WO2001084209A2 - Fully automatic rapid microscope slide scanner - Google Patents

Fully automatic rapid microscope slide scanner Download PDF

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Publication number
WO2001084209A2
WO2001084209A2 PCT/US2001/008028 US0108028W WO0184209A2 WO 2001084209 A2 WO2001084209 A2 WO 2001084209A2 US 0108028 W US0108028 W US 0108028W WO 0184209 A2 WO0184209 A2 WO 0184209A2
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WO
WIPO (PCT)
Prior art keywords
sample
image
scanner
microscope
window
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2001/008028
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English (en)
French (fr)
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WO2001084209A3 (en
WO2001084209B1 (en
Inventor
Dirk Soenksen
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Individual
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Individual
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Application filed by Individual filed Critical Individual
Priority to AU2001247403A priority Critical patent/AU2001247403A1/en
Priority to JP2001581174A priority patent/JP2004514920A/ja
Priority to EP10184724.2A priority patent/EP2282230B1/en
Priority to EP01920338.9A priority patent/EP1317685B2/en
Priority to DE60135562T priority patent/DE60135562D1/de
Publication of WO2001084209A2 publication Critical patent/WO2001084209A2/en
Anticipated expiration legal-status Critical
Publication of WO2001084209A3 publication Critical patent/WO2001084209A3/en
Publication of WO2001084209B1 publication Critical patent/WO2001084209B1/en
Ceased legal-status Critical Current

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Classifications

    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N23/00—Cameras or camera modules comprising electronic image sensors; Control thereof
    • H04N23/60—Control of cameras or camera modules
    • H04N23/66—Remote control of cameras or camera parts, e.g. by remote control devices
    • H04N23/661—Transmitting camera control signals through networks, e.g. control via the Internet
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/0004—Microscopes specially adapted for specific applications
    • G02B21/002—Scanning microscopes
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/0004—Microscopes specially adapted for specific applications
    • G02B21/002—Scanning microscopes
    • G02B21/0024—Confocal scanning microscopes (CSOMs) or confocal "macroscopes"; Accessories which are not restricted to use with CSOMs, e.g. sample holders
    • G02B21/0036—Scanning details, e.g. scanning stages
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/0004—Microscopes specially adapted for specific applications
    • G02B21/002—Scanning microscopes
    • G02B21/0024—Confocal scanning microscopes (CSOMs) or confocal "macroscopes"; Accessories which are not restricted to use with CSOMs, e.g. sample holders
    • G02B21/008—Details of detection or image processing, including general computer control
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/06—Means for illuminating specimens
    • G02B21/08—Condensers
    • G02B21/14—Condensers affording illumination for phase-contrast observation
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/24—Base structure
    • G02B21/241—Devices for focusing
    • G02B21/245—Devices for focusing using auxiliary sources, detectors
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/24—Base structure
    • G02B21/26—Stages; Adjusting means therefor
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/32—Micromanipulators structurally combined with microscopes
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/34—Microscope slides, e.g. mounting specimens on microscope slides
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/36—Microscopes arranged for photographic purposes or projection purposes or digital imaging or video purposes including associated control and data processing arrangements
    • G02B21/365—Control or image processing arrangements for digital or video microscopes
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/36—Microscopes arranged for photographic purposes or projection purposes or digital imaging or video purposes including associated control and data processing arrangements
    • G02B21/365—Control or image processing arrangements for digital or video microscopes
    • G02B21/367—Control or image processing arrangements for digital or video microscopes providing an output produced by processing a plurality of individual source images, e.g. image tiling, montage, composite images, depth sectioning, image comparison
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N1/00—Scanning, transmission or reproduction of documents or the like, e.g. facsimile transmission; Details thereof
    • H04N1/04—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa
    • H04N1/047—Detection, control or error compensation of scanning velocity or position
    • H04N1/053—Detection, control or error compensation of scanning velocity or position in main scanning direction, e.g. synchronisation of line start or picture elements in a line
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N1/00—Scanning, transmission or reproduction of documents or the like, e.g. facsimile transmission; Details thereof
    • H04N1/04—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa
