Classifications

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Definitions

• This invention generally relates to imaging moving objects or particles for purposes of analysis and detection, and more specifically, to a system and method for determining and analyzing the morphology of moving objects, such as cells, and for detecting the presence and composition of Fluorescence In-Situ Hybridization (FISH) probes within cells.
• FISH Fluorescence In-Situ Hybridization
• the target cells are fetal cells that cross the placental barrier into the mother's bloodstream.
• the target cells are sloughed into the bloodstream from nascent cancerous tumors.
• the target cells may be present in the blood at concentrations of one to five cells per billion. This concentration yields approximately 20-100 target cells in a typical 20 ml blood sample.
• any detection and analysis system employed in these applications be capable of processing an enriched sample of approximately 100 million cells within a few hours, corresponding to a minimum throughput of 10,000 cells per second.
• Cell processing includes the determination of cellular morphology parameters such as overall size, nuclear size, nuclear shape, and 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.
• the system must be able to collect cell images with a spatial resolution of approximately 1 micron.
• the system must have high spectral resolution and bandwidth to differentiate four or more fluorescent colors. Since some probes may label important cellular features with only a few thousand fluorescent molecules, the system must have high sensitivity and good measurement consistency to differentiate very weak signals.
• the predominant research laboratory protocols for non-invasive prenatal diagnosis employ a complex series of process steps that include gradient centrifugation to remove unnucleated cells, high speed cell sorting for fetal cell enrichment, and fluorescence microscopy for fetal cell identification and genetic analysis. These protocols often yield little or no fetal cells for analysis, because a fraction of the fetal cells are lost at each step of the protocol. Nevertheless, the protocols cannot be simplified because of limitations in existing analysis technology. Ideally, fetal cell identification and analysis would be performed in a few hours by a high speed cell sorter having the necessary speed and sample handling capacity.
• a paper published by Ong et al. [Anal. Quant. Cytol. Histol., 9(5):375-82] describes the use of a time delay and integration (TDI) detector in an imaging flow cytometer.
• TDI detector is any pixilated device in which the signal produced in response to radiation directed at the device can be caused to move in a controlled fashion.
• the pixels of a TDI detector 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.
• the approach disclosed by Ong et al. advanced the art by addressing the need for spatial resolution and high sensitivity for cells in flow. However, this approach does not address the remaining principal characteristics.
• U.S. Patent No. 5,644,388 discloses an alternative approach to an imaging flow cytometer.
• the patent discloses the use of a frame-based image collection approach in which a video camera views cells in flow, in a freeze frame fashion.
• This method requires the image collection system to be synchronized with the presence of cells in the imaging area, unlike the case of TDI, wherein the detector readout rate is synchronized with the velocity of the cells.
• the integration period must be very short to prevent blurring.
• a short integration time is achieved either with a strobed light source, or a continuous light source combined with a shuttered detector.
• the image represents the spatial distribution of light in object space.
• the spatial distribution is blurred as the light propagates past the image plane, through the spectral dispersing element and onto the image intensifier. Because there is no provision for re-imaging the intermediate aperture at the intensifier, the resulting signal distribution at the intensifier represents only the spectral distribution of the light and does not preserve the spatial distribution of the light from the object.
• the loss of spatial information limits the utility of the invention for applications such as fetal cell analysis. If multiple identical FISH spots are present in a cell, their spectra can be ascertained using this approach, but the number of spots cannot be determined. In addition, this approach disperses the wavelength spectrum parallel to the axis of flow.
• the patent discloses that a very short illumination height in the flow axis is used.
• the short illumination height decreases integration time, which necessitates the use of the image intensifier. Further, the short illumination height limits throughput by preventing the simultaneous imaging of multiple cells in the flow axis.
• the present invention is directed to an imaging system that is adapted to determine one or more characteristics of an object from an image of the object. There is relative movement between the object and the imaging system, and although it is contemplated that either (or both) may be in motion, the object will preferably move while the imaging system will be fixed.
• the present invention is preferably intended to be used with a plurality of objects and is particularly useful in connection with imaging a stream of objects.
• the present invention provides a method and apparatus utilizing multiple detectors to determine at least one characteristic of an object moving through a field a view, relative to the detectors.
• the detectors are stationary, although it should be understood that a critical aspect is that there be relative motion between the object and the detectors, thus the present invention anticipates embodiments in which the object is stationary and the detectors are in motion.
• the data provided by the present invention include simultaneous spatial and spectral images covering a large bandwidth at high resolution, and further that the present invention preserves the spatial origin of the spectral information gathered from the object.
• the use of multiple detectors ensures no distortion or convolution of the image occurs due to the emission bandwidth, and as a result, a deconvolution is not needed to correct the image.
• Sufficient detectors are employed to provide separate detectors for each spectrally decomposed image.
• a first series of embodiments are directed toward systems that include an imaging lens associated with each individual detector, and a second series of embodiments are directed towards systems that include a single imaging lens for the system.
• the system includes a collection lens disposed so that light traveling from the object is collimated by passing through the collection lens and travels along a collection path. At least one lens is disposed to receive light that has passed through the collection lens, and to generate an image.
• the disposition of such image lens, or lenses is a function of whether one image lens is employed for the system, or whether a separate lens is associated with each detector noted above. The relative dispositions will be discussed more in detail below.
• a plurality of light reflecting elements receive light that has passed through the collection lens, and reflecting having a predefined characteristic, while enabling light that does not have the predefined characteristic to pass.
• the light passing through the collection lens is in a plane substantially orthogonal to a direction of relative movement between the object and the imaging system.
• the object or the imaging system or both can be in motion relative to the other and for the sake of simplicity, this relative movement is hereinafter referred to simply as "the movement.”
• Each light reflecting element reflects light in a different direction, and for each light reflecting element there is a detector disposed to receive reflected light. Each detector is capable of producing a signal indicative of at least one characteristic of the object.
• each detector is a TDI detector, disposed to receive the image produced by the at least one imaging lens. As the movement occurs, the image of the object produced by the imaging lens moves from row to row across the TDI detector.
• Each TDI detector produces an output signal that is indicative of at least one characteristic of the object, by integrating light from at least a portion of the object over time.
• the collection lens in this embodiment, all light emitted from a first point in the object travels in parallel rays. Light emitted from a second point in the object will also travel in parallel rays, but at a different angle relative to light from the first point.
• spatial information in the object is transformed by the collection lens into angular information in the collection path.
• the plurality of different reflecting elements each reflect different characteristics of light, thereby acting on the collimated light such that different spectral components leave the plurality of different reflecting elements in different directions, preferably in a plane substantially orthogonal to the direction of the movement between the object and the imaging system. In this manner, both spatial and spectral information in the object are transformed into angular information.
• the at least one imaging lens acts on the collimated light to transform different light angles into different positions on each detector. Spatial information is preserved by the system since light from the different positions in the object is projected to different positions on the detector, for both axes. In addition, preferably light of different spectral composition that originates from the object is projected onto different detectors, in an axis substantially orthogonal to the movement. In this manner, the spatial information from the object is preserved, while spectral information covering a large bandwidth is simultaneously collected at high resolution.
• the use of a single detector for each different spectral component means that each detector can be focused independently for each color, thereby simplifying the optical design by eliminating the constraint of longitudinal color correction required for single detector systems.
