Abstract:
An imaging fountain flow cytometer allows high resolution microscopic imaging of a flowing sample in real time. Cells of interest are in a vertical stream of liquid flowing toward one or more illuminating elements at wavelengths which illuminate fluorescent dyes and cause the cells to fluoresce. A detector detects the fluorescence emission each time a marked cell passes through the focal plane of the detector. A bi-directional syringe pump allows the user to reverse the flow and locate the detected cell in the field of view. The flow cell is mounted on a computer controlled x-y stage, so the user can center a portion of the image on which to zoom or increase magnification. Several computer selectable parfocal objective lenses allow the user to image the entire field of view and then zoom in on the detected cell at substantially higher resolution. The magnified cell is then imaged at the various wavelengths.

Description:
This application is a Continuation in Part of U.S. patent application Ser. No. 10/323,535, filed Dec. 18, 2002 now U.S. Pat. No. 6,765,656, and incorporates that application by reference. 

   BACKGROUND OF THE INVENTION 
   1. Field of the Invention 
   The present invention relates to apparatus and methods for high resolution imaging and classification of sample particles in translucent or transparent flowing liquid. In particular, the present invention relates to high throughput analysis of imaged particles in a translucent flow. 
   2. Description of the Prior Art 
   Imaging and classification of low concentrations of selected target particles, cells in particular, in large volumes of fluid has a number of applications including: 1) bioterrorism and biowarfare defense, 2) food and water quality control, 3) clinical detection of cancerous cells, and 4) environmental monitoring. Cell imaging and classification systems developed to date usually suffer from 1) high cost, 2) unsatisfactory sensitivity, 3) slowness, 4) large size, 5) insufficient spectral and/or spatial resolution, and/or 6) labor-intensive preparation steps. 
   Direct detection may be accomplished using flow cytometry. Flow cytometry is a commonly used technique to measure the chemical or physical properties of cells. Cells flow by a measuring apparatus in single file while suspended in a fluid, usually air or water. In immunofluorescence flow cytometry, cells can be identified by attaching fluorescent antibodies to each cell:
         An antibody specific to the cell of interest is labeled with a fluorescent molecule or fluorochrome.   The labeled antibody is mixed in solution with the cell of interest. The antibodies attach to specific sites on the cells (called antigens).   The cells are passed in single file in a stream of liquid past a laser(s), which illuminates the fluorochromes and causes them to fluoresce at a different wavelength.   A photomultiplier or photodiode is used to detect a burst of fluorescence emission each time a marked cell passes in front of the detector.   The number of marked cells can then be counted. Antibodies can be chosen that are highly-specific to the cell(s) of interest.       

   Flow cytometry is currently used for a wide variety of applications including: measuring helper T-lymphocyte counts to monitor HIV treatment, measuring tumor cell DNA content in determining cancer treatment, and separating X- and Y-chromosome bearing sperm for animal breeding. 
     FIG. 1  (prior art) shows a typical flow cytometry system (from Shapiro, Practical Flow Cytometry, 2nd Edition). Putting flow cytometry into practice involves using two concentric cylindrical streams of fluid. The inner flow or core flow contains the cells to be sampled. The purpose of the outer stream or sheath flow is to reduce the diameter of the core flow. As the core and sheath fluids reach the tapered region of the flow, the cross-sectional area of the core flow is reduced. A small bore core flow (about 20 microns) allows for precision photometric measurements of cells in the flow, illuminated by a small diameter laser beam; all of the cells will pass through nearly the same part of the beam and will be equally illuminated. Why not just pass the cells through a small-bore transparent tube? Small diameter orifices are generally unworkable because they experience frequent clogging. All commercial flow cytometers now use a sheath/core flow arrangement. 
   Laser-induced fluorescence of fluorescent labels in a flow cytometer is a uniquely powerful method of making fast, reliable, and relatively unambiguous detections of specific microorganisms, such as food-borne pathogens. Several monographs describe the methods and applications of flow cytometry (e.g., Flow Cytometry: First Principles by A. L. Givan, 1992, and references therein). 