    • H04N1/19—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa using multi-element arrays
    • H04N1/1903—Arrangements for enabling electronic abutment of lines or areas independently scanned by different elements of an array or by different arrays
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N1/00—Scanning, transmission or reproduction of documents or the like, e.g. facsimile transmission; Details thereof
    • H04N1/04—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa
    • H04N1/19—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa using multi-element arrays
    • H04N1/191—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa using multi-element arrays the array comprising a one-dimensional array, or a combination of one-dimensional arrays, or a substantially one-dimensional array, e.g. an array of staggered elements
    • H04N1/192—Simultaneously or substantially simultaneously scanning picture elements on one main scanning line
    • H04N1/193—Simultaneously or substantially simultaneously scanning picture elements on one main scanning line using electrically scanned linear arrays, e.g. linear CCD arrays
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N1/00—Scanning, transmission or reproduction of documents or the like, e.g. facsimile transmission; Details thereof
    • H04N1/04—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa
    • H04N1/19—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa using multi-element arrays
    • H04N1/195—Scanning arrangements, i.e. arrangements for the displacement of active reading or reproducing elements relative to the original or reproducing medium, or vice versa using multi-element arrays the array comprising a two-dimensional array or a combination of two-dimensional arrays
    • H04N1/19505—Scanning picture elements spaced apart from one another in at least one direction
    • H04N1/19521—Arrangements for moving the elements of the array relative to the scanned image or vice versa
    • H04N1/19573—Displacing the scanned image
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N23/00—Cameras or camera modules comprising electronic image sensors; Control thereof
    • H04N23/56—Cameras or camera modules comprising electronic image sensors; Control thereof provided with illuminating means
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N23/00—Cameras or camera modules comprising electronic image sensors; Control thereof
    • H04N23/60—Control of cameras or camera modules
    • H04N23/63—Control of cameras or camera modules by using electronic viewfinders
    • H04N23/631—Graphical user interfaces [GUI] specially adapted for controlling image capture or setting capture parameters
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N23/00—Cameras or camera modules comprising electronic image sensors; Control thereof
    • H04N23/60—Control of cameras or camera modules
    • H04N23/63—Control of cameras or camera modules by using electronic viewfinders
    • H04N23/633—Control of cameras or camera modules by using electronic viewfinders for displaying additional information relating to control or operation of the camera
    • H04N23/635—Region indicators; Field of view indicators
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N7/00—Television systems
    • H04N7/18—Closed-circuit television [CCTV] systems, i.e. systems in which the video signal is not broadcast
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N7/00—Television systems
    • H04N7/18—Closed-circuit television [CCTV] systems, i.e. systems in which the video signal is not broadcast
    • H04N7/183—Closed-circuit television [CCTV] systems, i.e. systems in which the video signal is not broadcast for receiving images from a single remote source
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N2201/00—Indexing scheme relating to scanning, transmission or reproduction of documents or the like, and to details thereof
    • H04N2201/04—Scanning arrangements
    • H04N2201/047—Detection, control or error compensation of scanning velocity or position
    • H04N2201/04701—Detection of scanning velocity or position
    • H04N2201/04715—Detection of scanning velocity or position by detecting marks or the like, e.g. slits
    • H04N2201/04727—Detection of scanning velocity or position by detecting marks or the like, e.g. slits on a linear encoder
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04N—PICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N2201/00—Indexing scheme relating to scanning, transmission or reproduction of documents or the like, and to details thereof
    • H04N2201/04—Scanning arrangements
    • H04N2201/047—Detection, control or error compensation of scanning velocity or position
    • H04N2201/04753—Control or error compensation of scanning position or velocity
    • H04N2201/04755—Control or error compensation of scanning position or velocity by controlling the position or movement of a scanning element or carriage, e.g. of a polygonal mirror, of a drive motor

Definitions

  • NA numerical aperture
  • microscopist manually scan a slide at low magnification to obtain an overall
  • magnification fields of view the microscopist manually selects a higher magnification
  • a scanning system is used to move the sample, while a rectangular
  • optical sensor such as an area scan charge-coupled device (CCD) camera captures an image
  • image tiles into one coherent image.
