Patent ID: 12240770

The figures are not necessarily to scale. Like numbers used in the figures refer to like components. However, it will be understood that the use of a number to refer to a component in a given figure is not intended to limit the component in another figure labeled with the same number.

DETAILED DESCRIPTION

Embodiments described herein relate to devices, systems and methods for discriminating between different types of objects. The objects emanate output light in response to an excitation light that is directed toward the objects in a fluid column, such as a flow stream. As used herein the term “emanate” refers to both reflected and fluoresced electromagnetic radiation, such as light. As used herein the term “light” refers to both electromagnetic radiation at wavelengths in the visible spectrum as well as electromagnetic radiation at wavelengths in the infrared and ultraviolet spectrums. Such output electromagnetic radiation may include light reflected or fluoresced directly from an object as well as light reflected or fluoresced by a stain or dye associated the object. In some implementations, cell types are distinguished based on the intensity of the output electromagnetic radiation emanating from the objects. Intensity can be determined as a peak intensity or even as a total intensity, such as the integrated area under an intensity signal. Specific embodiments described herein are directed to distinguishing between X-chromosome sperm cells and Y-chromosome sperm cells. Further embodiments are concerned with distinguishing viable X-chromosome bearing sperm cells from objects other than viable X-chromosome bearing sperm cells, including Y-chromosome bearing sperm cells and non-viable cells of both sexes.

It will be appreciated that the approaches of this disclosure can be applied more generally to distinguishing between any objects of different types so long as the output electromagnetic radiation emanating from one object type generates a discernable difference in at least one characteristic when compared to the electromagnetic radiation emanating from another object type. In some examples provided, the fluid column is a flow stream that has a curved boundary or interface where refraction of electromagnetic radiation may occur. For example, the curved boundary of the fluid column may be generally circular in cross section. The fluid column can be bounded by solid walls, such as within a cuvette or within a microfluidic channel, or may be jetted into the air, such as in a jet-in-air flow cytometer. The objects may move along the fluid column through a central core shaped by a sheath fluid that at least partially surrounds the central core. In the case of sperm sorting applications, the central core may comprise a core stream of sample fluid containing sperm cells. The core stream may be conditioned into a generally ribbon shape or may have a generally elliptical cross section for the purpose of orienting aspherical sperm cells. Electromagnetic radiation emanating from the objects encounters at least one optical refraction boundary between the objects and other materials, such as at the interface between the fluid column and air.

Due at least in part to the different refractive properties of sheath fluid and air, the light collection efficiency external to the fluid column of light emanating from objects within the column depends upon the position of the objects for such systems. Light collection efficiency that varies with position is detrimental in applications where the light emanating from the objects must be precisely quantified and such precision is limited by random (not directly observable) position fluctuations of the objects. In the case of sex differentiating sperm specifically, such systems seek to differentiate very bright and closely related fluorescence intensities. Sperm cells and sperm nuclei are generally stained with Hoechst 33342 to make such differentiations. Hoechst 33342 is a bright, cell permeable dye that binds selectively with the A-T base pairs in the minor grove of double stranded nuclear DNA. The stoichiometric staining of sperm cells with Hoechst 33342 differentiates X-chromosome and Y-chromosome as having slightly different amounts of nuclear DNA. For example, many domestic animals have about a four percent difference. When sperm cells are properly stained and oriented, this small difference can be distinguished by the fluorescence intensity of the Hoechst 33342 associated with the nuclear DNA of the sperm cells when they are irradiated with an appropriate excitation source, such as a laser operating at or near a wavelength of 355 nm.

This four percent difference is difficult to detect for several reasons. First, sperm nuclear DNA resides within the sperm head, which is aspherical or has a paddle-like shape in most species. This asymmetry causes sperm to fluoresce differently out the flat side and more narrow side. Indeed, this fluctuation exceeds the four percent difference in DNA content, meaning sperm must be oriented in order to be differentiated based on nuclear chromosomal content. Orienting geometries tend to produce a core stream having a ribbon shape, or an elliptical cross section. This elliptical cross section provides sperm larger than normal latitude for placement in one axis.

The approaches disclosed herein enhance the precision of systems that may be limited by such fluctuations, such as jet-in-air flow cytometers. As described in more detail below, the positional variability of light intensity collected from objects in a fluid column can be addressed with an algorithm that corrects for the dependence of intensity on position.

The approaches outlined herein are particularly applicable to flow cytometry. However, the approaches can be applied to any system where light is collected on one side of an interface from objects emanating the light from the other side of the interface, wherein the interface causes a variation in the emanating light ray paths in a manner dependent on the object's position relative to the detector. Approaches herein correct for positional variation within the fluid column thus providing more accurate measurements for distinguishing types of objects.

The “jet-in-air” flow cytometer system100illustrated schematically inFIG.1is one type of discrimination system that can be used to discuss the concepts of the disclosure. The “jet-in-air” flow cytometer system100includes a fluid column forming structure that creates a flow stream comprising a fluid column150that jets out of the exit nozzle160of the chamber110at high velocity, e.g., about 20 m/s. The fluid column150expelled from the exit nozzle160can be roughly circular in cross-section and may have a diameter of about 10 μm to about 100 μm in some implementations. In some embodiments, the interior of the chamber110and/or the exit nozzle160are configured with an internal geometry that hydrodynamically orients sperm within the fluid column. As a non-limiting examples the nozzles like those described in U.S. Pat. Nos. 6,782,768 and 6,263,745 may be incorporated for the purpose of orienting sperm and generating the coaxial flow of a fluid column. The fluid column150is composed of a core stream151within a sheath stream152where the arrows inFIG.1indicate the direction of flow of the core and sheath streams151,152. The sheath stream152may have a generally circular cross section, while the core stream has generally elliptical cross section, with a major and a minor axis.