   Historically, flow cytometers have been very large, expensive, laboratory-based instruments. They consume large amounts of power, and use complex electronics. They are not typically considered within the realm of portable devices. The size (desktop at the smallest), power requirements, and susceptibility to clogging (requiring operator intervention) of conventional flow cytometers precludes their use for many applications, such as field monitoring of water biocontamination. 
   U.S. Pat. No. 6,309,886,“High throughput analysis of samples in flowing liquid,” by Ambrose et al. discloses an invention for the high throughput analysis of fluorescently labeled DNA in a transparent medium. This invention is a device that detects cells in a flow moving toward an imaging device. The flow is in a transparent tube illuminated in the focal plane from the side by a laser with a highly elongated beam. Although this invention does not suffer from the drawbacks listed above for alternative technologies, it is not suitable for applications where the flow medium is not transparent. It is also not an imaging technology, but rather a technology suitable for single-point photometric detection and characterization. 
   U.S. Pat. No. 6,473,176 (Baseji et al.), U.S. Pat. No. 6,249,341 (Baseji et al.), and U.S. Pat. No. 6,211,955 (Baseji et al.) describe a method to perform multi-spectral imaging of cells in a sample flowing in a flow cytometer using a technique called Time Delayed Integration or TDI. TDI is used with charge coupled device (CCD) detectors to produced enhanced signal-to-noise images of a moving scene (such as cells in a flow). The pixels of the CCD are arranged in rows and columns, and the signal is moved from row to row in synchrony with a moving image projected onto the device, allowing an extended integration time without blurring. Time Delayed Integration Multi-spectral flow cytometry, as described in the three above-mentioned patents, has advantages over previous flow cytometric techniques in that it recovers not only the fluorescence and/or scattering parameters from cells in the flow, but provides multi-spectral imaging as well. The latter allows for cell classification and differentiation based characteristics such as cell shape, overall size, nuclear size, nuclear shape, optical density, the detection and characterization of numerous fluorescent markers and FISH probes, the quantification of the total amount of DNA in the nucleus, and the detection of other cellular components at multiple wavelengths. The main disadvantage of this technique is that it requires TDI as well as conventional flow cytometry with all of its complexities including a hydrodynamically focused sheath flow. 
   A precursor invention, described in U.S. patent application Ser. No. 10/323,535 by the present inventor, is shown in  FIGS. 2 and 3 . This invention incorporates detection, but not high resolution imaging. 
   In  FIG. 2  (Prior Art), a sample of fluorescently tagged cells  210  flows up the tube  206  toward the CCD camera and foreoptics  208 . The cells are illuminated in the focal plane by a laser  228  through transparent end element  220 . When the cell(s) pass through the CCD camera focal plane  234  they are imaged by the CCD camera  218  and lens assembly  212 , through a transparent window and a filter  214  that isolates the wavelength of fluorescent emission. The fluid in which the cells are suspended then passes by the window and out the drain tube  230 . 
   In  FIG. 3  (Prior Art), a flow block  322  is used with a device like that shown in  FIG. 1 .  FIG. 3A  is a side schematic drawing of the aluminum flow block.  FIG. 3B  is a top plan view of the flow black.  FIG. 3C  shows a detail of the device flow and imaging. The sample enters the flow block through Tygon tube  312  and stainless steel tube  310  and exits through stainless steel tube  324  and Tygon tube  315 . Two 2-mm holes have been drilled into the aluminum flow block  322 , an entrance hole  302  and an exit hole  306 . As the sample flows up the internal entrance hole  302 , it passes through the focal plane of the CCD camera  326 . This hole is generally painted black to reduce scattered light. Component  320  is a Teflon tape gasket. The gasket is sandwiched between the aluminum flow block and a circular window  220 , and tightly held with a screw-on brass cap  318 . The gasket is cut to form a channel  304  through which the fluid is diverted into the exit hole  306 .  FIG. 3D  is a photograph of a working flow block with attached tubing. The block is mounted onto a black-anodized plate. 
   A need remains in the art for improved apparatus and methods for high throughput, high resolution imaging analysis of samples in a translucent flowing liquid. 