  • the BLISS system is designed primarily for the anatomic pathologist who has a
  • the BLISS system BLISS system
  • the BLISS system user interface provides
  • a tiled image is constructed by assembling several adjacent, original
  • the data structure is obtained by
  • a pathologist may interactively select
  • the remote user is thus provided with a
  • the BLISS system is integrated around a computer-controlled, automated
  • microscope such as the Axioplan-2 microscope system sold by Carl Zeiss, Inc., Thornwood, NY. This type of high-end microscope has capabilities for computer-
  • the microscope objective lens subsystem the microscope objective lens subsystem, the filtering subsystem, as well as
  • the BLISS system is also equipped with a computer
  • pixels, and an image frame grabber are also integrated into the BLISS system.
  • the BLISS system is that it takes a long time, typically twenty minutes or longer to
  • Image tiling is relatively slow because of the need to minimize
  • the width of a single pixel is within less than one pixel. For example, at a 40x magnification, the width of a single
  • image tile captured by a one-half inch format CCD camera corresponds to 160
  • the image tile should be captured only after the mechanical stage has settled
  • image tiling systems by proposing an alternate method that combines image tiling using
  • the total acquisition time for such a macro-image is about one minute.
  • magnification macro-image is practically limited to samples in which anatomic
  • the BLISS system thus has limited utility for non-reference information
  • histological samples such as Pap smears, because such cytological samples inherently
  • a fourth disadvantage of the BLISS system is its complexity and expense.
  • BLISS system is based largely on off-the-shelf components, including a high-end, fully
  • objective lens turret is rotated automatically to change microscope objective lenses, for
  • intensity of illumination will be needed to optimally fill the dynamic range of the CCD.
  • microscope objective lenses can be eliminated.
  • the resolution of the microscope objective lens are captured by the digital image.
  • magnification images can be created using standard computational algorithms.
  • portion of a sample be searched for defects or for the presence or absence of a special
  • Patent No. 5,922,282 (Ledley et al.), are based on storing the x/y stage coordinates of
  • circuitry that is applied to the intensity information measured by a line scan camera that
  • an area scan sensor such as a video camera can be used as the basis for
  • Patent No. 4,700,298 (Palcic et al.) uses a linear array CCD attached to a commercially
  • This method is based on recording the x/y stage coordinates of all fields
  • imagery data set in lieu of, or in addition to, manually scanning an entire slide.
  • the present invention provides an apparatus for and a method of fully automatic rapid scanning and digitizing of an entire microscope sample, or a substantially large
  • invention also provides a method for composing the image strips obtained from
  • the invention also provides a method for dynamically displaying, with
  • portions of the contiguous digital image are portions of the contiguous digital image.
  • all elements of the scanner are part of a single-
  • enclosure that has a primary connection to a network such as the Internet or a local
  • the preferred sample type is a microscope slide and the
  • illumination and imaging optics are consistent with transmission mode optics optimized
  • FIG. 1 is a block diagram of a preferred embodiment of an optical microscopy
  • FIG. 2 is a block diagram of a second embodiment of an optical microscopy
  • FIGS. 3A-3C illustrates a manner in which contiguous image strips acquired by
  • a linear array detector digitizes a portion of a sample according to the present invention:
  • FIG. 4 is a simplified flow chart of the operation of an optical microscopy
  • FIGS. 5A-5B are a schematic diagram of an image viewing frame according to
  • FIGS. 6A-6B are a schematic diagram of a dynamic image viewing frame
  • FIG. 1 a block diagram of a preferred embodiment of an optical sensor
  • microscopy system 10 according to the present invention is shown.
  • the heart of the microscopy system 10 is shown.
  • system 10 is a microscope slide scanner 11 that serves to scan and digitize a specimen or
  • sample 12 can be anything that may be interrogated by optical
  • the sample 12 may be a microscope slide or other sample
  • specimens that include tissues and cells, chromosomes,
  • DNA DNA, protein, blood, bone marrow, urine, bacteria, beads, biopsy materials, or any other
  • the sample 12 may also be an array of any type of DNA or DNA-
  • microarrays including any and all samples commonly known as a microarrays.
