Patent Publication Number: US-11378808-B2

Title: Laser systems and optical devices for laser beam shaping

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of U.S. Provisional Application No. 62/700,194, filed Jul. 18, 2018, titled “Laser Systems and Optical Devices for Laser Beam Shaping.” This application is related to U.S. patent application Ser. No. 12/940,004, filed Nov. 4, 2010, titled “Compact, Thermally Stable Multi-Laser Engine,” which is a continuation-in-part of U.S. patent application Ser. No. 12/418,537, filed Apr. 3, 2009, titled “Compact, Thermally Stable Multi-Laser Engine,” which claims the benefit of U.S. Provisional Application No. 61/042,652, filed Apr. 4, 2008. This application is also related to U.S. patent application Ser. No. 14/103,709, filed Dec. 11, 2013, titled “Optical Systems,” which claims the benefit of U.S. Provisional Application No. 61/736,500, filed Dec. 12, 2012. This application is also related to U.S. Patent Application Publication 2009/0257054 and corresponding U.S. patent application Ser. No. 12/418,494, filed Apr. 3, 2009 and titled “Compact, Thermally Stable Fiber-Optic Array Mountable to Flow Cell,” as well as U.S. Provisional Application No. 61/042,640, filed Apr. 4, 2008. Each of the above-referenced applications is incorporated herein by reference in their entirety. 
    
    
     BACKGROUND 
     Field 
     This disclosure generally relates to optical (e.g., fluorescent, spectroscopic, scatter) analysis of biological samples contained in flow cells and/or optical fibers connected to confocal microscopes or “lab-on-a-chip” devices, and to, for example, compact, thermally stable multi-laser systems configured to couple to flow cells, optical fibers, or other target objects and to provide illumination thereto. 
     This disclosure also relates generally to optical systems for directing light to a sample contained in a flow cell, and more particularly to a compact, thermally stable, optical fiber array attachable to a flow cell for directing laser light to the flow cell for optical measurements such as laser-induced fluorescence. 
     Description of Related Art 
     Optical analysis of samples contained in flow cells, such as laser-induced fluorescence, involves illuminating biological samples with laser light in order to test samples which may, for example, be tagged with fluorescent dyes. Fluorescent dyes absorb light at certain wavelengths and in turn emit their fluorescence energy at a different wavelength. This emission can be detected to ascertain properties of the sample contained in the flow cell. Existing systems for fluorescent analysis of flow cells, however, suffer from various drawbacks, such as measurement error. 
     SUMMARY 
     Embodiments described herein have several features, no single one of which is solely responsible for their desirable attributes. Without limiting the scope of the invention as expressed by the claims, some of the advantageous features will now be discussed briefly. 
     Various embodiments described herein provide the ability to perform optical measurements on samples contained in flow cells while addressing some of the drawbacks encountered with conventional approaches, such as laser beam alignment to the flow cell, achieving uniform intensity over a cross-sectional area of the flow cell and/or achieving a sufficiently small spot size configured to selectively illuminate a portion of the flow cell. 
     Various embodiments described herein provide advantages such as uniformity of intensity of light, spot size of the illuminating light and intensity noise in the illuminating light. A wide range of embodiments are disclosed. 
     Various embodiments disclosed herein, for example, comprise a laser system for directing light for optical measurements, such as laser-induced fluorescence. The laser system can include a thermally conductive housing defining an interior chamber, and a thermoelectric controller thermally coupled to the housing. The laser system can include a plurality of optical input ports, and the optical input ports can be configured to engage a plurality lasers and or light emitting diodes (LEDs). The lasers and or LEDs can be free-space, fiber coupled or a combination of free space and fiber coupled. The plurality of lasers and or LEDs can be collimated to generate a plurality of laser and or LED beams which can be combined using dichroic beam combiners to produce a single beam of multiple wavelengths. This single multi-wavelength beam can then be focused towards a moving diffuser with a focusing lens. The size of the beam on the moving diffuser can be controlled by the separation between the lens and the moving diffuser, the focal length of the lens and the diameter of the single multi-wavelength beam incident on the focusing lens. 
     The thermoelectric controller can be configured to maintain the interior chamber at a substantially constant temperature. 