   SUMMARY OF THE INVENTION 
   It is an object of the present invention to provide improved apparatus and methods for high throughput, high resolution imaging analysis of samples in a translucent flowing liquid. This object is accomplished by utilizing flow cytometry to first detect particles and then to reposition and magnify detected particles for high resolution imaging. 
   The present invention provides apparatus and methods for high throughput, high sensitivity imaging and classification of samples in a translucent or transparent flowing liquid. This object is accomplished by providing a relatively large cross section axial flow, in which cells or other target particles suspended in a liquid are observed as they are quickly passed through a tube oriented generally along the optical axis of imaging optics. When a rare cell of interest is detected, it is slowly passed back through the tube and imaged. This allows for real time high resolution imaging of rare cells, including multi-spectral imaging, without having to resort to labor-intensive microscopy or more complex and expensive MSIFC. 
   The present invention has advantages over Multi-Spectral Imaging Flow Cytometry (MSIFC), including detection of individual cells, at a much lower complexity, and thus cost. This invention is especially useful for real-time imaging of rare cells in a sample flow. This invention is based on taxonomic identification using fluorescent dyes. 
   Cells of interest are dyed with one or more fluorescent probes or markers designed to stain regions of the cell that are of particular interest. The cells are passed in a vertical stream of liquid toward a laser diode, LED, gas laser, or the like, or a combination of the above at one or more wavelengths which illuminate the fluorescent dyes and cause them to fluoresce at a longer wavelength than the wavelength of illumination. 
   In order to substantially increase the power of this invention, the following features are included in various preferred embodiments: 
   1) By using several computer selectable parfocal objective lenses the user can image the entire field of view and then zoom in on a particular cell at substantially higher resolution. 
   2) By mounting the flow cell on a computer controlled x-y stage, the user can center a portion of the image on which to zoom or increase magnification. 
   3) By using a computer-controlled syringe pump that is bidirectional (can pump forward or backward) along with a computer selectable set of parfocal objective lenses and a computer controlled x-y stage on which to mount the flow cell. 
   A low-cost CCD (charge coupled device) 2-D detector images the fluorescence emission each time a marked cell illuminated by the laser diode passes through the focal plane of the detector. 
   Background fluorescence from unbound dye or out-of-focus target particles/cells, can be removed by use of high-pass filtering of the images or by structured illumination techniques as outlined in Neil, Juskaitis, &amp; Wilson (1997, Opt. Lett. 22, 1905–1907) and Fukano and Miyawaki (2003, Applied Optics 42, 19, 4119–4124). 
   Multi-spectral cell images are processed to retrieve morphology parameters such as overall size, nuclear size, nuclear shape, optical density, the detection and characterization of numerous fluorescent markers and FISH probes, the quantification of the total amount of DNA in the nucleus, and the detection of other cellular components such as fetal hemoglobin. Cells can then be classified according to these parameters or alternatively with automated classification algorithms such as Principal Component Analysis. 
   The present invention includes apparatus and methods for imaging particles in a sample of liquid flowing within a flow channel along a flow axis including a transparent element transverse to the flow axis for terminating the flow channel and diverting the sample, a waste conduit adjacent to the transparent element for discharging the sample, an illumination beam(s) positioned to illuminate an illumination zone within the sample, and an imaging element(s) for imaging a focal plane transverse to the flow axis within the illumination zone. 
   Generally the focal plane is spaced apart from the transparent element and a clear volume separates the transparent element and the imaging element. 
   The imaging element comprises a color filter, optics, and a CCD camera. 
   The waste conduit may comprise an opening formed in the flow channel, or a specially designed flow block. The flow block includes an input tube for providing the sample to the flow block, an output tube for discharging the sample from the flow block, and a flow path formed within the flow block and connected to the input tube and the output tube. The flow path passes adjacent to the transparent element, and the focal plane is located in the flow path before the sample passes adjacent to the transparent element. 
   The illumination may be provided by a laser or by an LED, combined with the use of dichroic mirrors to allow multiple wavelength simultaneous illumination. 
   In the case of detection of pathogenic microorganisms in human blood, the resulting sample would contain red blood cells, and would likely be optically thick over circa 1 mm or greater distance necessitating a transparent gap (air or immersion liquid) between imaging optics and the focal plane of the instrument. 