  • the sample 12 may be a microtiter plate, for example a 96-well plate.
  • Other examples of the sample 12 include integrated circuit boards, electrophoresis records, petri dishes,
  • the scanner 1 1 includes a motorized stage 14, a microscope objective lens 16, a
  • the sample 12 is positioned on the line scan camera 18, and a data processor 20.
  • the sample 12 is positioned on the line scan camera 18, and a data processor 20.
  • the motorized stage 14 for scanning.
  • the motorized stage 14 is connected to a stage
  • controller 22 which is connected in turn to the data processor 20.
  • the data processor 20 is connected to the data processor 20.
  • the motorized stage 14 moves the
  • a piezo positioner 24 such as the PIFOC from Polytec PI
  • the microscope objective 16 and is connected to and directed by the data processor 20
  • a means of providing a coarse focus adjustment may also be
  • the motorized stage 14 includes a high
  • the motorized stage 14 could be any type of excellent straight line and flatness accuracy.
  • the motorized stage 14 could be any type of excellent straight line and flatness accuracy.
  • the motorized stage 14 could be any type of excellent straight line and flatness accuracy.
  • the motorized stage 14 could be any type of excellent straight line and flatness accuracy.
  • motorized stages 14 are also suitable for the scanner 11, including stacked single axis stages based on ways other than ball bearings, single- or multiple-axis positioning stages
  • motorized stage 14 includes two stacked single-axis positioning
  • stage 14 can be equipped with mechanical or optical position encoders which has the
  • preferred embodiment does not include position encoders. However, if one were to use
  • Position commands from the data processor 20 are converted to motor current or
  • the stage controller 22 includes a 2-axis servo/stepper motor controller (Compumotor
  • the relatively large single 1.8 degree motor step For example, at a microstep of 100, the
  • sample 12 can be commanded to move at steps as small as 0.1 micrometer.
  • stage 14 and the stage controller 22 depends on many factors, including the nature of the
  • the microscope objective lens 16 can be any microscope objective lens
  • the microscope objective lens 16 is of the infinity-
  • the sample 12 is illuminated by an illumination system 28 that includes a light
  • the light source 30 in the presently preferred
  • source 30 could also be any other type of arc-lamp, laser, or other source of light.
  • illumination optics 32 in the presently preferred embodiment include a standard K ⁇ hler
  • the illumination optics 32 are representative of the bright-field illumination optics that
  • a second conjugate plane includes (i) the filament of the bulb that is part of the light source 30, (ii) the aperture of
  • the sample 12 is illuminated and imaged in
  • the scanner 11 of the present invention is equally suitable for detecting optical
  • microscope objective lens 16 is selected to be compatible with phase-contrast
  • microscopy should be readily apparent. Overall, the scanner 11 is suitable, with
  • the line scan camera focusing optics 34 that focus the optical signal captured by
  • lens and an external imaging port consist of an optical element known as a tube lens
  • the tube lens that is part of a microscope's observation tube. Many times the tube lens consists of
  • accessory elements like dichroic mirrors or filters can be
  • Infinity-corrected microscope objective lenses are typically inscribed with an
  • a tube lens with a focal length of 180 millimeters will be used as the objective lens.
  • a tube lens with a focal length of 180 millimeters will be used as the objective lens.
  • a 20x objective lens from Olympus a company that uses a
  • the tube lens is part of a critical fixed element of the
  • the line scan camera focusing optics 34 include a tube lens optic mounted inside
  • imaging microscope such as provided by the present scanner 11 is limited.
  • magnification sometimes known as electric zoom
  • scanner 11 is to provide high quality digital images, in lieu of visual observation
  • the scanner 11 provides diffraction- limited digital imaging by selection
  • this objective lens at a wavelength of 500 nanometers is approximately 0.6 micrometers
  • pixels is used to detect a portion of the sample 12.
  • the tube lens must be selected to achieve a magnification of 46.7.
  • optic focal length is therefore about 420 millimeters, obtained by multiplying 46.7 by 9.