     The plurality of beams of light produced by the one or more optical elements can comprise a plurality of substantially elliptical beams of light. The one or more optical elements can comprise a plurality of anamorphic microlenses. The laser system can include one or more output windows, and the one or more output windows can be configured to transmit the beams of light out of the internal chamber. 
     The flow cell connector can be configured to attach the flow cell to the outside of the housing. The housing can be hermetically sealed. 
     Certain innovations disclosed here are related to optical analysis of biological samples contained in flow cells. Certain innovations disclosed here are related to optical fibers connected to confocal microscopes, or “lab-on-a-chip” devices. For example, certain innovations are related to compact, thermally stable multi-laser systems configured to couple to flow cells, optical fibers, or other target objects and to provide illumination thereto. Aspects of this disclosure are related to, and can be used in, optical systems for directing light to a sample contained in a flow cell. Aspects of this disclosure are related to, and can be used in, a compact, thermally stable, optical fiber array attachable to a flow cell for directing laser light to the flow cell for optical measurements such as laser-induced fluorescence. 
     An innovation includes an illumination system that can be used to direct light at targets for optical measurements. The illumination system can include one or more lasers. The illumination system can include a thermally conductive housing defining an interior chamber, and a thermoelectric controller thermally coupled to the housing. The illumination system can include a plurality of optical input ports, and the optical input ports can be configured to engage a plurality of input optical fibers and receive light from the input optical fibers. The illumination system can include a plurality of waveguides contained within the interior chamber, and the waveguides can be configured to receive the light from the optical input ports and output the light into the internal chamber. The illumination system can include one or more optical elements configured to receive the light output by the waveguides and output a plurality of beams of light. The illumination system can include a flow cell connector configured to attach a flow cell to the housing, and the flow cell connector can be configured to position the flow cell to intersect the beams of light. 
     An innovation includes an illumination system, including one or more lasers configured to output light having at least one wavelength, one or more beam combiners each aligned to receive light from a corresponding one of the one or more lasers, the one or more beam combiners configured to direct the received light along a path, a focusing optical element configured to receive light from the one or more beam combiners and focus the received light towards a focus point, a diffuser positioned spaced apart from the focus point to receive defocused light from the focusing element, the diffuser configured to diffuse the received defocused light and output diffused light, an actuator coupled to the diffuser and configured to vibrate the diffuser, a collimating optical element configured to receive light output by the diffuser and configured to substantially collimate the light, and a microlens array configured to receive light output by the diffuser and configured to alter the distribution of light. 
     Various embodiments of the illumination systems disclosed here can include one, all, or any combination of features of this paragraph, or other features disclosed herein. The one or more lasers can include a plurality of lasers. The one or more beam combiners can include one or more dichroic mirrors. The illumination system can include at least one filter configured to filter a portion of the light output by a corresponding one of the one or more lasers. The diffuser of the illumination system can be positioned (or located) between the focusing optical element and the focus point to diffuse the light as the light is converging towards the focus point. The diffuser of the illumination system can be positioned (or located) between the focus point and the collimating optical element to diffuse the light as the light is diverging away from the focus point. The diffuser can be positioned (or located) so that light from the focusing element forms a spot on the diffuser, the spot having a first width along a first direction and a second width along a second direction that is orthogonal to the first direction, the first width being larger than the second width, and wherein the actuator is configured to vibrate the diffuser in the first direction. The focusing element can be configured so that light from the focusing element forms a spot on the diffuser, the spot having a first width along a first direction and a second width along a second direction that is orthogonal to the first direction, the first width being larger than the second width, and wherein the actuator is configured to vibrate the diffuser in the first direction. The diffuser can be positioned so that light from the focusing element forms a spot on the diffuser, the spot having a first width along a first direction and a second width along a second direction that is orthogonal to the first direction, the first width being larger than the second width, and wherein the actuator is configured to vibrate the diffuser in the first direction. The diffuser can be positioned at a location, and the focusing element can be configured, so that light from the focusing element forms a spot on the diffuser, the spot having a first width along a first direction and a second width along a second direction that is orthogonal to the first direction, the first width being larger than the second width, and wherein the actuator is configured to vibrate (or rapidly move) the diffuser in the first direction. The actuator can be configured to vibrate (or rapidly move) the diffuser in a one-dimensional motion. The actuator can be configured to vibrate (or rapidly move) the diffuser in a two-dimensional motion in a plane that is substantially orthogonal to the optical axis of the focusing optical element. The actuator can be configured to vibrate the diffuser in a circular motion. The microlens array can be configured to output a substantially flat-top distribution of light. The diffuser can be positioned at least about 0.2 mm from the focus point, for example, at a location so that the light focused by the focusing optical element is incident of the diffuser before the light reaches the focus point, or at a location so that the light focused by the focusing optical element is incident on the diffuser after the light propagates through the focus point. The focusing optical element can be configured to focus the light to a spot having a first area at the focus point. The diffuser can be positioned so that the light focused by the focusing optical element forms a spot on the diffuser that has a second area larger than the first area. The second area can be at least about 50% larger than the first area. The illumination system can further include one or more additional optical elements configured to receive light from the micro-lens array and focus the received light onto a target. 