Within the chamber110, a sample injection element111introduces the core stream151containing objects171,172which may be of multiple types. The core stream151is bounded by a sheath stream152comprising sheath fluid and shaped by hydrodynamic forces in the chamber110. The sheath stream152at least partially surrounds the core stream151, and the sheath stream152and the core stream151do not substantially mix. The sloping or angled walls115of the chamber110impart forces that shape the core stream151and accelerate objects171,172within the core stream151. The movement of the sheath stream152constrains the objects171,172in the core stream151to move toward the center of the fluid column150when the fluid column150is ejected from the chamber110. The fluid column150delivers the objects171,172to a measurement region175of the fluid column150, e.g., in single file.

As the objects pass through the measurement region175of the fluid column150, light from an excitation source180provides excitation light to the objects171,172. The excitation source180can provide light in a broad wavelength band or in a narrow wavelength band. For example, the excitation source180may be a laser. Any laser suitable for producing a response from the object or a dye associated with the object may be employed. Pulsed lasers and continuous wave lasers are each well suited to produce appropriate responses. In some configurations, electromagnetic radiation generated by the excitation source, such as excitation light, may be modified by an optical element181. For example, the excitation light may be focused on the measurement region175by a one or more lenses181. Lenses may be used to focus the excitation electromagnetic radiation into a suitable beam shape focused on the measurement region. Objects172ain the measurement region175emanate light, e.g., scattered or fluorescent light, in response to the excitation source180.

Objects of a first type171will emanate output electromagnetic radiation that differs in at least one characteristic as compared to output electromagnetic radiation that emanates from objects of the second type172. For example, in some scenarios, objects of the first type171will emanate light having a higher intensity than the light that emanates from objects of the second type172.

An optical collection arrangement190is positioned to collect the output electromagnetic radiation161emanating from the object172awithin the measurement region175that crosses the optical refraction boundary of the fluid column150at the fluid-air interface153. In some embodiments, the optical arrangement190may be configured to modify the output electromagnetic radiation161to provide modified output electromagnetic radiation162that focuses output electromagnetic radiation emanating from the object172ain the measurement region175onto a detector185. In some embodiments, the optical collection arrangement190may include an element that reduces the positional dependence of the output electromagnetic radiation161. The detector185receives the modified output electromagnetic radiation162and, in response, generates an electrical signal representative of characteristics of the modified output electromagnetic radiation. As but an example, the detector185may be a forward fluorescence detector. Of course, other detectors may be incorporated to detect characteristics of interest, such as scatter, decay, phase shifts or other characteristics of interest. As but non-limiting examples, the detector may be a photomultiplier tube (PMT), silicon photomultiplier (SiPM) a photodiode array, or a split detector. In some embodiments, the detector185may represent more than one detectors. In some embodiments, a second position detector may be utilized. In other embodiments a side detector may be employed to detect side scatter or side fluorescence. Still other embodiments may incorporate both a position detector and a side detector in addition to the detector185.

In some scenarios, the amplitude of the electrical signal may be different for different object types. The electrical signal is used by an analyzer187to distinguish between different types of objects171,172. For example, the analyzer187may be configured to compare the amplitude of the electrical signal to a threshold to discriminate between objects of the first type171and objects of the second type172. The analyzer187may include one or more analog circuits and/or digital processors for manipulating one or more signals from one or more detectors. As but one example, a side detector may be employed 90 degrees relative to the detector185to detect side scatter or side fluorescence. In the case of sperm sorting, side fluorescence allows the analyzer187to differentiate properly oriented sperm from unoriented sperm.

The analyzer187may include a processor188having executable instructions stored thereon. In addition to those instructions198known for the purpose of collecting, comparing and manipulating information from detector signals, the processor may include instructions192for normalizing the intensity value of the output electromagnetic radiation in the represented in the electrical signal from the detector based on the position of the object172ain the fluid column150at the measurement region175. The intensity value may be normalized in any number of ways. As but one example, hand drawn lines or curves may be input by a user into a graphical user interphase based on an initial sampling of data including fluorescence intensities and positional information.

The processor188may also include instructions182for discriminating objects.FIG.2shows an x-y plane cross section of the fluid column150in the measurement region175depicted inFIG.1. In the x-y cross section of the measurement region175, the core stream151is elliptical in shape, and the fluid of the core stream151comprises at least one object172asuspended in a buffer solution, which may also be referred to as sample. The sheath stream152substantially surrounds the core stream151. In a particular example used for this discussion in this disclosure, the objects171,172are sperm cells and the system100is implemented to discriminate X-chromosome sperm from Y-chromosome sperm.

A focused laser beam generated by the excitation source180irradiates the sperm cell172awithin the measurement region175. The cells171,172are stained with a fluorescent dye, and the excitation electromagnetic radiation causes the cell172awithin the measurement region175to emanate fluorescent output electromagnetic radiation. The purpose of the generally elliptical core stream151is to orient a sperm cell172asuch that the flat sides of the sperm cell are facing to the left and the right as shown inFIG.2. In this orientation, the flat sides of the sperm cell172aface the laser180and the optical collection arrangement190, respectively. When each cell171,172is presented in a similar orientation at the measurement region175, random variability based on orientation can be greatly reduced. However, the elliptical cross section which aids in this orientation also provides significant latitude with respect to the position of the cell within the fluid column150.