   
     BRIEF DESCRIPTION OF THE DRAWINGS 
       FIG. 1  (Prior Art) is a schematic drawing showing a conventional flow cytometry system. 
       FIG. 2  (Prior Art) is a simplified schematic drawing showing apparatus for detecting particles in a translucent flow according to a precursor of the present invention. 
       FIG. 3A  (Prior Art) shows a side cutaway view of a flow block which may be used in the apparatus of  FIG. 2 .  FIG. 3B  (Prior Art) is a top plan view of the flow block. 
       FIG. 3C  is a detail side view of the flow block illustrating depth of focus.  FIG. 3D  is photograph of the flow block of  FIG. 3A . 
       FIG. 4A  is a block diagram illustrating a first embodiment of a high resolution imaging fountain flow cytometer according to the present invention.  FIG. 4B  is a simplified view of a filter wheel of  FIG. 4A , end on.  FIG. 4C  is a simplified view of a filter wheel of  FIG. 4A , from the side. 
       FIGS. 5A–5D  are schematic drawings illustrating two images of the same cell at different wavelengths.  FIG. 5A  shows the cell itself.  FIG. 5B  shows an image of the cell of  FIG. 5A  at a first wavelength.  FIG. 5C  shows an image of the cell of  FIG. 5A  at a second wavelength.  FIG. 5D  shows a composite figure combining the images at both wavelengths. 
       FIG. 6A  is a block diagram illustrating a second embodiment of a high resolution imaging fountain flow cytometer according to the present invention with two focal planes and a variation on the filter wheel element.  FIG. 6B  is a simplified view of a filter slide element from the side.  FIG. 6C  is a simplified view of a flat filter wheel from the side. 
       FIG. 7  shows a side cutaway view of a variation of the flow block of  FIG. 3 , utilizing side illumination.  FIG. 7A  shows an end-on view of the laser port of  FIG. 7 . 
   

   DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS 
   The present invention includes apparatus and methods for high resolution imaging of fluorescent particles in a fountain flow cytometry set up. (A precursor invention, described in U.S. patent application Ser. No. 10/323,535 by the present inventor, is shown in Prior Art  FIGS. 2 and 3 . This previous invention incorporates detection, but not high resolution imaging.) To review the flow cytometry detection process, a flow channel defines a flow direction for samples in a flow stream and has a viewing plane nearly perpendicular to the flow direction. A clear volume between the illuminated flow volume and the imaging optics is provided in some embodiments. A beam of illumination is formed as a column having a size that can effectively cover the viewing plane, and illuminates the flow end on or nearly end on. Imaging optics are arranged to view the focal plane to form a low-resolution image of the multiple fluorescent sample particles in the flow stream. In this step, particles of interest are identified. 
   In th identification step, as a microorganism passes up the delivery tube its spot size (the size that the image of the microorganism occupies on the CCD) decreases as it approaches the focal plane of the CCD camera; above the focal plane the spot size increases. The spot size reaches it minimum in the focal plane of the CCD fore-optics. In order to minimize the blur of imaged cells, low resolution detection imaging should occur in a thin (relative to the camera focal length) focal plane and light emitted from outside of this region should be attenuated. This can be achieved by illumination of the flow with an elongated laser beam orthogonal to the flow (as in U.S. Pat. No. 6,309,886 by Ambrose et al.), or the use of structured illumination with a grating in the conjugate focal plane (Neil, Juskaitis, &amp; Wilson, 1997, Opt. Lett. 22, 1905–1907) or using a micro-mirror array (Fukano and Miyawaki, 2003, Applied Optics 42, 19, 4119–4124). 
   Once a particle of interest has been detected, the present invention provides apparatus and methods for repositioning the particle, magnifying it, and forming a high resolution image of the image. For the present application, “low resolution” generally refers to an image on the order of 10–100 pixels. Such an image identifies that a spatially unresolved cell or particle is present. “High resolution” indicates a spatially resolved image of a particle, having 500 to 1000 or more pixels. 