• a still further advantage is that the quantum efficiency of each detector can be individually optimized for its particular color band, thereby increasing the overall sensitivity of the system.
• each light reflecting element is a dichroic filter, or dichroic mirror, which are arranged to reflect light within predefined bandwidths at predefined angles.
• dichroic filter or dichroic mirror, which are arranged to reflect light within predefined bandwidths at predefined angles.
• all light within a predefined bandwidth incident on the dichroic element at a common angle leaves a given dichroic element at the same angle. Therefore, there is no convolution between the emission spectrum of the light leaving the object and the image of that object.
• light of a first spectral bandwidth reflects off the first dichroic element at a predefined nominal angle.
• Light of a second spectral bandwidth is passed through the first dichroic element to the next dichroic element and is reflected therefrom at a different predefined nominal angle.
• Light of a third spectral bandwidth is passed through the first and second dichroic elements to a third dichroic element and reflected therefrom at a third predefined nominal angle.
• the dichroic elements are selected to cover the desired light spectrum with the appropriate spectral passbands.
• the angle of each dichroic element is set such that light reflected from it within the corresponding spectral bandwidth for the dichroic element is focused onto a different detector.
• a single image lens is disposed in the collection path.
• the positions of the detectors are manipulated such that the distance from each detector to the single image lens is substantially equivalent.
• Each reflective element is disposed in between the image lens and the corresponding detector.
• each dichroic reflecting element is a cube substrate.
• each dichroic reflecting is a pellical, while in other embodiments each dichroic reflecting element is a plate substrate. Note that for most embodiments, light from the object passes through each light reflecting element only once. Particularly in embodiments employing a single lens, optical distortions are increased after light passes through each dichroic reflecting element.
• such distortions are reduced by employing cube substrates wherein a numerical aperture associated with each cube substrate is sufficiently small so as to substantially eliminate coma and astigmatism.
• a correction plate is disposed between each successive light reflecting element, each correction plate being oriented relative to an immediately preceding light reflective element such that any astigmatism imparted by the immediately preceding light reflective element is substantially eliminated.
• the orientation of the correction plate is substantially orthogonal relative to an axis about which the immediately preceding light reflective element is rotated to direct reflected light toward one of the plurality of detectors.
• the predefined characteristic which the reflecting elements employ to reflect or pass light is color
• each individual TDI detector is separately focused for a specific color of light, so that each individual TDI detector is properly focused for a specific color of light directed toward that TDI detector by a corresponding reflecting element.
• each individual TDI detector is independently optimized for the specific color to be directed toward that TDI detector.
• One embodiment includes an aperture stop disposed adjacent to and preceding the at least one image lens, the aperture stop enabling control of a numerical aperture associated with the at least one image lens.
• Other embodiments include an objective lens and an imaging slit disposed along the light collection path, in between the object and the collection lens.
• a light source can be disposed to provide an incident light that illuminates the object. It should be noted that the use of a TDI detector in the present invention results in an extended imaging region along the axis of motion and a correspondingly long integration time. Several light sources can be simultaneously projected into the imaging region, increasing the amount of light incident upon objects therein.
• the combination of an extended imaging region and the orthogonal orientation of the spectral dispersion axis relative to the axis of the motion allows multiple objects to be imaged simultaneously.
• the long integration time and parallel image acquisition of this embodiment allows sensitive and consistent imaging performance to be combined with high throughput.
• the light from the object comprises an unstimulated emission from the object, i.e., the object emits light without requiring a light source to stimulate the emission.
• a light source is disposed to provide an incident light that illuminates the object.
• the object may scatter the incident light so that the light scattered from the object at least in part passes through the collection lens, or the incident light illuminating the object may stimulate the object to emit the light that passes through the collection lens.
• the incident light may at least be partially absorbed by the object, so that the light passing through the collection lens does not include a portion of the light absorbed by the object.
• the incident light from the light source may be reflected from the object toward the collection lens.
• the light source or sources that are used preferably comprise at least one of a coherent light source, a non-coherent light source, a pulsed light source, and a continuous light source.
• the object may be entrained within a fluid stream that moves the object past the collection lens, or alternatively, can be carried on a support, or simply move without the benefit of a support or flowing medium.
• the present invention is not limited to the imaging of microscopic or small objects.
• the TDI detector preferably responds to the image of the object by producing a signal that propagates across the TDI detector. Pixels of a typical TDI detector are arranged in rows and columns, and the signal propagates from row to row. However, the present invention is not limited to TDI detectors employing a rectilinear arrangement of pixels (e.g., a microchannel plate-based TDI detector). A propagation rate of the signal across the TDI detector can either be synchronized with a motion of the image of the object on the TDI detector as a result of the movement, or can be non-synchronized with the movement. Other aspects of the present invention are directed to methods for imaging an object. These methods implement steps that are generally consistent with the imaging system discussed above.
• FIGURE 1 is a plan view of a first embodiment of the present invention in which particles conveyed by a fluid stream depicted as flowing into the sheet;
• FIGURE 2 is a side elevational view of the first embodiment shown in
• FIGURE 1
• FIGURE 3 is an isometric view of the first embodiment of FIGURE 1;
• FIGURE 4 is an isometric view of a confocal embodiment that includes a slit that is used for spatial filtering of extraneous light;
• FIGURE 5 is an isometric view showing different locations for a light source in connection with the first embodiment;
• FIGURE 6 is an alternative to the first embodiment in which a second set of imaging components and TDI detector is included for monitoring light from a particle, to avoid interference between FISH probes, and showing alternative locations for light sources;
• FIGURE 7 is an isometric view of an embodiment in which an object is supported by or comprises a slide that moves past a collection lens, showing different locations for a light source;
• FIGURES 8 A and 8B are respectively a plan view and a side elevational view of an alternative to the embodiment of FIGURE 7 that is used to produce a scattered pattern on the TDI detector;
• FIGURE 9 is a plan view of yet a further embodiment in which light forming a scatter patterned image and spectrally dispersed light from the object are imaged on separate portions of a TDI detector;
• FIGURE 10 is a plan view of a still further embodiment in which light forming a scatter patterned image and spectrally dispersed light from the object are imaged by two different TDI detectors;
• FIGURE 11 is a schematic diagram illustrating the optical convolution of a narrow FISH emission spectrum by the present invention, to resolve two FISH probes in a cell;
• FIGURE 12 is a schematic diagram showing the optical convolution of two different colors of narrow FISH emission spectra, to resolve the image of the FISH probes on the TDI detector;
• FIGURE 13 is a schematic diagram illustrating how for a wider FISH emission spectrum, a deconvolution is provided by the present invention to resolve the image of two FISH probes of a single color;
• FIGURE 14 is a schematic diagram showing the deconvolution of two color FISH spectra that are relatively wide, to resolve the image of the FISH probes;
• FIGURE 15 is a schematic block diagram of the system used to process the signal produced by a TDI detector in the present invention.