To obtain the desired orientation, the elliptical core stream151, presents a major axis that parallels the x-axis depicted inFIG.2. The sperm cell172acan take any number of positions along the x-axis within the core stream151.FIG.2shows three representative possible positions for the sperm cell172ain the elliptical core151, although it may be appreciated sperm may be located anywhere in between the depicted positions. In the orientation shown inFIG.2, the first possible position for the sperm cell172ain the core stream151is approximately at the center of the elliptical core151(on the optical axis199of the optical collection arrangement190), a second possible position is at the top of the core stream151(above the optical axis199), and a third possible position is at the bottom of the core stream151(below the optical axis199). A position-dependent refraction of the output light rays emanating from the sperm cell172aoccurs at the fluid-air interface153at the different positions within the core stream151. As used herein terms of relative position such as “top,” “bottom,” “upper,” and “lower” should be understood as descriptive regarding the relationships between depicted features in the figures and not limiting on the claims, especially the position of sperm in a core stream151.

When the sperm cell172ais located at the first position and the fluid column150has a circular cross section as shown inFIG.2, the in-plane rays of light emanating from the sperm cell172aare approximately normally incident on the fluid-air interface153. Rays that emanate from points of the sperm cell172aaway from its center, or rays that emanate out of the plane of the figure, are not exactly normally incident on the interface153; these rays are not considered in this simplified discussion, but one of ordinary skill in the art can see how the discussion could be generalized to include them. Thus, to the extent any refraction of light occurs at the fluid-air interface153it occurs in a more uniform manner with respect to the detector185.

The diagram ofFIG.3shows uniform light refraction of the output electromagnetic radiation298emanating from a sperm cell172aas the electromagnetic radiation crosses the interface153when the sperm cell172ais at the 1st position within the elliptical core151shown inFIG.2. Correspondingly, the in-plane density of the light rays298exiting the fluid column150inFIG.3is uniform with respect to ray angle. Uniform angular density of light rays corresponds to uniform radiance as a function of ray angle.

In contrast, when a sperm cell172ais off the optical axis199and is nearer to the top or bottom of the elliptical core151, e.g., at the 2nd and 3rd positions of the elliptical core151shown inFIG.2, at least some of the output rays emanating from the sperm cell172aencounter the fluid-air interface153at an oblique angle. These output rays are refracted in a non-uniform fashion at the fluid-air interface153in contrast to the normal incidence scenario described above. The most oblique rays are the most severely refracted. Refraction of the light rays causes the radiance distribution of the fluorescent light exiting the fluid column150across the fluid-air interface153to become non-uniform and to vary with position of the cell172aalong the x axis. That is, this refraction changes the radiance distribution of output electromagnetic radiation emanating from sperm cell172aoutside of the fluid column150.

For example, when the cell172ais located off the optical axis199, e.g., at the 2nd or 3rd positions shown inFIG.2, the density of light rays and thus the radiance on the air side of the interface153is higher at positive or negative ray angles, respectively, with respect to the optical axis199when compared to the radiance on the air side of the interface153at angles parallel to the optical axis199or at negative or positive ray angles, respectively. Positive and negative refer to the sign of the ray angle γ inFIG.5.FIG.4is a diagram illustrating light rays299emanating from a cell172aand exiting the fluid column150through the fluid-air interface153when the cell172ais located at the 2nd position of the elliptical core151. In this scenario, the density of light rays, or radiance, at positive ray angles is greater than the density of the light rays parallel to optical axis199or at negative ray angles. For an optical system with a predetermined numerical aperture (NA), the amount of light collected by the system from cells of the same type (e.g., the collection efficiency) may vary depending on whether the cell is in the first position or the second position. The positional dependence of the system collection efficiency leads to inaccuracies in determining cell type.

With reference toFIG.5, an analytical formula for the light ray density as a function of ray angle γ and sperm position x is determined using Snell's law, where γ is the angle of a light ray, with respect to the optical axis, emanating from the object after refraction at the fluid-air interface. This analysis considers only rays within, or tangential to, the two-dimensional cross-section of the flow stream.

We wish to solve for the density of the light rays with respect to the angle γ, which we can use to determine the density of rays at the entrance pupil of an optical collection system for each sperm position x. This can be written:
Iγ(γ)  (1)

For our purposes we can assume that the sperm cell emanates light uniformly in all directions, so the density of emanated light rays with respect to the angle θ is:
Iθ(θ)=1/π  (2)
that is, uniformly distributed from θ=−π/2 to θ=π/2. By geometrical analysis:

θ=tan-1(cos⁢∅-xsin⁢∅)(3)∞=π/2-∅-θ;and(4)γ=π/2-∅-β,(5)
wherein the angles γ, θ, ϕ, α, β, and the distance x are shown inFIG.5. As the flow stream has index of refraction n, Snell's law yields another relation between the angles:
sinβ=nsin∝  (6)

The density of light rays external to the interface I_β (β) is related to the density of light rays internal to the interface I_α (α) by the following formula, with T(α) representing the average, across both polarizations, of the transmission through the interface:

Iβ(β)=I∝(∝)⁢T⁡(∝)⁢❘"\[LeftBracketingBar]"d∝d⁢β❘"\[RightBracketingBar]"(7)

The transmission is related to the Fresnel reflection coefficients for s- and p-polarization, R_s(α) and R_p(α), with the following formulas:

T⁡(∝)=1-R⁡(∝),(8)R⁡(∝)=Rs(∝)+RP(∝)2,(9)Rs(∝)=❘"\[LeftBracketingBar]"cos∝-n⁢cos⁢βcos∝+n⁢cos⁢β❘"\[RightBracketingBar]"2,and(10)Rp(∝)=❘"\[LeftBracketingBar]"cos⁢β-n⁢cos∝cos⁢β+n⁢cos∝❘"\[RightBracketingBar]"2.(11)