   The low resolution imaging can be done on the fly with the high throughput apparatus shown in  FIG. 2  (Prior Art). The ability to stop temporarily and form high resolution images of particles of interest, and then continue with the high throughput operation, is the key to the present invention. 
   A preferred embodiment of the present invention is shown in  FIG. 4A . Refer also to Prior Art FIGS.  2  and  3 A– 3 D.  FIG. 2  illustrates illumination and detection of a target particle  210 , and  FIGS. 3A–3D  illustrate a flow block which is useful in the present invention.  FIG. 4A  is a block diagram illustrating a high resolution imaging fountain flow cytometer  400  according to the present invention. The sample  314  is illuminated in this embodiment by multiple lasers  448 ,  450  through the microscope objective  444 . 
   Multispectral imaging may be accomplished by using two separate lasers  448 ,  450  to illuminate sample  314  at different light frequencies, as shown in  FIG. 4A . As an alternative, an illumination beam at a single frequency could result two different wavelengths of light being emitted from the particle in the sample, for example by illuminating two fluorescent dyes that emit at two different frequencies. In either case, two (or more) frequencies of light end up issuing from the particle (via reflection, emission, scattering, or the like) and are imaged, resulting in a multi-spectral image. 
   The flow cell  300  sits on a computer controlled x-y stage  446  that allows the field of view to be centered on any target particle  210  passing through the flow cell orifice. The microscope objective  444  can be swapped by computer control to allow for multiple magnifications (say 2×, 40×, and 100×). A filter wheel  440  allows imaging at multiple wavelengths. The syringe pump  460  is under computer control and may be programmatically stopped and run in either direction. 
   In this preferred configuration, the illumination geometry is an epi-illumination geometry, that is sample  314  is illuminated through the same microscope objective  444  that is used to image the sample, as is common with epi-fluorescent microscopes. 
   Whenever a cell of interest,  210 , is detected passing through flow cell  300  by means of its fluorescence at a specific wavelength, the syringe pump  460  is used to slowly back cell  210  through the focal plane  326  of flow cell  300  by operating it in reverse at slow speed. As an alternative, or in addition, syringe pump  460  may be operated to stop the cell in the focal plane temporarily. Then x-y stage  446  is used to center cell  210  in the field of view while a high magnification objective lens  444  is selected and used to zoom in on the cell at higher magnification. Then a series of high resolution fluorescence images (see  FIG. 5 ) at a series of absorption/emission wavelengths is taken for multispectral analysis by (for example) use of a computer controlled filter wheel  440 . When completed, computer  470  resets filter  440 , x-y stage  446 , and microscope objective  444  so that syringe pump  460  can be set in forward motion at high speed again. All of this allows high speed detection of rare cells at high volume throughput, with high resolution imaging of cells of interest after detection from emission at a single wavelength (by using an appropriate selective stain, such as an immuno-label). 
     FIG. 4B  is a simplified view of filter wheel  440  of  FIG. 4A , shown end on.  FIG. 4C  is a simplified view of filter wheel  440 , from the side. Filter wheel  440  and its operation are described in more detailed in U.S. patent Ser. No. 10/323,535. A summary of that discussion follows. Two-color emission is illustrated in  FIGS. 4A–4C , but three or more colors may be detected by using more than two filter portions  440   a ,  440   b , etc. While filter wheel  440  is not necessary for the present invention, since the two images can be taken at separate times, it is still useful in some embodiments for spatially separating the two (or more) resulting images. 
   The basic premise for the filter wheel system is that multicolor light emission  434  from focal plane  326  of flow cell  300  is sent through tilted filter wheel  440 , which is rotating. As filter wheel  440  rotates it alternates between passing emission from a first emission wavelength and a second emission wavelength through the system onto CCD  408 . 
   When a beam of light passes through tilted filter portions  440   a ,  440   b , the beam is displaced by an amount that depends on the index of refraction and the thickness of each filter portion. Filter portions  440   a ,  440   b , are designed to have slightly different thicknesses/indices, creating a multiple image for each bacterium or other imaged particle, one image for each emission color. 