     Another innovation includes an illumination system including one or more light sources, 
     a focusing optical element configured to receive light emitted by the one or more light sources and focus the received light towards a focus point, and a dynamic diffuser positioned to receive light propagating through the focusing optical element and to vibrate to diffuse the received light, the position of the optical element being at a location other than the focus point. The focusing optical element of the illumination system can include an aspherical lens. The dynamic diffuser can be positioned (or located) between the focusing optical element and the focus point so that the light being focused by the focusing optical element impinges on the dynamic diffuser before reaching the focus. The dynamic diffuser can be positioned (or located) so that the light being focused by the focusing optical element impinges on the dynamic diffuser before reaching the focus point. The focusing optical element can be configured such that light focused by the focusing optical element forms a spot of light on the dynamic diffuser that is generally elliptical in shape, having a major axis and a minor axis. The dynamic diffuser is configured to move in at least one dimension in the same direction (or substantially the same direction) as the major axis. The system can include an actuator that vibrates (or moves) the diffuser. In some embodiments, the dynamic diffuser is configured to move in a direction along a line that is parallel, or substantially parallel, to the major axis. 
     An innovation includes a method of illuminating a target, the method comprising receiving light from one or more lasers by one or more beam combiners, each of the one or more beam combiners aligned to receive light from a corresponding one of the one or more lasers; combining, by the one or more beam combiners, the received light and directing the received light along a common path, receiving propagating along the common path at a focusing optical element and focusing the light towards a focus point, receiving the focused light at a diffuser positioned at a location spaced apart from the focus point, diffusing the light, at least in part by vibrating the diffuser, and outputting diffused light, receiving light output by the diffuser at a collimating optical element configured to collimate the light from the diffuser, and receiving the collimated light at a microlens array, the microlens array configured to alter the distribution of the collimated light for illuminating a target. The target can be a flow cell, or contained in a flow cell. The diffuser can be positioned between the focusing optical element and the focus point. The diffuser can be positioned between the focus point and the collimating optical element. The method can further include vibrating the diffuser by moving the diffuser in a circular motion. Vibrating the diffuser includes moving the diffuser in a two-dimensional motion in a plane. The two-dimensional motion can be substantially orthogonal to an optical axis of the focusing optical element. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The following drawings and the associated descriptions are provided to illustrate embodiments of the present disclosure and do not limit the scope of the claims. 
         FIG. 1  depicts an example embodiment of a multi-laser system. 
         FIG. 2  depicts another example embodiment of a multi-laser system. 
         FIG. 2A  depicts another example embodiment of a multi-laser system in which the beam positioning/combining system comprises mirrors. 
         FIG. 2B  depicts an example embodiment of a triangular prism. 
         FIG. 2C  depicts an example embodiment of a rectangular prism. 
         FIG. 2D  depicts an example embodiment of a multi-laser system including a prism beam positioning/combining system. 
         FIG. 2E  depicts an example embodiment of a prism beam positioning/combining system. 
         FIG. 3  depicts the front view of the system of  FIG. 2 . 
         FIG. 4  depicts the side view of the system of  FIG. 2 . 
         FIG. 5  depicts an example embodiment of a multi-laser system further including a plurality of beam adjusters. 
         FIG. 6  depicts an example embodiment of a multi-laser system further including focusing optics. 
         FIG. 7  depicts an example embodiment of a multi-laser system in which the beam adjusters comprise Risley prism pairs. 