• FIGURE 16 is a schematic diagram illustrating how the present invention is used to determine whether a cell is from a male or female;
• FIGURE 17 is a plan view of an alternate embodiment that employs a spectral dispersion component comprising a plurality of stacked dichroic filters employed to spectrally separate the light;
• FIGURE 18 is an X-Y plot of several typical passbands for the dichroic filters employed in the embodiment shown in FIGURE 17;
• FIGURE 19 is a schematic illustration of a detection filter assembly that may optionally be placed in front of the TDI detector in the embodiment of FIGURE 17 to further suppress out-of-band light;
• FIGURES 20A-20E are X-Y plots of transmission vs. wavelength for corresponding passbands of the filter segments of the detection filter assembly that may optionally be placed in front of the TDI detector;
• FIGURE 21 is a plan view of another embodiment of the configuration of FIGURE 17, wherein the spectral dispersion filter system comprises a plurality of dichroic cube filters orientated at various angles to create the spectral dispersing effect;
• FIGURE 22 illustrates an exemplary set of images projected onto the TDI detector when using the spectral dispersing filter system of the FIGURE 17
• FIGURE 23 is a schematic isometric view of yet another embodiment, in which spectral decomposition occurs in an axis that is generally parallel to a direction of motion of a substrate carrying an object;
• FIGURE 24 is a schematic plan view of a spectrally segmented detector for use in detecting and imaging light of several different spectral compositions
• FIGURE 25 is an isometric view of an alternate embodiment, employing separate TDI detectors and separate imaging lenses for each spectrally decomposed image;
• FIGURE 26 is an isometric view of an alternate embodiment employing separate TDI detectors, with a common imaging lens placed prior to the spectral decomposition elements;
• FIGURE 27 is an isometric illustration of correction plates added to correct for astigmatism induced by a plate beam splitter placed in convergent space;
• FIGURE 28 is an isometric view of an alternate embodiment employing separate TDI detectors receiving both light transmitted through and reflected by spectral decomposition elements.
• the present invention offers considerable advantages over systems employed for cell and particle analysis in the prior art. These advantages arise from the use in the present invention of an optical dispersion system in combination with a TDI detector that produces an output signal in response to the images of cells and other objects that are directed on the TDI detector. Multiple objects can be imaged on the
• the image of each object can be spectrally decomposed to discriminate object features by absorption, scatter, reflection or probe emissions using a common TDI detector for analysis.
• the present invention can be employed to determine morphological, photometric, and spectral characteristics of cells and other objects by measuring optical signals including light scatter, reflection, absorption, fluorescence, phosphorescence, luminescence, etc.
• Morphological parameters include nuclear area, perimeter, texture or spatial frequency content, centroid position, shape (i.e., round, elliptical, barbell-shaped, etc.), volume, and ratios of any of these parameters. Similar parameters can also be determined for the cytoplasm of cells with the present invention.
• Photometric measurements with the invention enable the determination of nuclear optical density, cytoplasm optical density, background optical density, and the ratios of any of these values.
• An object being imaged with the present invention can either be stimulated into fluorescence or phosphorescence to emit light, or may be luminescent, producing light without stimulation.
• the light from the object is imaged on the TDI detector of the present invention to determine the presence and amplitude of the emitted light, the number of discrete positions in a cell or other object from which the light signal(s) originate(s), the relative placement of the signal sources, and the color (wavelength or waveband) of the light emitted at each position in the object.
• FIGURES 1, 2, and 3 A first preferred embodiment of an imaging system 20 in accord with the present invention is schematically illustrated in FIGURES 1, 2, and 3, in connection with producing images of moving objects such as cells that are conveyed by a fluid flow 22 through the imaging system.
• fluid flow 22 entrains an object 24 (such as a cell, but alternatively, a small particle) and carries the object through the imaging system.
• object 24 such as a cell, but alternatively, a small particle
• the direction of the fluid flow in FIGURE 1 is into (or out of) the sheet, while in FIGURES 2 and 3, the direction of flow is from top to bottom, as indicated by the arrow to the left of the Figures.
• Light 30 from object 24 passes through collection lenses 32a and 32b that collect the light, producing collected light 34, which is approximately focussed at infinity, i.e.
• the rays of collected light from collection lens 32b are generally parallel. Collected light 34 enters a prism 36, which disperses the light, producing dispersed light 38. The dispersed light then enters imaging lenses 40a and 40b, which focuses light 42 onto a TDI detector 44.
• positions 26 and 28 can represent the location of two separate objects, which are simultaneously imaged on the detector at positions 26' and 28'.
• imaging system 20 and all other imaging systems illustrated herein, it will be understood that the lenses and other optical elements illustrated are shown only in a relatively simple form.
• the collection lens is illustrated as a compound lens comprising only collection lenses 32a and 32b.
• Lens elements of different designs, either simpler or more complex, could be used in constructing the imaging system to provide the desired optical performance, as will be understood by those of ordinary skill in the art.
• the actual lenses or optical elements used in the imaging system will depend upon the particular type of imaging application for which the imaging system will be employed.
• the TDI detector that is used in the various embodiments of the present invention preferably comprises a rectangular charge-coupled device (CCD) that employs a specialized pixel read out algorithm, as explained below.
• CCD charge-coupled device
• Non-TDI CCD arrays are commonly used for 2-dimensional imaging in cameras.
• TDI detector 44 which comprises a CCD array
• the CCD array remains exposed to the light as the pixels are read out.
• the readout occurs one row at a time from the top toward the bottom of the array. Once a first row is read out, the remaining rows are shifted by one pixel in the direction of the row that has just been read. If the object being imaged onto the array moves in synchrony with the motion of the pixels, light from the object is integrated for the duration of the TDI detector's total readout period without image blurring.
• the signal strength produced by a TDI detector will increase linearly with the integration period, which is proportional to the number of TDI rows, but the noise will increase only as the square root of the integration period, resulting in an overall increase in the signal-to-noise ratio by the square root of the number of rows.
• One TDI detector suitable for use in the present invention is a Dalsa Corp., Type IL-E2 image sensor, although other equivalent or better image sensors can alternatively be used.
• the Dalsa image sensor has 96 stages or rows, each comprising 512 pixels; other types of image sensors useable in the present invention may have different configurations of rows and columns or a non-rectilinear arrangement of pixels.
• the Dalsa sensor has approximately 96 times the sensitivity and nearly 10 times the signal-to-noise ratio of a standard CCD array.
• the extended integration time associated with TDI detection also serves to average out temporal and spatial illumination variations, increasing measurement consistency.
• a flow-through cuvette or a jet (not shown) contains the cells or other objects being analyzed.
• the velocity and cellular concentration of the fluid may be controlled using syringe pumps, gas pressure, or other pumping methods (not shown) to drive a sample solution through the system to match the pixel readout rate of the TDI detector.
• the readout rate of the TDI detector can be selectively controlled, as required, to match the motion of the sample solution.
• optical magnifications can be used to achieve a desired resolution of the object that is being imaged on the light sensitive regions (pixels) of the TDI detector. It is contemplated that in most embodiments, the optical magnification will fall within a range of 1:1 to 50:1, providing a substantial range in the number of light sensitive regions on the TDI detector on which images of the object are formed, also depending of course, on the actual size of the object being imaged and its distance from the imaging system. It is envisioned that the present invention can have applications ranging from the analysis of cells and other microscopic objects to the imaging of stellar objects.
• TDI detectors are CCD types of TDI detectors.
• Other types of TDI detectors such as complementary metal oxide semiconductor (CMOS) and multi-channel plate imaging devices might also be used for the TDI detector in the present invention.
• CMOS complementary metal oxide semiconductor
• CMOS complementary metal oxide semiconductor
• the signal will move in synchrony with a moving image projected onto the device, thereby increasing the integration time for the image, without causing blurring.