Using Eq. (7) with the above and the following additional relations:

I∅(∅)=Iθ(θ)⁢❘"\[LeftBracketingBar]"d⁢θd⁢∅❘"\[RightBracketingBar]",(12)I∝(∝)=I∅(∅)⁢❘"\[LeftBracketingBar]"d⁢∅d∝❘"\[RightBracketingBar]",and(13)Iγ(γ)=Iβ(β)⁢❘"\[LeftBracketingBar]"d⁢βd⁢γ❘"\[RightBracketingBar]",(14)
we have an expression for the density of rays with respect to γ:

Iγ(γ)=Iθ(θ)⁢❘"\[LeftBracketingBar]"d⁢θd⁢γ|T⁡(γ)(15)

Now, the optical collection arrangement's NA is given by the sine of the maximum ray angle γ_0, so we can solve for this angle in terms of NA:
γ0=sin−1(NA)  (16)

Finally, the relative collected light intensity, as a function of sperm position x, is given by integrating Eq. (15) from −γ0to γ0and normalizing by that integral value at x=0:

Relative⁢Intensity=∫-γ0γ0Iγ⁢d⁢γ∫-γ0γ0Iγ(x=0)⁢d⁢γ.(17)

Using the formula for ray density distribution of Eq. (15), the angular dependence of ray density (radiance) for different sperm positions can be plotted as inFIG.6. InFIG.6, each of the lines represents the density of rays as a function of angle γ for a given sperm position x, where the angle γ is in radians. The plots correspond to a series of positions that lie in a range symmetric about x=0, (corresponding to graph404inFIG.6), which is where the ray density (radiance) is uniform as a function of angle. When x is positive (e.g., 2nd position inFIG.2, corresponding to graph402), relative radiance is higher for positive ray angles γ and lower for negative ray angles γ, and the opposite is true when x is negative (e.g., 3rd position inFIG.2, corresponding to graph403).

If the numerical aperture of the collection optics (optical collection arrangement190inFIGS.1and2) is large, e.g., approaching one, the variation in collected optical intensity with respect to position for light emanating from an object within the elliptical core is relatively small. This is because essentially all light emanating from the object and directed to the right would be collected by the collection optics, regardless of the exact ray direction, and the total amount of emanating light is invariant to object position (given uniform excitation). In contrast, a small numerical aperture results in a relatively large collected intensity variation with respect to object position, because changes in object position affect the radiance distribution, and a small numerical aperture implies only a portion of this changing radiance distribution is collected. Practical systems may have NAs that are significantly less than one, e.g., less than 0.5, or less than 0.3. The family of graphs provided inFIG.7illustrates the relative intensity of light collected from an object, as a function of object position x, through collection optics with different NAs.FIG.6illustrates the range of angles γ captured by the different numerical apertures ofFIG.7.

In the family of graphs ofFIG.7, graph412illustrates the relative intensity with respect to position along the x axis for collection optics (e.g., optical collection arrangement190shown inFIGS.1and2) having a numerical aperture (NA) of 0.2; graph414shows the relative intensity with respect to position along the x axis for collection optics having an NA of 0.4; graph416shows the relative intensity with respect to position along the x axis for collection optics having an NA of 0.6; graph418shows the relative intensity with respect to position along the x axis for collection optics having an NA of 0.8; and graph419shows the relative intensity with respect to position along the x axis for collection optics having an NA of 0.9. It is clear fromFIGS.6and7that collection optics having smaller NAs produce a larger variation in collected light intensity with respect to object position when compared to collection optics having larger NAs. Additionally, collection optics with larger NAs collect light rays having a wider range of refraction angles than collection optics having smaller NAs, and therefore have a higher overall collection efficiency.

With respect to sperm discrimination or sorting application in particular, it can be understood that the elliptical major axis of the core stream151(FIGS.1and2) may be about 50 μm in length, providing sperm about 25 μm in latitude to move in either direction. Referring back toFIG.7, it can be seen a NA of 0.2 only captures about 90% of an objects relative intensity when the object is about 17 μm off center. Similarly, a NA of 0.4 captures only 92% of the relative intensity for objects that are about 17 μm off center and a NA of 0.6 captures a little more than 94% of the relative intensity at the same position. It may be further appreciated that the NA of collection optics for a sperm sorter may be between about 0.3 and 0.6. WhileFIG.7illustrates the benefit of increasingly large numerical apertures, such numerical apertures are increasingly expensive and have a shallower field of depth, meaning the larger aperture must be placed closer to the nozzle. There is, however, a limit on how close the collection optics can be placed in sperm sorting applications. In typical sperm sorting instruments, the apertures may be between about 0.5 and 0.6. Embodiments described herein correct for the positional dependency on measured intensity allowing lower numerical aperture collection optics to perform like higher numerical aperture collection optics.

Sperm located in the core stream151at positions approaching the 2nd and 3rd positions ofFIG.2, therefore, emanate a significantly lower overall intensity of electromagnetic radiation that is ultimately detected for analysis and discrimination. Indeed, the core stream151may have an elliptical major axis that is about 50 μm in length at high event rates (in the magnitude of 60,000 events per second and greater). Some sperm will be off center by 20 μm or even up to about 25 μm either side of the 1st position. In the context of extremely bright and closely related fluorescence signals, this variation can overshadow the roughly 4% difference in stained nuclear DNA differentiating X-chromosome bearing sperm from Y-chromosome bearing sperm.

