. As shown in Fig.
`
`5, a beamsplitter can be positioned in a scan housing 62. The beam splitter 46
`
`20
`
`may be mounted in the scan housing by any suitable method and at any suitable
`
`angle. In the example shown in Fig. 5, the beam splitter is attached to the scan
`
`housing by an adjustable two-position mount 64. In certain embodiments, the
`
`beam splitter is a dielectric beam splitter that reflects the incoming excitation
`
`light, but permits the emission light to pass through it to the optical detection
`system 20.
`
`25
`
`In the embodiments shown in Figs. 1-5, the reflecting surface of the beam
`
`splitter 46 is arranged at a forty-five degree angle to