• the motion of the signal can be selectively desynchronized from the motion of the radiation image, as required to achieve a desired affect.
• FIGURE 4 illustrates an imaging system 45, which is a second preferred embodiment of the present invention and which is similar in many ways to imaging system 20.
• imaging system 45 is a confocal embodiment that includes a slit 52 that substantially prevents extraneous light from reaching TDI detector 44.
• light 46 from object 24 is focussed by an objective lens 48 onto a slit 52.
• Slit 52 is sufficiently narrow to block light, which is not focussed onto the slit by objective lens 48 from passing through the slit.
• Light 30' passes through the slit and is collected by collection lens 32 as discussed above, in regard to imaging system 20.
• Collected light 34 is spectrally dispersed by prism 36, and is imaged by imaging lens 40 onto TDI detector 44, also as discussed above.
• the TDI detector produces an output signal that corresponds only to the actual images of the object, and the signal is not affected by the extraneous light, which has been excluded. If not excluded in this manner, the ambient light reaching TDI detector 44 might otherwise produce "noise" in the output signal from the TDI detector.
• each of imaging systems 20 and 45 a light source has not been shown. These first two embodiments have been illustrated in their most general form to make clear that a separate light source is not required to produce an image of the object, if the object is luminescent, i.e., if the object produces hght.
• many of the applications of the present invention will require that one or more light sources be used to provide light that is incident on the object being imaged. The location of the light sources substantially affects the interaction of the incident light with the object and the kind of information that can be obtained from the images on the TDI detector.
• FIGURE 5 several different locations of light sources usable to provide light incident on object 24 are illustrated. It should be understood, however, that light sources can be located at many other positions besides those shown in FIGURE 5.
• the location of each one or more light source employed will be dependent upon the kind of imaging of the object, and the kind of data for the object, to be derived from the signal produced by the TDI detector.
• employing a light source 60a or a light source 60b, as shown in the Figure will provide light 58 that is incident on object 24 and which is scattered from the object into the optical axis of collection lens 32.
• the optical axis of collection lens 32 is at about a 90° angle relative to the directions of the light incident upon object 24 from either light source 60a or 60b.
• a light source 62 is disposed so that light 58 emitted from the source travels toward the object in a direction that is generally aligned with the optical axis of collection lens 32, so that the image formed on TDI detector 44 will not include light absorbed by object 24. Light absorption characteristics of the object can thus be determined by illuminating the object using a light source 62.
• a light source 64 is disposed to illuminate object 24 with hght directed toward the object along a path that is approximately 30-45° off the optical axis of collection lens 32. This light 58, when incident on object 24 will be reflected (scattered) from object 24, and the reflected or scattered light will be imaged on TDI detector 44.
• a more directly reflected light is provided by an epi light source 66, disposed so as to direct its light 58 toward a partially reflective surface 68 that is disposed so that a portion of the hght is reflected through collection lens 32 and onto object 24. The light reaching the object will be reflected from it back along the axis of collection lens 32 and will at least in part pass through partially reflective surface 68 to form an image of the object on TDI detector 44.
• a dichroic mirror may be employed instead of, and in the position of, partially reflective surface 68 to direct light from epi light source 66 to excite fluorescence or other stimulated emission from object 24. Emission from object 24 is then at least partially collected by collection lens 32 and passes through the dichroic mirror for spectral dispersion and detection by the TDI detector.
• a light source can also be used to stimulate emission of hght from the object.
• FISH probes that have been inserted into cells will fluoresce when excited by hght, producing a corresponding characteristic emission spectra from any excited FISH probe that can be imaged on TDI detector 44.
• light sources 60a, 60b, 64, or 66 could alternatively be used for causing the excitation of FISH probes on object 24, enabling TDI detector 44 to image FISH spots produced by the FISH probes on the TDI detector at different locations as a result of the spectral dispersion of the hght from the object that is provided by prism 36.
• Each of the light sources illustrated in FIGURE 5 produces hght 58, which can either be coherent, non-coherent, broadband or narrowband light, depending upon the application of the imaging system desired.
• hght 58 can either be coherent, non-coherent, broadband or narrowband light, depending upon the application of the imaging system desired.
• a tungsten filament hght source can be used for applications in which a narrowband light source is not required.
• narrowband laser light is preferred, since it also enables a spectrally-decomposed, non-distorted image of the object to be produced from light scattered by the object.
• This scattered light image will be separately resolved from the FISH spots produced on TDI detector 44, so long as the emission spectra of any FISH spots are at different wavelengths than the wavelength of the laser light.
• the light source can be either of the continuous wave (CW) or pulsed type. If a pulsed type illumination source is employed, the extended integration period associated with TDI detection can allow the integration of signal from multiple pulses. Furthermore, it is not necessary for the light to be pulsed in synchronization with the TDI detector.
• Pulsed lasers offer several advantages over CW lasers as a hght source in the present invention, including smaller size, higher efficiency, higher reliability, and the ability to deliver numerous wavelengths simultaneously.
• Another advantage of pulsed lasers is their ability to achieve saturating levels of fluorescence excitation of fluorescent probes used in cells. Fluorescence saturation occurs when the number of photons encountering a fluorescent molecule exceeds its absorption capacity. Saturating excitation produced by a pulsed laser is inherently less noisy than unsaturafing CW laser excitation because variations in pulse-to-pulse excitation intensity have little effect on the fluorescence emission intensity.
• Prism 36 in the imaging systems discussed above can be replaced with a diffraction grating, since either is capable of spectrally dispersing the optical signals from the cells over the pixels of the TDI detector.
• spectral dispersion can be used to reduce measurement noise.
• the light source wavelength differs from the emission spectra of the fluorescent probes
• the light from the source that is scattered into the collection system is spatially isolated from the fluorescence signals. If the light source wavelength overlaps the emission spectra of the fluorescent probes, the pixels of the TDI detector in which light of the wavelength of the source falls can be isolated from those pixels on which the remaining fluorescence signals fall. Further, by dispersing the fluorescence signals over multiple pixels, the overall dynamic range of the imaging system is increased.
• a third preferred embodiment is a stereoscopic arrangement 70 of the first preferred embodiment, as illustrated in FIGURE 6.
• This arrangement allows the imaging of the object from two different directions in order to distinguish features that would otherwise overlap when viewed from a single direction.
• the third preferred embodiment can be employed for objects on moving substrates such as microscope slides, it is particularly useful for analyzing multi-component objects in solution, such as cells containing FISH probes.
• Such probes appear as point sources of hght anywhere within the cell's three-dimensional nucleus.
• two or more FISH probes may appear in an overlapping relationship along the optical axis of the imaging system. In such cases, one of the FISH probes may obscure the others, making it difficult to determine the number of probes present in the cell.
• the stereoscopic imaging system 70 in FIGURE 6 includes two TDI detectors 44a and 44b, and their associated optical components, as discussed above in connection with imaging system 20.
• the optical axes of collection lenses 32 for the two TDI detectors so that they are spaced apart, for example, by 90°, it is possible to separately resolve the FISH spots imaged from two or more FISH probes on at least one of TDI detectors 44a or 44b. If two or more FISH probes overlap in regard to the image produced on one of the detectors, they will be separately resolved in the spectrally dispersed images produced on the other TDI detector.