Furthermore, increasing the number of events at a given sperm concentration within a sample of buffer requires increasing the volume of sample per unit time in the fluid column passing through the measurement region. Increasing the number of events detected per second in this manner also increases the elliptical cross section of the core stream within the fluid column, including the length of the major axis. As a natural consequence, and as those of skill in the art are aware, generally increasing the sorting speed by increasing the flow rate of sample decreases the sensitivity of sperm sorting equipment. Therefore, embodiments described herein not only improve sperm sorting precision at customary speeds, but may also provide for sperm sorting at increased overall speed in terms of throughput without suffering losses in fidelity.

An approach for identifying objects traveling in a fluid column in the presence of positional variation is illustrated in the flow diagram ofFIG.8. The process includes creating510a fluid column containing objects at differing positions within the fluid column. The fluid column may be a coaxial stream of fluid created by a jet-in-air flow cytometer. Such a fluid column may comprise a core stream with an elliptical cross section having a major axis along which objects may be positioned. The core stream may be coaxially contained within a sheath stream. In some embodiments the fluid column may have an air-fluid interface whereby refraction occurs. In other embodiments the fluid column may be formed within a cuvette or a microfluidic channel. In such cases there may be a liquid-glass interface and possibly a glass-air interface and emanating light may be refracted twice. Such twice refracted light is expected to benefit greatly from the angular dependency correction of certain embodiments.

The process continues by generating520excitation electromagnetic radiation and directing530the excitation electromagnetic radiation toward objects in the fluid column at a measurement region. Objects within the fluid column emanate output electromagnetic radiation in response to the excitation electromagnetic radiation at the measurement region. The output electromagnetic radiation is collected540from the objects in the fluid column, including objects having different position within the fluid column at a measurement region and a detector generates550an electrical signal responsive to the intensity of the output electromagnetic radiation collected by the optical arrangement.

Next, an analyzer or other suitable means normalizes560the intensity represented by the output signal based on the position of the object in the fluid column. The normalization may be performed by means of a correction, whereby signals generated off the central axis, such as toward and including the second and third positions ofFIG.2, are amplified by an appropriate correction factor based on their position. The magnitude of appropriate correction factors can be seen inFIG.7. Once normalized by correction the method continues by discriminating570a first type of object from other objects. The discrimination may take place in a flow cytometer analyzer and may include one or more additional manipulations. For example, univariate histograms may be generated illustrating a distribution of fluorescence intensities. Bivariate histograms may also be generated with the corrected signal and with further calculated values. Such corrected and calculated values may be compared against gating regions in a flow cytometer analyzer or compared against look-up-tables to discriminate a first type of object from other types of objects.

As exemplary objects sperm may be discriminated as either X-chromosome bearing or Y-chromosome bearing sperm. Further, sperm may be stained with a DNA selective dye in addition to a secondary quenching dye. A quenching dye typically permeates membrane compromised sperm cells, such as dead or dying sperm cells, and greatly reduces the fluorescence produced by the DNA selective dye associated with those compromised cells. Such quenched cells are effectively removed from the closely related populations undergoing discrimination/sorting. In this way a system can discriminate live or viable sperm cells from dying or compromised sperm cells. The system may also discriminate viable X-chromosome bearing sperm from all remaining cells, Y-chromosome bearing sperm from all remaining cells, or even simultaneously viable X-chromosome bearing sperm and Y-chromosome bearing sperm from all other sperm cells.

FIG.9illustrates a first embodiment of the discrimination system substantially similar to the discrimination system depicted inFIGS.1and2in which output electromagnetic radiation161emanating from an object172alocated in the measurement region is collected by an optical collection arrangement190. The optical collection arrangement190may include a collection lens that focuses a modified output electromagnetic radiation onto a detector185. In the depicted embodiment, the detector functions to both measure a characteristic of the modified output electromagnetic radiation as well as a position detector186for determining the position of the object172awithin the core stream151of the fluid column150.

The detector185suitable for determining both a characteristic of the modified output electromagnetic radiation162and for determining the location of the object172ain the measurement region may comprise split detectors or a detector array of PMTs, SiPM, pin photodiodes or the like. These detectors may be located in the image plane of the object or in the Fourier plane to determine the position of the object. In the image plane the detectors directly measure the position of the object, whereas in the Fourier plane the position information will be extracted from the lateral intensity distribution (e.g. the left-right asymmetry).

Flow cytometry applications often require very sensitive (down to single photon counting) and fast (objects are moving with ˜20 m/s through 10 μm) detectors. Detectors with the requisite speed and sensitivity are typically those detectors that provide an internal gain. In photomultiplier tube (PMT) or a silicon photomultiplier (SiPM), also known as pixelated avalanche photodiode, a single photon creates a cascade of up to about 106 electrons. Both detector types are commercially available as detector arrays. SiPM may be better suited for use in detector arrays suitable for determining the position of the object because they are fabricated by standard techniques on silicon wafer. Some detector, such as SiPMs may be particularly well suited to be placed in a Fourier plane in order to distribute light over a larger area of the detector.

FIG.10illustrates an alternative embodiment in which a beam splitter191, or other suitable optics, redirect a fraction of the power of the modified output electromagnetic radiation162. The majority of the modified output electromagnetic radiation162is directed to and focused on the detector185. In this embodiment the detector185comprises a first detector176for detecting a characteristic of interest. The first detector176may be any detector conventionally suited to quantify the particular characteristic of interest. In typical flow cytometer applications photodiodes, photomultiplier tubes (PMTs) and silicon photomultipliers may be particularly well suited to detect scattered or fluoresced electromagnetic intensity.