  • millimeters will therefore be capable of acquiring images with the best possible spatial
  • the scanner 11 utilizes a
  • scan camera focusing optics 34 are modular elements of the scanner 11 and can be
  • lens 16 with a numerical aperture corresponding to the highest spatial resolution
  • the presently preferred embodiment of the scanner 1 1 provides for only one
  • the presently preferred embodiment of the scanner 1 1 is based on a Dalsa
  • each pixel having a dimension of 14 by 14 micrometers.
  • linear array whether packaged as part of a camera or custom-integrated into an imaging
  • embodiment effectively provides eight bits of quantization, but other arrays providing
  • RGB red-green-blue
  • TTI time delay integration
  • TDI arrays provide a substantially better signal-to-noise ratio (SNR) in the
  • TDI arrays can comprise multiple stages of linear arrays. TDI arrays
  • the scanner 1 1 also supports
  • linear arrays that are manufactured in a variety of formats including some with 512 pixels, some with 1024 pixels, and others having as many as 4096 pixels. Appropriate,
  • focusing optics 34 may be required to accommodate larger arrays. Linear arrays with a
  • any type of line scan camera 18 is that the sample 12 can be in motion with
  • the output signal of the line scan camera 18 is connected to the data processor
  • the data processor 20 in the presently preferred embodiment includes a central processing unit (CPU) 22.
  • the data processor 20 in the presently preferred embodiment includes a central processing unit (CPU) 22.
  • processing unit with ancillary electronics, for example a motherboard, to support at least
  • one signal digitizing electronics board such as an imaging board or a frame grabber.
  • the imaging board is an EPIX PIXCID24 PCI bus
  • imaging board there are many other types of imaging boards or frame
  • An alternate embodiment could be a line scan camera that uses an interface such
  • IEEE 1394 also known as Firewire, to bypass the imaging board altogether and store
  • a data storage 38 such as a hard disk.
  • the data processor 20 is also connected to a memory 36, such as random access
  • RAM random access memory
  • the data processor 20 is connected to a
  • LAN local area network
  • WAN wide area network
  • MAN metropolitan area network
  • intranet an intranet
  • the memory 36 and the data storage 38 are also connected to an extranet, or the global Internet.
  • the memory 36 and the data storage 38 are also connected to an extranet, or the global Internet.
  • the data processor 20 is also capable of executing computer
  • the data processor 20 can be based on
  • operating systems such as Windows, Linux, OS/2,
  • a personal computer such as a Dell Dimension XPS T500 that features a Pentium III 500
  • the computer elements which include the data processor 20, memory 36.
  • the scanner 11 in the presently preferred embodiment of the invention,
  • the communication port 40 provides a means for rapid communications with the
  • communications protocol for the communications port 40 is a carrier-sense multiple-
  • the scanner 11 is intended to work with
  • any type of transmission media including broadband, baseband, coaxial cable, twisted
  • imagery data captured by the scanner 1 1 are performed on a computer 44 that is
  • the computer 44 in its presently preferred embodiment,
  • a display monitor 46 is connected to a display monitor 46 to provide imagery information to an operator.
  • plurality of computers 44 may be connected to the network 42.
  • the computer 44 communicates with the scanner 11 using a
  • network browser such as Internet Explorer from Microsoft or Netscape Communicator
  • Images are stored on the scanner 11 in a common compressed format such a JPEG which is an image format that is compatible with standard image-decompression
  • the scanner 1 1 is a webserver providing an operator interface
  • the browser on the computer 44 uses the hypertext transmission protocol
  • applets is equally feasible and may be desirable for selected future
  • PC personal computer
  • Spectrally resolved images are images in which
  • spectral information is measured at every image pixel. Spectrally resolved images could
  • the imaging spectrograph uses a two-dimensional CCD
  • FIG. 2 a block diagram of a second embodiment of an optical system
  • microscopy system 10 according to the present invention is shown.
  • this system 10 is shown.