• the use of two TDI detectors in imaging system 70 in what might be referred to as a "stereo or three-dimensional configuration" allows flexibility in the configuration of each leg of the system, including parameters such as the relative TDI readout rates, axial orientations, inclinations, focal plane positions and magnification. Multiple cells or other objects may be imaged onto each detector simultaneously in the vertical direction. Since the objects may move in synchronicity with the signal on the TDI, no gate or shutter is required to prevent blurring of the image.
• the present invention can use a pulsed or CW light source without need for a trigger mechanism to time a pulse coincident with particle arrival in the field of view.
• a pulsed hght source the extended field of view in the axis of motion associated with TDI detection allows the cell or object in motion to be illuminated by multiple pulses during its traversal.
• a TDI system can produce a single unblurred image of the object that integrates the signal from multiple pulses.
• the signal generated by the object will be collected throughout the entire traversal of the object through the field of view, as opposed to only a small segment in time when a shutter is open. Therefore, the amount of signal collected and imaged on the detector in the present invention is substantially greater than that of the prior art frame-based imaging systems.
• FIGURE 6 Also illustrated in FIGURE 6 are several exemplary positions for hght sources, which are useful for different purposes in connection with the imaging system illustrated therein.
• light source 62 provides illumination of object 24 from a direction so that absorption characteristics of the object can be determined from the image produced on the TDI detector.
• hght provided by light source 62 that is scattered from object 24 can be used to produce a scatter image and spectrally dispersed images on TDI detector 44b.
• Light source 74 can be employed to produce spectrally dispersed and scattered images on both TDI detectors 44a and 44b.
• light sources 62 and 72 are of different wavelengths and an appropriate filter is provided to block the wavelength from the light source aligned with the optical axis of the respective collections lenses 32, these two light sources can be used for producing scattered light from the object. For example, suppose light source 72 produces light of a wavelength A that scatters from object 24 and is directed toward TDI detector 44a. By including a filter (not shown) that blocks wavelength B produced by light source 62, the hght at wavelength B will not directly affect the images produced on TDI detector 44a. Similarly, the light from light source 72 would be blocked with an appropriate filter (not shown) so that it does not interfere with the imaging of light produced by light source 62 that is scattered from object 24 onto TDI detector 44b.
• Epi light source 66 is also illustrated for use in producing images on TDI detector 44a in conjunction with partial reflector 68.
• Light source 64 can be used to generate reflected light to produce images on TDI detector 44a, while scattered light from this source is directed toward TDI detector 44b.
• FIGURE 7 an imaging system 80 is illustrated that is similar to imaging system 20, except that it is used for imaging object 24 on a slide 82.
• Object 24 is supported by shde 82 and the slide moves relative to the imaging system as shown in FIGURE 7.
• shde 82 may be the object that is imaged.
• the object may be a semiconductor wafer, paper, or other object of interest since the object may be imaged using reflected incident light.
• a light source placed at one of several different locations can be employed.
• Exemplary light sources 62, 64, and 66 illustrate some of the locations at which light sources useful in this embodiment may be disposed.
• Light 58 emitted by any of the light sources can be either coherent or non-coherent light, pulsed or CW, and can be directed through slide 82 (if it is transparent) from light source 62 or can be reflected from the object or slide, if light sources 64 or 66 are employed.
• epi light source 66 illuminates the object in connection with a partially reflective surface 68.
• FIGURES 8 A and 8B show two different views of a fourth preferred embodiment, which is an imaging system 90 that produces a scattered pattern image of object 24 on TDI detector 44.
• Light 30 from object 24 passes through collection lenses 32a and 32b, and collected light 34 is directed onto a cylindrical lens 92, as in the previous embodiments.
• Cylindrical lens 92 focuses light 94 on TDI detector 44, generally along a line that is aligned with a central axis 96 of cylindrical lens 92.
• Central axis 96 is shown in FIGURE 8B, and it will be apparent that it is orthogonal to the direction in which object 24 moves through the imaging system.
• an illustration of a fifth preferred embodiment is provided of an imaging system 100 that produces both a . scattered pattern image and a spectrally dispersed image of object 24 on TDI detector 44.
• hi imaging system 100 light 30 from object 24 passes through collections lenses 32a and 32b, which produce infinitely focussed light 34 directed toward a dichroic filter 102.
• Dichroic filter 102 reflects hght of a specific wavelength, e.g., the wavelength of a hght source (not shown) that is incident upon object 24. Light of any other wavelength is transmitted through dichroic filter 102 toward a diffraction grating 112.
• Diffraction grating 112 spectrally disperses the hght transmitted through dichroic filter 102, which typically would be hght produced by the fluorescence of FISH probes on object 24, so that a plurality of FISH spots corresponding to the number of different FISH probes and objects being imaged are produced on TDI detector 44.
• Light 104 which is reflected from dichroic filter 102 is transmitted into cylindrical lens 106 and is focussed along a line as a scattered pattern image in a region 110 on the TDI detector.
• the spectrally dispersed images of FISH spots or other aspects of object 24 having wavelengths different than that reflected by dichroic filter 102 are imaged as light 116 by imaging lenses 114a and 114b onto a region 118 of the TDI detector.
• signals corresponding to the scattered pattern image and the spectrally dispersed images are both produced by TDI detector 44.
• a sixth preferred embodiment, as illustrated in FIGURE 10, is an imaging system 120 that is slightly different than the preceding fifth embodiment, since a dichroic filter 102' is employed that is angled in a different direction, toward a second TDI detector 44b.
• a dispersed pattern image represented by light 108' is produced by a cylindrical lens 106' in this embodiment.
• hght transmitted through dichroic filter 102' is focussed onto TDI detector 44a.
• imaging system 120 is substantially identical in operation to imaging system 100.
• imaging system 100 could be constructed to include two separate TDI detectors instead of a single TDI detector, if desired.
• the present invention provides substantial utility in resolving FISH spots on the TDI detector, even when the FISH probes are disposed in spatially close relationship within the cell.
• spectral imaging occurs in the present invention, the spatial distribution of light in the object is convolved with the spectral distribution of that light to produce the image of the object at the TDI detector. This convolution can result in blurring in the dispersion axis, depending on the spectral bandwidth of the hght.
• Narrow spectral bandwidths will result in little or no blurring depending on the spectral resolution of the system, i the present invention, it is contemplated that the spectral resolution will be approximately 3 nm per pixel, with a spatial resolution in object space of approximately 1 micron. However, the spatial and spectral resolution can be adjusted to match the requirements of the particular application.
• FIGURE 11 illustrates the present invention with a spectral resolution of approximately 10 nm per pixel and a spatial resolution of approximately 0.5 microns.
• This Figure further illustrates how the present invention is used to image a cell 140 having a nucleus 142 in which are disposed two FISH probes 144a and 144b having the same emission spectrum, hi FIGURE 11, the emission spectrum 146 of the FISH probes 144a and 144b is approximately 10 nm in width, such as would be produced by "quantum dots" or a narrow-band fluorescent dye.
• the optical convolution of the narrow bandwidth spectrum results in minimal blurring of FISH spots 148a and 148b, enabling them to be readily resolved on TDI detector 44.
• a cell 150 is illustrated having a nucleus 152 in which are disposed FISH probes 154 and 156 having different emission spectra.
• FISH probes are designed so that different emission spectra correspond to different DNA sequences.