The beam splitter191may comprise a dielectric mirror197, however those of skill in the art will appreciate other suitable optical components such as cube beam splitters, prism beam splitters and the like may be used for redirecting a portion of the modified output electromagnetic radiation162power. Regardless of the manner in which the output power is split, a first beam fraction164is directed along a first path to the detector and a second beam fraction165is directed along a different path to a second detector173in the form of a position detector177. The position detector can be a camera, a position sensitive device (“PSD”) such as an isotropic sensor or a charged coupled device (CCD), split detectors, a detector array of PMTs, SiPM, pin photodiodes or the like.

Turning toFIG.11, a simulation was performed illustrating the viability of a split detector for determining positional information in a flow cytometry system. The simulation employed a split SiPM detector comprising 3 mm SiPM detectors mounted side by side. The edge at which the detectors met was calibrated as a central x coordinate position, simulating the beam axis of an interrogation laser as well as the symmetric center of a fluid column. A 1.5 mm spot size was swept across the split detectors from an x position between about −12 mm to 12 mm and the relative intensity was measured by each detector was recorded. A first graph601illustrates the relative intensity recorded for the beam spot from one of the detectors from x positions ranging from about −12 mm to about 12 mm, where the x position corresponds to a plane of the SiPM detector. A graph602illustrates the corresponding relative intensity detected by the other detector for the beam spot in a range of x positions from about −12 mm to about 12 mm. As can be seen, the positional difference in the two detectors results in differing measured intensities based on the x position of the 1.5 mm spot. These differences correlate to position and can be translated through processing means to approximate positional information. Noise was included in the simulation, but it was independent of intensity. At max intensity the noise corresponds to 0.8% coefficient of variation. The simulation demonstrated that x position can be determined in a split detector arrangement based on the relative intensity detected by each SiPM in a split detector arrangement. Those of skill in the art can appreciate, embodiments of the present invention are not limited to this configuration and that other detector configurations suitable for determining the position of a particle within a fluid column are also contemplated for use herein. As but one example, other detectors may be employed in a split detector arrangement. Those of skill in the art will appreciate that detectors should have low noise, as the combined signals must have a sufficiently low coefficient of variation.

FIG.12illustrates the result of an experiment incorporating positional correction for sperm nuclei in a fluid column resulting in significant improvements in differentiating X and Y-chromosome bearing sperm nuclei. Sperm nuclei stained with Hoechst 33342 were processed through a Genesis III sperm sorting instrument manufactured by Cytonome. The instrument was outfitted with a SiPM split detector. Sample and sheath pressure were adjusted to establish an event rate of 35,000 events per second. Nuclei were interrogated with a Coherent Genesis CW-355 laser at an average power of 150 mW. Plot610depicts a bivariate histogram illustrating a sum of fluorescence intensives from each detector in the split detector plotted against the positional delta of nuclei in the fluid column. As previously described, the range of the positional delta represents the major axis of the elliptical core stream along which nuclei may enter the measurement region. A population of X-chromosome bearing nuclei612is seen in a crescent shape. As expected, measured intensities are greatest near a position delta of 0 with reductions curving downward as nuclei move away from the central position. A population of Y-chromosome bearing nuclei614is seen as a second crescent just below the X population and, again, the highest intensities are seen near a position delta of 0 with significant losses in relative intensity as the nuclei move away from the central position.

Plot620presents a univariate histogram of the summed fluorescence intensities that corresponds to the intensities charted in plot610. While the distinct population of X-chromosome bearing nuclei612and population of Y-chromosome bearing nuclei614can be seen, a comparison of plot610with plot620makes apparent that off center X-chromosome bearing sperm nuclei increasingly overlap with the well centered Y-chromosome bearing sperm nuclei. Indeed, the peak to valley ratio is calculated at 76.8%.

In accordance with embodiments of the invention, a correction factor616is illustrated as a curved line in plot610. The correction factor616illustrates the degree of correction required to the detected fluorescence intensity to remove the variation introduced by the random positions of events. A corresponding correction was applied to the fluorescence sum values depicted in plot630to produce a corrected population of X-chromosome bearing nuclei632and a corrected population of Y-chromosome bearing nuclei634. The corrected population of X-chromosome bearing nuclei632form a generally rectangular shape and no longer demonstrates fluctuation based on the position of the nuclei in the fluid column. A more distinct gap can be seen in plot630between the corrected population of X-chromosome bearing nuclei632and a corrected population of Y-chromosome bearing nuclei634. Plot640illustrates the corresponding univariate histogram, which has a 94% peak to valley ratio between the corrected population of X-chromosome bearing nuclei632and the corrected population of Y-chromosome bearing nuclei634. The stark contrast between plot620and plot640is visually apparent. Furthermore, the difference is a quantifiable with at 17.2 percentage points higher.

FIG.13illustrates the results of an example incorporating correction in accordance with embodiments described herein. Live sperm stained with Hoechst 33342 were processed through a Genesis III sperm sorting instrument manufactured by Cytonome. Sample and sheath pressures were adjusted to reach an event rate of 43,000 events per second and the sperm was interrogated with a Coherent Genesis CW-355 laser operated at an average power of 100 mW. Plot710illustrates a bivariate histogram of the summed fluorescence intensity and the relative positions of live sperm in the core stream. Again, the population of X-chromosome bearing sperm712can be seen as a first population above a population of Y-chromosome bearing sperm714. A correction factor716for normalizing the summed intensity values is also depicted in plot710. Plot720illustrates the univariate histogram of uncorrected summed intensities and demonstrates a peak to valley ratio of 75.3% between the population of X-chromosome bearing sperm712and the population of Y-chromosome bearing sperm714.