   Filter wheel  440  rotates very rapidly compared to the integration (exposure) time, so that beam  434  is incident on each filter portion for (typically) half of the integration time. The two slightly displaced, colored beams then focus onto CCD  408 , forming spots  502  and  504  in  FIG. 5 . The filter segment sizes can be adjusted to compensate for the difference in intensity at each wavelength. 
   Multicolor detection of three or more colors can easily be implemented with the invention. A motorized filter wheel  440  containing multiple filter segments (one to select each wavelength of multiple emission wavelengths) is inserted so that each segment will pass through beam  434  before striking the CCD  408  (or other imaging detector). The filter motor (not shown) is driven at a high rotation rate so that the time of rotation is much faster than the time it takes a particle to move in the image or across the focal plane. The filters are of differing index of refraction and/or thickness, so that the image of a particle on the detector will move (chop) significantly and in a direction and distance on the detector that can be calibrated. The detection of multiple spots on the detector with an appropriate distance and direction of separation can then be taken as a detection in one or more wavelength bands. 
     FIGS. 5A–5D  are schematic drawings illustrating two images of the same cell  502  at different wavelengths.  FIG. 5A  shows the cell  502  itself.  FIG. 5B  shows an image  504  of the cell of  FIG. 5A  at a first wavelength, and  FIG. 5C  shows an image of the cell of  FIG. 5A  at a second wavelength. For example, if cell  502  was labelled with a blue fluorescent dye absorbed by the DNA of the nucleus, and a red fluorescent dye absorbed by the mitochondria, image  504  could be the image resulting applying a blue filter, and image  506  could be the image resulting from applying a red filter. Essentially, images  504 ,  506  are cartoons showing two MSFFC images of a cell, side-by-side, at two emission wavelengths. Each shows a different morphology, which can be used for cell identification/discrimination.  FIG. 5D  shows a composite  figure 508  combining the images at both wavelengths. For example, image  508  could be an image formed by false coloring and adding images  504  and  506 . 
     FIG. 6A  is a block diagram illustrating a second embodiment  600  of a high resolution imaging fountain flow cytometer according to the present invention with two focal planes  628 A and  628 B and possible variations  640  on the filter wheel element. In the embodiment of  FIG. 6 , microscope objective  444  comprises a low power objective  644 A and a high power objective  644 B. Low power objective  644 A has a first focal plane  628 A, and High power objective  644 B has a second focal plane  628 B, which is downstream of focal plane  644 A. 
   In use, low power objective  644 A is used most of the time, while imaging cytometer  600  is doing high-speed detection of target particles. When a target particle  210  is detected, microscope objective  444  switches resolutions, for example by sliding low power objective  644 A out of the optical axis and sliding high power objective  644 B into the optical axis in its place. XY stage  446  operates to center particle  210  within high power objective  644 B. Flow control element  460  sows the flow through flow cell  300 B. Hence, by the time target particle  210  passes through second focal plane  628 B, it can be imaged by high power objective  644 B. Processor  670  detects target particle  210 , and then changes objectives, centers the particle, and controls the flow for high resolution imaging. 
     FIG. 6B  is a simplified view of a filter slide element  640 A from the side.  FIG. 6C  is a simplified view of a flat filter wheel  640 B from the side. These filter elements include filters  641 ,  642  at two or more wavelengths (colors) for multispectral imaging. Since the flow is slowed or stopped while high resolution imaging occurs, these flat filter elements may be used in place of the filter wheel  440  shown in  FIG. 4 . They do no spatially displace the images, but the images are displaced in time. 
     FIG. 7  shows a side cutaway view of a variation  300 C of the flow block  300  of  FIG. 3 , utilizing side illumination. Imaging is still done through transparent element  220 , but in some cases it is convenient to utilize side illumination. Port  730  allows laser beam  734  to illuminate focal plane  728  through window  732 . 
   A number of alternative embodiments are within the scope of the present invention. For example, while the preferred embodiment of  FIG. 4  includes multi-spectral imaging, one-color imaging is also quite useful. The flow cell of  FIG. 3  is a particularly useful element of the invention, but can be replaced with a simpler element such as that shown in  FIG. 2 .