• Each of the emission spectra of FISH probes 154 and 156 are relatively narrow, as indicated by wavebands 158 and 160, and therefore, as in FIGURE 11, minimal blurring occurs in FISH spots 162 and 164.
• the spectral dispersion of the present invention which maps wavelength into lateral position on TDI detector 44, produces a relatively wide physical displacement of FISH spots 162 and 164, despite the close proximity of FISH probes 154 and 156 in the cell.
• FIGURES 11 and 12 illustrate how the present invention discriminates FISH probes of the same or different color, thereby enabling the simultaneous enumeration of numerous genetic traits.
• the present invention is well suited to the requirements of fetal cell analysis, where there may be ten or more probes of different colors present in the cell at one time. Further, those skilled in the art will appreciate that the present invention is not limited to the analysis of fetal cells using FISH probes.
• FIGURES 13 and 14 illustrate that the present invention can also be used with light of wide spectral bandwidth. In this case an additional signal processing step is performed to correct for lateral blurring due to the wide emission spectra.
• a cell 140 having a nucleus 142 is shown, and FISH probes 170a and 170b having a common emission spectram are disposed in the nucleus.
• FISH probes 170a and 170b are characterized by producing a relatively wide emission spectrum 172.
• FISH spots 174a and 174b are produced on TDI detector 44, but their images are laterally blurred across TDI detector 44, as a result of their relatively wide emission spectrum.
• a deconvolution is carried out on the signal produced by TDI detector 44, with the known FISH emission spectrum, thereby producing accurate FISH spot representations 178a and 178b on a display 176.
• the deconvolution step enhances the ability to enumerate the number of FISH spots.
• FIGURE 14 illustrates a corresponding relationship between FISH probes 180 and 182, which are disposed within a nucleus 152 of a cell 150.
• FISH probes 180 and 182 are characterized by each producing relatively wide band emission spectra 184 and 186, as shown in the Figure.
• the corresponding images shown on display 176 of FISH spots 192 and 194 are recovered.
• the spectral dispersion of the present invention which maps wavelength into lateral position on TDI detector 44, produces a relatively wide physical displacement of FISH spots 192 and 194, despite the close proximity of FISH probes 180 and 182 in the cell, hi this manner, it is possible to resolve these images of FISH spots produced by FISH probes having different and relatively wide emission spectra.
• FIGURE 15 A system 230 for analyzing the signal produced by TDI detector 44 and performing the deconvolution steps described above is illustrated in FIGURE 15.
• the signal from TDI detector 44 is apphed to an amplifier 232, which buffers the signal and amplifies it to achieve a level required by an analog to digital (A-D) converter 234.
• A-D converter converts the analog signal from amplifier 232 into a digital signal that is input into a TDI line buffer 236.
• TDI line buffer 236 temporarily stores the digital signal until it can be processed by a CPU 238.
• a spectral buffer 240 is loaded with the known emission spectrum for each of the FISH probes being used so that their emission spectra can be deconvolved with the signal stored in TDI line buffer 236.
• CPU 238 is a high speed processor programmed to carry out the deconvolution and other analysis procedures, enabhng the identification of desired characteristics or parameters of the object being imaged.
• the output from CPU 238 is temporarily stored in an image line buffer 242 that enables the image to be displayed or otherwise recorded for later analysis.
• FIGURE 16 illustrates a practical application of the present invention for identifying a male cell 200 and a female cell 208 and for producing their corresponding scatter images 212 and 220.
• Male cell 200 includes a nucleus 202 that has been stained with a yellow fluorescent dye.
• a FISH probe 204 produces a fluorescent orange emission, indicating the presence of an X-chromosome in the nucleus
• a FISH probe 206 produces red fluorescence emission, indicating the presence of a Y-chromosome.
• Spectral decomposition of the fluorescence emissions from male cell 200 when the cell is illuminated with light from a green laser, results in a series of images on TDI detector 44, separated as a function of the wavelength of the light that is imaged.
• the FISH probes responsive to X and Y chromosomes are detected, enabling the user to determine that ceU 200 is a male ceU, since it includes both the X and Y chromosome.
• female cell 208 when spectrally decomposed, also includes the characteristic yellow fluorescence of nucleus 210, but unlike the male cell, includes two FISH spots 216 corresponding to FISH probes 204, which indicates the presence of two X-chromosomes.
• TDI detector 44 also distinguishes the spatial position of male cell 200 and female cell 208, the corresponding spectral decompositions for these cells are readily separately resolved as both cells pass through the imaging system in the direction indicated by the arrow to the lower left of FIGURE 16. Again, it should be noted that a deconvolution can be apphed to the signal produced by TDI detector 44 to provide better resolution of the corresponding FISH spots that are illustrated.
• FIGURE 17 illustrates a seventh preferred embodiment of the invention corresponding to such a non-distorting spectral dispersion system 250 that employs a five color stacked wedge spectral dispersing filter assembly 252.
• This seventh embodiment is substantially similar to the embodiment shown in FIGURES 1, 2, and 3, except that spectral dispersing prism element 36 (of FIGURES 1, 2 and 3) is replaced by spectral dispersing filter assembly 252.
• the spectral dispersing filter assembly splits the light into a plurality of hght beams having different bandwidths. Each light beam thus produced is directed at a different nominal angle so as to fall upon a different region of TDI detector 44.
• the nominal angular separation between each bandwidth produced by the spectral dispersing filter assembly 252 exceeds the field angle of the imaging system in object space thereby preventing overlap of the field images of various bandwidths on the detector.
• Spectral dispersing filter assembly 252 comprises a plurality of stacked dichroic wedge filters, including a red dichroic filter R, an orange dichroic filter O, a yellow dichroic filter Y, a green dichroic filter G, and a blue dichroic filter B.
• Red dichroic filter R is placed in the path of collected light 34, oriented at an angle of approximately 44.0° relative to an optic axis 253 of collection lenses 32a and 32b.
• Light of red wavelengths and above, i.e., > 640 nm, is reflected from the surface of red dichroic filter R at a nominal angle of 1°, measured counter-clockwise from a vertical optic axis 257.
• Example spectral reflectance characteristics R' of red dichroic filter R are plotted in FIGURE 18, along with example spectral reflectance characteristics corresponding to the other dichroic filters used in spectral dispersing filter assembly 252.
• O' indicates the spectral reflectance characteristics of orange dichroic filter O
• Y' indicates the spectral reflectance characteristics of yellow dichroic filter Y, etc.
• the hght reflected by red dichroic filter R leaves spectral dispersing filter assembly 252 and passes through imaging lenses 40a and 40b, which cause the hght to be imaged onto a red light receiving region of TDI detector 44, which is disposed toward the right end of the TDI detector, as shown in FIGURE 17.
• Orange dichroic filter O is disposed a short distance behind red dichroic filter R and is oriented at an angle of 44.5 degrees with respect to optic axis 253. Light of orange wavelengths and greater, i.e., > 610 nm, is reflected by orange dichroic filter O at a nominal angle of 0.5° with respect to vertical optic axis 257. Because the portion of collected hght 34 comprising wavelengths longer than 640 nm was already reflected by red dichroic filter R, the light reflected from the surface of orange dichroic filter O is effectively bandpassed in the orange colored region between 610 nm and 640 nm.