Plot730provides a type of bivariate histogram common in sperm sorting applications. In this case, a corrected forward fluorescence intensity is plotted against a side fluorescence. A forward fluorescence vs side fluorescence histogram is useful for sorting live sperm because the side fluorescence provides information on the orientation of each cell. In contrast, sperm nuclei are sonicated and removed from the aspherical sperm head. As such, orientation is not an issue when sorting sperm nuclei. For this reason, nuclei are easier to sort and are often used to calibrate sperm sorting flow cytometers. Plot730depicts a corrected population of X-chromosome bearing sperm732and a corrected population of Y-chromosome bearing sperm734

Much like the previous example, plot740still correlates in the Y axis to the corrected forward fluorescence of graph730. In the univariate plot of graph740, the corrected population of X-chromosome bearing sperm732and the corrected population of Y-chromosome bearing sperm734can be seen as more distinct peaks having a machine calculated peak to valley ratio of 81.0%. And again, the corrected histogram presents a significant improvement over plot720demonstrating the value of positional correction for live sperm.

In another aspect, embodiments described herein may provide systems and methods that substantially ease an alignment process in a flow cytometer. In the case of sperm for example, the measurement region, detectors, and even the structure forming the sheath flow must be properly and precisely aligned in order to generate and collect sufficiently clear signals for differentiating the very bright and closely related X and Y-chromosome bearing sperm populations. Even in a precise and proper alignment, oriented sperm in a fluid column can assume any number positions along the major axis of core stream. As described above with respect toFIGS.3-7, this means that even when the components of the flow cytometer are in perfect alignment, there is an angular dependency to the detected output electromagnetic radiation. This angular dependency introduces noise like variations because the cells may be randomly positioned within the core stream.

In commercial sperm sorting applications, technicians typically undertake a number of course adjustments followed by a number of fine adjustments for multiple components in multiple axis in order to align the instrument. Due to the sensitivity of the instrument to each adjustment, the very closely related nature of the detected signals, and the number of possible adjustments, such alignments can be time consuming tasks for technicians operating sperm sorting instruments. When switching between samples machine alignments for commercially sorting sperm can take a few minutes, even up to five minutes. After declogging a nozzle or otherwise removing, replacing or adjusting other components that require calibration, it may take a technician 5 minutes, 15 minutes, and in rare cases as long as 30 minutes in order put an instrument in suitable alignment for commercially sex sorting sperm.

FIG.14illustrates the results of an example in which the alignment process is greatly reduced for discriminating sperm nuclei. Sperm nuclei stained with Hoechst 33342 were processed through a Genesis III sperm sorter manufactured by Cytonome. The instrument was fit with an SiPM split detector. The forward fluorescence detection was aligned for less than one minute resulting in a rough alignment. Sperm nuclei were run at an event rate of 33,000 nuclei per second and interrogated with a Coherent Genesis CW-355 laser operated at an average power of 150 mW. Plot810illustrates the bivariate histogram showing the summed forward fluorescence plotted against the position detected by each event by the SiPM. The poor alignment is evident in each of the population of X-chromosome bearing nuclei812and the population of Y-chromosome bearing nuclei814. In poor alignment the crescent shapes are asymmetric and the fluorescence intensity values drop dramatically in the positive x direction as compared to the negative x direction. The population of Y-chromosome bearing nuclei814demonstrate the same skew.

The correction factor816is illustrated as a line between the two populations. This correction factor816illustrates the degree of correction that will be performed to summed fluorescence values at each x location. Stated differently, the correction factor816, represents a curved line that will be normalized by correction to a flat line. Each summed fluorescence value at a corresponding x position along line receives the same magnitude of increase or decrease as the correction factor816.

The distortion caused by rough alignment is more pronounced in the histogram of fluorescence intensities of plot820, where increased overlap results in a peak to valley ratio of 72.3% between the population of X-chromosome bearing nuclei812and the population of Y-chromosome bearing nuclei814.

In plot830, the corrected forward fluorescence summed value is plotted in a bivariate histogram against the detected position of each event. It can be seen, again, that by normalizing the fluorescence intensity values with a correction factor816based on the position of the cells, two clean populations of cells emerge. A corrected population of X-chromosome bearing nuclei832and a corrected population of Y-chromosome bearing nuclei834are more clearly and distinctly grouped in plot830. Importantly, the orthogonal relationship of these populations translates in the univariate fluorescence intensity histogram seen in plot840, where two distinct univariate peaks have a calculated peak to value ratio of 94.4%.

In addition to the use of correction, some embodiments disclosed herein include elements that reduce the variation in collected light intensity with respect to object position in a flow stream. Some embodiments described herein can provide modified output light that has less than about a 3%, or less than about a 2%, or even less than about a 1% measured intensity variation for a deviation in position of the object that is less than 60% of a radius of the flow stream away from a center of the flow stream along an axis perpendicular to the optical axis. Many applications are sensitive to intensity measurement errors, which may arise from a variety of sources. Due to the difficulty in reducing intensity fluctuations by precisely controlling the position of objects within the flow stream, it is useful to instead reduce the variation in collected light intensity with respect to object position by careful design of the optical collection arrangement. For applications such as X/Y sperm sorting, it is often the case that two or more cell populations are to be separated based on the difference in measured fluorescence intensity between the populations. If the random position fluctuations lead to fluctuations in collected light intensity that are greater in magnitude than the nominal difference in fluorescence intensity of the two populations, it is not possible to distinguish them with simultaneously high yield and high purity. The fluorescence intensity difference between X and Y sperm cells is typically only a few percent (e.g., ˜4% for bovine sperm). Current sperm sorter systems can in theory achieve high throughput by increasing the flow rate of the core stream, but this has the effect of increasing the width of the core stream. Consequently, there would be a large uncertainty of the sperm position within the core of the flow stream. This position uncertainty and the resultant fluctuations in collected fluorescence intensity limit the maximum throughput of current sperm sorter systems to levels which do not obscure the small fluorescence intensity difference between X and Y sperm.