  • the scanner 1 1 is more complex and expensive than the currently preferred embodiment
  • FIG. 2 is
  • FIG. 2 provides for a much greater level of
  • the connection to the light source 30 may control the voltage
  • the light source 30 is a halogen bulb in the presently preferred embodiment.
  • the connection between the data processor 20 and the illumination optics is a halogen bulb in the presently preferred embodiment.
  • the second embodiment of FIG. 2 also provides for a fluorescence
  • filter cube 50 that includes an excitation filter, a dichroic filter, and a barrier filter.
  • fluorescence filter cube 50 is positioned in the infinity corrected beam path that exists
  • optical signal to be split into at least two paths.
  • the primary path is via the line scan
  • a second path is provided via an area scan camera
  • the area scan camera 56 can be
  • the area scan camera 56 provides a traditional imaging system configuration for the scanner 11.
  • the area scan camera 56 is connected to the data processor 20. If
  • two cameras are used, for example the line scan camera 18 and the area scan camera 56,
  • both camera types could be connected to the data processor using either a single dual-
  • display monitor 58 and to also provide local input devices such as a keyboard and
  • the second embodiment shown in FIG. 2 also provides for a much greater level
  • the second embodiment also provides for a motorized nose-piece 62 to
  • the motorized nose-piece 62 is connected to
  • sample 12 could be modified to comprise scanning of the microscope objective lens 16
  • microscope objective lens 16 or scanning both the sample 12 and the microscope
  • the scanner 11 also provides a general pu ⁇ ose platform for automating many
  • the illumination system 28 could be modified
  • FIGS. 3A-3C the manner in which contiguous image strips are
  • the line scan camera field of view 70 comprises the region of the sample 12 of
  • FIG. 1 that is imaged by a multitude of individual pixel elements 72 that are arranged in
  • each of the pixel elements 72 being 14 micrometers square.
  • the line scan camera field of view 70 corresponds to a region of
  • pixel element 72 images an area about 1.4 micrometers by 1.4 micrometers.
  • FIG. 3C illustrates that during digital scanning of the sample 12, an image 76 is
  • the scanning may be either top-to-bottom or bottom-to-top or may start any point on the
  • the digital scanning may also involve vertical image strips rather than
  • the image 76 can comprise the entire sample 12 or
  • the scanning and digitization is performed in a direction of travel 84 that alternates
  • the capabilities of the line scan camera 18 typically determine whether scanning can be done bi-directionally, as in the currently preferred embodiment of the scanner 1 1.
  • Uni-directional systems often comprise more than one linear array
  • FIG. 3B The color array 86 detects the RGB intensities required for obtaining a color
  • An alternate embodiment for obtaining color information uses a prism to split
  • the TDI array 88 could be
  • FIG. 4 a simplified flow chart of the operation of an optical sensor
  • microscopy system 10 according to the present invention is shown.
  • the sample 12 is
  • sample loading is for an
  • sample loading is performed manually to reduce system
  • the scanner 11 is initialized at step 201 by commands issued from the computer
  • buttons 44 or similarly from buttons that may be part of an alternate embodiment of the scanner
  • the portion of the sample 12 to be digitized to create the image 76, and the name of a relevant calibration file are entered by an operator at step 201.
  • the scanner 11 defaults
  • steps 202 through 210 are orchestrated by the data processor 20
  • step 202 the motorized stage
  • Optical limit switches are provided in the motorized stage 14 of the presently preferred embodiment of the scanner 11 to indicate when it is time to
  • step 204 the digitization process continues with step 202.
  • step 206 Because the focus will not change dramatically from one image
  • sample 12 to be digitized at a magnification of lOx is 50 millimeters by 25 millimeters
  • strip 77 would comprise about 36,000 by 1024 pixel elements, with the entire image 76
  • step 208 the positioning of the sample 12 for a new
  • Step 210 includes movement of the motorized stage 14 from
  • the total time required to acquire the image 76 is proportional to the line rate at
  • the line rate is 27,600 lines per second, or 28.3 million
  • each image strip 77 comprising, for pu ⁇ oses of
  • the motorized stage 14 in the present embodiment thus moves at
  • the motorized stage 14 is returned at maximum stage velocity to the same left reference position along the x-axis and all image strips,
  • deceleration depends on the x-axis performance of the motorized stage 14 and the x-axis
  • the acceleration and deceleration times using S-curve profiles for smooth motion and
  • step 210 the line scan camera 18 moves off the edges of the portion of the
  • the new scan set-up time depends on the particular -
  • controller 22 is approximately one -half second in the presently preferred
  • example is therefore about one minute for a bi-directional scanning embodiment.