• This light travels at a nominal angle of 0.5° from vertical optic axis 257, and is imaged by imaging lenses 40a and 40b so as to fall onto an orange light receiving region disposed toward the right hand side of TDI detector 44 between a center region of the TDI detector and the red light receiving region, again as shown in FIGURE 17.
• Yellow dichroic filter Y is disposed a short distance behind orange dichroic filter O and is oriented at an angle of 45° with respect to optic axis 253.
• Light of yellow wavelengths i.e., 560 nm and longer, is reflected from yellow dichroic filter Y at a nominal angle of 0.0° with respect to vertical optic axis 257.
• Wavelengths of hght reflected by yellow dichroic filter Y are effectively bandpassed in the yellow region between 560 nm and 610 nm and are imaged by imaging lenses 40a and 40b near vertical optic axis 257 so as to fall on a yellow light receiving region toward the center of TDI detector 44.
• dichroic filters G and B are configured and oriented so as to image green and blue light wavebands onto respective green and blue light receiving regions of TDI detector 44, which are disposed toward the left-hand side of the TDI detector.
• spectral dispersing filter assembly 252 collectively works to focus light within predefined wavebands of the light spectrum onto predefined regions of TDI detector 44.
• the filters used in the spectral dispersing filter assembly 252 may have spectral characteristics that differ from those described above and in FIGURE 18. Further, the spectral characteristics may be arbitrary and not limited to dichroic in order to achieve the desired dispersion characteristics.
• the wedge shape of the dichroic filters in the preceding discussion allows the filters to be placed in near contact, in contact or possibly cemented together to form the spectral dispersing filter assembly 252.
• the angle of the wedge shape fabricated into the substrate for the dichroic filter allows easy assembly of the spectral dispersing filter assembly 252, forming a monolithic structure in which the wedge-shaped substrate is sandwiched between adjacent dichroic filters. If the filters are in contact with each other or cemented together, the composition of the materials that determine the spectral performance of the filter may be different from those which are not in contact.
• flat, non wedge-shaped substrates could be used to fabricate the spectral dispersing filter assembly 252.
• non-distorting spectral dispersion system 250 may optionally include a detector filter assembly 254 to further attenuate undesired signals in each of the light beams, depending upon the amount of rejection required for out-of-band signals.
• FIGURE 19 illustrates the constraction of an exemplary detector filter 254 corresponding to the five color bands discussed above and includes a blue spectral region 256, a green spectral region 258, a yellow spectral region 260, an orange spectral region 262, and a red spectral region 264, all of which are disposed side-by-side, as shown in the Figure.
• FIGURES 20A-20E The corresponding spectral characteristics of the blue, green, yellow, orange, and red spectral regions or wavebands are respectively shown in FIGURES 20A-20E.
• the detection filter assembly shown in FIGURE 19 may be constructed by cementing separate filters in side-by-side arrangement on a common substrate or by other means well known to those or ordinary skill in the art. Additionally, the ordinary practitioner in the art will understand that the filter may alternatively be placed at an intermediate image plane, instead of directly in front of TDI detector 44. In the embodiment shown in FIGURE 17, light may pass through each dichroic filter in the spectral dispersing filter assembly 252 twice before exiting spectral dispersing filter assembly 252. This condition will further attenuate out-of-band signals, but will also attenuate in-band signals.
• FIGURE 21 illustrates an eighth embodiment of the present invention in which the light does not pass through another dichroic filter after reflection.
• a plurality of cube dichroic filters including a red cube filter 266, a yellow cube filter 268, a green cube filter 270, and a blue cube filter 272 are spaced apart sufficiently to ensure that light does not pass through any of the cube filters more than once.
• the cube dichroic filters are oriented at appropriate angles to image light within a predefined bandwidth to distinct regions on a TDI detector 274.
• hght is reflected from each of cube dichroic filters 266, 268, 270 and 272, it is directed toward imaging lenses 40a and 40b, and different bandpass portions of the light are focussed upon corresponding red, yellow, green, and blue hght receiving segments or regions defined on a hght receiving surface of TDI detector 274.
• an optional detector filter assembly 276 of similar construction to detector filter assembly 254 may be used to increase the rejection of out-of-band signals. It should be apparent to those skilled in the art that separate spaced apart plate, or pelhcal elements could also be used in this application instead of the cube filters.
• the image lenses 40a and 40b must be placed a sufficient distance away from the plurality of cube filters to minimize the clear aperture requirement for lenses 40a and 40b.
• the clear aperture in the plane orthogonal to the page can increase as the distance between the lenses and plurality cube filters increases. Therefore, the placement of lenses 40a and 40b must be chosen to appropriately accommodate the clear aperture in both planes.
• spectral dispersing component with more or fewer filters may be used in these configurations in order to construct a system covering a wider or a narrower spectral region, or different passbands within a given spectral region.
• spectral resolution of the present invention may be increased or decreased by appropriately choosing the number and spectral characteristics of the dichroic and or bandpass filters that are used.
• angles or orientation of the filters may be adjusted to direct light of a given bandwidth onto any desired point on the TDI detector.
• FIGURE 22 illustrates the distribution of images on TDI detector 44 corresponding to imaging a plurality of cells 200 when using non-distorting spectral dispersion system 250.
• the resultant images on the TDI detector are similar in many ways.
• all wavelengths within the predefined bandwidth of each dichroic filter are reflected from the filter at the same nominal angle, so image components that fall within that passband suffer no positional distortion on the detector.
• the field angle orthogonal to flow in object space is also indicated on FIGURE 22.
• the field angle in object space is less than +/- 0.25°.
• the field angle can be made larger or smaller. To the extent that the field angle is made larger, for example, to image cells over a wider region on a shde or in a broad flat flow, the field angle at the detector will increase in proportion to the number of colors used.
• broad flat flow can easily be created using commercially available flow cells as shown in FIGURE 25, which incorporates containing flow cell 306.
• Flow cell 306 has a cross section that is elongated in an axis perpendicular to both the flow and optical axes. The generation of a broad flat flow is discussed in many references, including U.S. Patent No. 5,422,712.
• flow cell 306 enables a broad flat flow to be achieved, hi embodiments incorporating flow cell 306, or other means to provide a broad flat flow, preferably the field angle in increased by an amount that is sufficient to enable any objects entrained in such a broad flat flow to be imaged and that image captured by a detector.
• the field angle also must increase in a proportional fashion, to ensure all objects in that flow volume can be imaged as they pass through the field of view.
• FIGURE 22 illustrates the image projected onto the detector when three cells 280, 282 and 284 are flowing through the field of view. Light scatter images of cells 280, 282, and 284 are seen on the left hand side of the detector denoted as the BLUE area.
• Probe 204 stains the X chromosome with an orange fluorescing dye
• probe 205 stains the Y chromosome with yellow fluorescing dye
• probe 206 stains the inactive X chromosome in female cells with a red fluorescing dye.
• Cell 282 is imaged onto the detector as shown in FIGURE 22. An image 286 of probe 204 from cell 282 is seen in the ORANGE area of the detector.
• cells 280 and 284 contain probes 204 and 206, which create images 290 and 292 in the ORANGE area of the detector, and images 294 and 296 in the RED area of the detector, indicating that these cells are female, respectively.
• FIGURES 25, 26 and 28 Alternate embodiments of the present invention utilizing multiple detectors for spectral dispersing and imaging are illustrated in FIGURES 25, 26 and 28.