One approach for intensity-position correction may be understood with reference toFIGS.6and7. The brackets inFIG.6highlight regions of integration that correspond to fluorescence collection optics with a given NA. Graphs of the collected intensity variation with respect to object position for the NAs ofFIG.6are provided inFIG.7. InFIG.7, for a given NA, integration over the fluorescence collection region is performed such that the intensity of collected light can be plotted as a function of each sperm position. It is evident fromFIG.7that increasing the NA of the collection optics helps to decrease the influence of object position on the fluorescence intensity gathered via the collection optics.

In some embodiments collection optics (e.g., the optical collection arrangement190inFIGS.1and2) may be modified with elements that reduce collected light intensity variation with respect to object position as described above. Such embodiments are described in more detail in U.S. patent application Ser. No. 16/133,531, which is incorporated herein by reference. According to some such embodiments, the collection optics operate by masking certain rays in “angle space”, that is, the collection optics selectively collect, attenuate, and/or block rays from different angles γ in order to achieve a desired intensity vs. position profile. In practice, an “angle space” masking function can be applied at a pupil (e.g., entrance pupil, exit pupil, or aperture stop) of an optical system, where the position of a ray intersection with the pupil plane corresponds to the angle γ. In some embodiments, the collection optical arrangement achieves a desired, e.g., flatter, intensity vs. position profile by preferentially collecting higher angle (pointing away from the optical axis) light rays to the exclusion of certain lower angle light rays.

FIGS.15and16illustrate how excluding low-angle refracted rays, at a given NA, causes the intensity-vs-position curve to flatten out. Excluding the low angle rays excludes the rays that produce the most variation in the intensity vs. position profile, whereas the angular variation of radiance at high positive angles tends to cancel the corresponding variation at high negative angles.FIG.15shows plots of the relative radiance vs. ray angle, γ, for different positions of the object along the x axis where the angle γ is in radians. InFIG.15, each graph corresponds to an object position, x, within the core of a flow stream, as indicated inFIG.5. The brackets inFIG.15show the portion of the light rays that will be excluded by the collection optics for each position x, when rays having angle magnitude less than 0.3 rad are excluded (bottom bracket inFIG.15) and when rays having angle magnitude less than 0.4 rad are excluded (top bracket inFIG.15).

FIG.16shows the relative collected light intensity vs. position of the object along the x axis when no angles are excluded (graph900), when rays having angles between −0.3 rad and +0.3 rad are excluded (graph903) and when rays having angles between −0.4 rad and +0.4 rad are excluded (graph904). Graph16shows that when lower angle rays are excluded, the relative intensity vs. position graph exhibits less intensity variation with respect to position.

FIG.17illustrates the results of an experiment incorporating both a software based positional correction and a hardware based element in the collection light path that reduces collected light intensity variation with respect to object position as described. Sperm nuclei stained with Hoechst 33342 were processed through a Genesis III sperm sorter manufactured by Cytonome. The sperm sorter was fit with an SiPM split detector having a wire placed in the light collection path in order to exclude low collection angle electromagnetic radiation produced from the sperm nuclei. Suitable wires and other elements for blocking low collection angle electromagnetic radiation are described in U.S. patent application Ser. No. 16/133,531.

Sample and sheath pressures were adjusted to reach an event rate of 60,000 events per second and the nuclei was interrogated with a Coherent Genesis CW-355 laser operated at an average power of 90 mW. In plot1010it can be seen the wire mitigates some effect of the intensity dependence on nuclei position within the fluid column. There is still however, a significant decrease in relative intensity as nuclei move further in the positive direction along the x axis. A population of X-chromosome bearing nuclei1012and a population of Y-chromosome bearing nuclei1014are seen sagging significantly in the positive direction in the x axis. The corresponding peak to valley ratio calculated from the fluorescence intensity histogram of plot1020is 81.5%. Again, X-chromosome bearing nuclei that are located toward one end of the fluid column are not sufficiently detected. As a result, the summed fluorescence intensity of the nuclei at this end have similar intensity values as centered Y-chromosome bearing nuclei within the population of Y-chromosome bearing nuclei1014. This skew is evident in the univariate histogram of plot1020in the form of a shoulder shifting downward and an exaggerated peak of the population of Y-chromosome bearing nuclei1014.

A correction factor1016is illustrated on graph1010. For each position, a correction value is added to the detected fluorescence intensity corresponding correction factor. Plot1030illustrates a bivariate histogram having a corrected population of X-chromosome bearing nuclei1032and a corrected population of Y-chromosome bearing nuclei1034, which are more distinct rectangular populations. Plot1040provides the corresponding univariate histogram of corrected summed intensity values independent of the location of each event. The corrected population of X-chromosome bearing nuclei1032and the corrected population of Y-chromosome bearing nuclei1034are more distinct having roughly equal peaks heights and a peak to valley ratio of 92.6%.

The foregoing description of various embodiments has been presented for the purposes of illustration and description and not limitation. The embodiments disclosed are not intended to be exhaustive or to limit the possible implementations to the embodiments disclosed. Many modifications and variations are possible in light of the above teaching.