  • the scanner 11 can be further optimized to minimize the total acquisition time of
  • the image acquisition time that can be achieved by the
  • each line image is captured in about
  • linear array such as linear
  • stage 14 while increasing the line integration time, all without a reduction in total
  • optical signal without vignetting and other optical aberrations. It is even possible to use
  • the scanner 11 in its presently preferred embodiment, performs the digitization
  • the entire sample or portions of the sample 12 may be scanned without any
  • the image 76 of the sample 12 can be
  • step 220 either a conventional optical microscope as indicated in step 222 or
  • a higher resolution embodiment of the scanner 11 as shown in step 224 can be used for
  • microscope slide or large portions of the sample 12, may not be practical or cost-
  • step 206 The need for focusing during scanning is indicated in step 206 and is very much
  • the scanner 11 uses a
  • motorized stage 14 can be used for autofocus, although the presently preferred method
  • One of the benefits of the scanner 11 is the rapid digitization of a large portion of
  • the scanner 1 in its most basic embodiment, does not require the
  • the scanner 11 provides extensive autofocus capabilities using an ancillary area scan
  • the spatial information for autofocusing is part of the sample 12, for example, a glass
  • the overall quality of the image 76 is related to the ability of the sample 12 to be
  • the scanner 11 supports different approaches for capturing data in synchrony
  • Capabilities are provided in the data processor 20
  • high-resolution images utilizes position feedback from the motorized stage 14.
  • the scanner 1 1 is able to generate high quality
  • example is captured at eight bits (one byte) of quantization per pixel, 648 million bytes
  • embodiment of the invention is to scan the sample 12 so as to slightly overlap the image
  • strips 77 for example by 10-20 pixels, and to use these overlapping pixels to fine-tune
  • individual image strips 77 can be reduced to five to ten percent, or less, of their original
  • the scanner 11 is also capable of eliminating from the image 76
  • step 214 the
  • analysis of the image 76 that represents a digitized portion of the sample 12, comprises a
  • analysis methods functions might include counting or measuring
  • step 214 do not
  • step 214 requires that the sample 12 be physically present or available. The methods of step 214
  • step 218 If the decision logic in step 218 does not return the analysis to the
  • step 220 determines whether the
  • step 222 or using the scanner 11 as per step 224. It should be realized that
  • scanner 1 1 comprises step 224 and includes the ability to remotely control the scanner
  • piezo positioner 24, and the illumination intensity of the light source 30 may be under remote control of the operator during step 224.
  • Real-time imagery for example from
  • the area scan camera 56 may be the basis for this review rather than digitized
  • step 224 Autofocus would be utilized as required based on the size of the portion of the
  • FIGS. 5A-5B a schematic of an image viewing frame 100
  • image 76 that may be on the order of 36,000 by 18,000 pixels or larger, such as the
  • zoom image 104 that corresponds to a portion of the image 76.
  • the region of the macro image 102 that is displayed in the zoom image 104 is indicated on the macro image 102
  • zoom region 106 itself as a zoom region 106 that can be interactively sized and moved over the entire
  • the zoom region 106 is a
  • the zoom region 106 provides a critical reference between
  • FIG. 5B highlighting the presence, for illustrative pu ⁇ oses only, of
  • objects 01 108 and 02 112 are within the zoom region 106 and are thus displayed in the
  • zoom image 104 that is part of an operator sizable zoom window 124.