• Spectral decomposition is implemented using dichroic filters, generally as described above. However, as illustrated in FIGURE 25, separate imaging lenses and detectors are used for each spectral region. Dichroic filters 301- 305 are disposed in infinite space with respect to the object from which light is being spectrally decomposed to minimize optical aberrations. After each dichroic filter, separate imaging lenses 311- 315 are used to form an image of the object onto corresponding detectors 321- 325. In this configuration, each detector has fewer pixels than in the embodiments described above, enabling the present embodiments to operate at high pixel line rates.
• the images projected on each detector appear as shown on one zone of the detector illustrated in FIGURE 17. The images on the detector configured to receive hght in the red portion of the spectrum appear like those in the right-most zone of FIGURE 17.
• FIGURES 25, 26 and 28 have an advantage in optical efficiency over other embodiments, because the light from the object only passes through each dichroic filter once.
• a further advantage of the multiple detector embodiments is that each detector can be focused independently for each color, thereby simplifying the optical design by removing constraints on longitudinal color correction.
• a still further advantage is that the quantum efficiency of each detector can be individually optimized for its particular color band. Those of ordinary skill in the art will readily recognize that such optimization can be accomplished through doping of the semiconductor materials utilized in the detector.
• one or more lenses as exemplified by lens 311), may have a different focal length, thereby enabling simultaneous image collection with differential magnifications.
• the clock rate on detector 321 will be proportionally higher to maintain synchronization, which is expected to be useful when one channel is used with a higher magnification for brightfield image collection, to more accurately analyze morphological detail.
• the configuration shown in FIGURE 25 also allows channel independent control of numerical aperture, as illustrated by the disposition of optional aperture stop 330. It should be noted that an object plane 348a as shown in FIGURE 25 is larger than object planes 348 illustrated in other Figures, due to the characteristics of flow cell 306. As noted above, flow cell 306 enables a broad flat flow to be achieved, such that multiple objects passing through object plane 348a simultaneously can be imaged simultaneously, as long as each image covers a sufficiently large field angle.
• the field angle needs to be matched to the size of the object plane (such as object plane 348a) so that the images produced encompasses substantially all of the object plane.
• the object plane is defined by the perimeter of the fluid channel employed.
• FIGURE 26 illustrates another embodiment of the multiple detector approach. While similar to the embodiment illustrated in FIGURE 25, the embodiment of FIGURE 26 has the advantage of reducing the number of imaging lenses required to project an image upon the detectors, hi the embodiment of FIGURE 26, an image lens 340 is placed before dichroic filters 345- 347. Those skilled in the art will appreciate that the functions of collection lens 32 and image lens 340 can be carried out by a single element. Detectors 341- 344 are placed at the appropriate positions along the optical path to image an object plane 348 on the surface of each detector.
• Detectors 341 - 343 are placed in a path of light from the object that is reflected off dichroic filters 345, 346 and 347, while detector 344 is placed in a path of hght from the object transmitted through dichroic filter 347.
• the filters are disposed in convergent space with respect to the image of the object and therefore each filter, depending upon its design, may impart astigmatism, coma, spherical, and chromatic aberration into the imagery at each downstream detector. Progressively, more of each of these aberrations are added by each subsequent filter.
• the numerical aperture (i.e., the product of the index of refraction and the sine of the half cone angle of iUumination) in the filter space is approximately 0.03. Therefore, if cube substrates are employed for the dichroic filters, coma and astigmatism are neghgible, while spherical aberration is substantially eliminated, being less than 0.15 waves peak. Longitudinal chromatic aberration is effectively canceled by moving the detectors to the plane of best focus for their respective color band. Pellicles can also be used in place of the cubes for the substrates of the dichroic filters, with excellent theoretical optical performance.
• correction plate 360 As shown in FIGURE 27, of approximately the same thickness, incident angle, and glass type.
• correction plate 360 must be rotated 90 degrees about axis Z with respect to dichroic filter 361.
• Correction plate 360, and dichroic filter 361 impart an equal but opposite amount of astigmatism in the transmitted wavefront, thereby canceling each other. Therefore, light striking detector 342 is free of astigmatism. This configuration leaves a small amount of residual coma. Yet, the optical performance is very close to the diffraction limit.
• the correction plate can be placed in many alternative positions, with adjustments in its thickness, material, and/or angle, relative to the propagation of the hght.
• Any of the non-distorting spectral dispersing embodiments can be constructed using an additional objective lens 48 and sht 52, to form a confocal stop arrangement as shown in FIGURE 26.
• FIGURE 28 illustrates an embodiment similar to FIGURE 25 using multiple imaging lenses, however, the majority of detectors are place in the transmission path of dichroic filters. Either of the multiple detector embodiments may constructed such that the detectors receive hght transmitted through the dichroic filters, reflected by the dichroic filters or in a combination of transmission and reflection as illustrated in both FIGURES 26 and 28.
• ceUs or other objects may be oriented side-by-side such as may be found in broad flat flow, or on microscope slides and microtiter plates. This configuration enables more objects to be imaged simultaneously than could otherwise be possible if objects were aligned in a single file orientation.
• FIGURE 23 illustrates an embodiment of the present invention that facilitates imaging of a wide field.
• motion of a substrate 73 is generally parallel or aligned with an axis of spectral decomposition provided by dichroic element 252.
• Optional epi illuminator 60a which may comprise a laser or other type of illumination source, can be used to illuminate objects carried on substrate 73, while there is relative movement between the substrate and the imaging system in the direction of the double-headed arrow.
• another illuminator 60b is provided to provide bright field illumination of the objects on the substrate with hght reflected from a reflective surface 77.
• Collection lens 32 collimates the light from the slit and directs the light onto dichroic element 252, which spectrally disperses the light passing through lens 40 and onto different regions of detector 44.
• Segmented detector 300 (FIGURE 24) is used for detector 44 in FIGURE 23, and spectral dispersing filter assembly 252 is oriented to decompose light in an axis parallel to the movement of the image across detector 44.
• the field of view of substrate 73 in FIGURE 23 may be illuminated in bright field with bright field illuminator 60b or with epi-illumination by illuminator 60a. In either case the iUuminated field of view, when imaged by the optical system, is equivalent in size to one segment of detector 300.
• spectral dispersing filter assembly 252 when spectral dispersing filter assembly 252 is employed, light is split into a plurality of light beams each having a different bandwidth. Each hght beam thus produced is directed at a different nominal angle so as to fall upon a different segment of detector 300.
• the nominal angular separation between each bandwidth produced by spectral dispersing filter assembly 252 exceeds the field angle of the imaging system in object space, thereby preventing overlap of the field images of various bandwidths on the detector. Therefore, each detector segment sees the same field of view, however, each segment sees hght composed of a different spectral bandwidth.
• Slit 55 may be provided to eliminate any stray hght from outside the intended field of view from passing through the system and landing on an inappropriate zone of detector 300.
• segmented detector 300 comprises four segments or zones 302a-302d, each zone receiving light of a different characteristic.
• the detector is segmented into these zones such that the charge corresponding to an incident image flows across a segment in concert with the image movement across that segment The charge is then read out of the segment and not permitted to enter an adjacent segment or zone where hght of a different characteristic is imaged.
• the charge corresponding to an image received by each zone is integrated over a length of the zone and readout from the tap provided for the zone.
• the rate at which the charge is readout from each zone is independently controllable.

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