  • the user has the
  • these icons would be clicked using a mouse as a pointing device
  • Command icons are known in the art and can be used here as well. Command icons may be
  • an electronic zoom icon can be part of the zoom window 124. As the electronic zoom is increased, the size of the zoom
  • region 106 is decreased on the macro image 102 so as to maintain a constant sized zoom
  • a macro window 128 might display
  • the size of the macro image 102 in pixels the size of the zoom region 106 in pixels, and
  • the zoom window 124 might
  • window 128 and the zoom window 124 can be changed interactively by the operator,
  • step 214 the application of specialized computer programs to the
  • object window 130 in the presently preferred embodiment of this invention comprises a
  • object image 132 that each correspond to different
  • images 132 can be displayed as reduced resolution thumbprint images in an image
  • the object window 130 are based on the specialized computer programs that are applied to the image 76 in step 214.
  • the specialized computer program that are applied to the image 76 in step 214.
  • results could be displayed in an analysis window 134 of the image viewing frame 100.
  • the analysis window 134 in the present example could contain the total count of
  • the analysis window 134 in a variety of formats.
  • image viewing frame 100 provides a window for interactively selecting the attributes of
  • FIGS. 6A-6B a schematic of a dynamic image viewing frame
  • reviewing the image 76 is intended to offer a digital imaging alternative to manually
  • One of the objects of the presently preferred invention is to provide a
  • image 76 that is a digitization of a portion of the sample 12, and preferably a diffraction-
  • the digital imagery data can increase the productivity of an operator charged with
  • the dynamic image viewing frame 150 includes the same macro image 102 within the macro window 128 as that in the previously discussed image viewing frame
  • the dynamic image viewing frame 150 also includes the zoom image
  • window 124 in the dynamic image viewing frame 150 will typically be smaller than in
  • the movie image 152 is displayed with sufficient resolution within a movie window 154.
  • the movie image 152 is displayed with sufficient resolution within a movie window 154.
  • image 152 could be generated by dividing the large image 76 into multiple movie image
  • strips 156 that can be displayed at a user-selectable resolution on the display monitor 46.
  • a series of movie images 152 that differs from each other as described can comprise the individual frames of a digital movie that is played and displayed in the
  • the sample 12 is that objects in the movie image 152 are typically in motion, making it
  • This alternate process comprises dividing the
  • movie image strip 156 into contiguous image fields of, for example, 600 by 600 pixels
  • 600 by 600 pixel image is only meant to illustrate the principles of the idea, as images
  • a scan tracker 158 could be shown on the macro
  • image 102 itself to indicate those regions of the image 76 that have previously been
  • the operator may spend more time on some areas than on
  • the scan tracker 158 could be color coded, for example, to indicate relative dwell times, providing immediate feedback to the operator regarding the thoroughness

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  • Multimedia (AREA)
  • Signal Processing (AREA)
  • Optics & Photonics (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • General Physics & Mathematics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Human Computer Interaction (AREA)
  • General Engineering & Computer Science (AREA)
  • Microscoopes, Condenser (AREA)
  • Investigating Materials By The Use Of Optical Means Adapted For Particular Applications (AREA)
  • Analysing Materials By The Use Of Radiation (AREA)
  • Image Input (AREA)
  • Facsimile Scanning Arrangements (AREA)
  • Investigating Or Analysing Materials By Optical Means (AREA)
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PCT/US2001/008028 2000-05-03 2001-03-13 Fully automatic rapid microscope slide scanner Ceased WO2001084209A2 (en)

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AU2001247403A AU2001247403A1 (en) 2000-05-03 2001-03-13 Fully automatic rapid microscope slide scanner
JP2001581174A JP2004514920A (ja) 2000-05-03 2001-03-13 全自動迅速顕微鏡用スライドスキャナ
EP10184724.2A EP2282230B1 (en) 2000-05-03 2001-03-13 Fully automatic rapid microscope slide scanner
EP01920338.9A EP1317685B2 (en) 2000-05-03 2001-03-13 Fully automatic rapid microscope slide scanner
DE60135562T DE60135562D1 (de) 2000-05-03 2001-03-13 Vollautomatischer schneller mikroskopprobenabtaster

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US09/563,437 US6711283B1 (en) 2000-05-03 2000-05-03 Fully automatic rapid microscope slide scanner
US09/563,437 2000-05-03

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