         FIGS. 8A-8B  depict example embodiments of a multi-laser system in which the beam adjusters comprise Risley prisms and plane parallel plates. 
         FIG. 9  depicts an example embodiment of a multi-laser system in which the target object comprises an optical fiber or waveguide. 
         FIG. 10  depicts an example embodiment of a multi-laser system in which the target object comprises an adjuster mount. 
         FIGS. 11A-11N  depict example spatial arrangements of laser beams in multi-laser systems. 
         FIG. 11A  depicts parallel collimated beams with identical beam separations, d 0 . 
         FIG. 11B  depicts parallel collimated beams with different beam separations, d 1  and d 2 . 
         FIG. 11C  depicts converging collimated beams with identical angular separations, θ 0 . 
         FIG. 11D  depicts converging collimated beams with different angular separations, θ 1  and θ 2 . 
         FIG. 11E  depicts diverging collimated beams with identical angular separations, θ 0 . 
         FIG. 11F  depicts diverging collimated beams with different angular separations, θ 1  and θ 2 . 
         FIG. 11G  depicts co-linear collimated beams. 
         FIG. 11H  depicts parallel focused beams with identical beam separations, d 0 . 
         FIG. 11I  depicts parallel focused beams with different beam separations, d 1  and d 2 . 
         FIG. 11J  depicts converging focused beams with identical angular separations, θ 0 . 
         FIG. 11K  depicts converging focused beams with different angular separations, θ 1  and θ 2 . 
         FIG. 11L  depicts diverging focused beams with identical angular separations, θ 0 . 
         FIG. 11M  depicts diverging focused beams with different angular separations, θ 1  and θ 2 . 
         FIG. 11N  depicts co-linear focused beams. 
         FIG. 12  schematically shows an optical system that can be used to direct light to samples for performing optical measurements such as laser-induced fluorescence and spectroscopic analysis. 
         FIG. 13  is a cross-sectional view of an embodiment of an optical fiber array. 
         FIG. 14  schematically shows another optical system that can be used to direct light to samples for performing optical measurements such as laser-induced fluorescence and spectroscopic analysis. 
         FIG. 15  schematically shows another optical system that can be used to direct light to samples for performing optical measurements such as laser-induced fluorescence and spectroscopic analysis. 
         FIG. 16  illustrates an embodiment of an optical system configured to analyze a sample, for example using laser induced fluorescence. 
         FIG. 17  illustrates another embodiment of an optical system configured to analyze biological and/or chemical samples using laser-induced fluorescence. 
         FIG. 18  illustrates an example of a flow cell comprising an array of tiles. 
         FIG. 19A  depicts the intensity profile for light output by an example light source. 
         FIG. 19B  depicts an example of a uniform intensity profile obtained by shaping the intensity profile for light output by an example light source shown in  FIG. 19A  using a beam shaping optical system. 
         FIG. 20  depicts the incident path of an embodiment of an optical system configured to analyze samples (e.g., biological and/or chemical samples), such as using laser-induced fluorescence. 
         FIG. 21  shows the variation of the beam diameter and the intensity noise at the output of a dynamic diffuser as a function of the distance between a focusing lens and the dynamic diffuser. 
         FIG. 22  illustrates an embodiment of a fiber coupled illuminator comprising two laser diodes. 
         FIGS. 23A-23E  show the variation in the beam profile at the output of the dynamic diffuser as the spacing between the dynamic diffuser and a focusing lens is increased from a value less than the focal distance to a value greater than the focal distance.  FIG. 23D  shows the beam profile with the spacing between the dynamic diffuser and focusing lens equal to the focal distance. 
         FIG. 24  is a flow diagram illustrating a method of illuminating a target. 
     
    
    
     DETAILED DESCRIPTION 
     Although certain preferred embodiments and examples may be disclosed herein, inventive subject matter extends beyond the specifically disclosed embodiments to other alternative embodiments and/or uses of the inventions, and to modifications and equivalents thereof. Thus, the scope of the inventions herein disclosed is not limited by any of the particular embodiments described below. For example, in any method or process disclosed herein, the acts or operations of the method or process may be performed in any suitable sequence and are not necessarily limited to any particular disclosed sequence. 
     For purposes of contrasting various embodiments with the prior art, certain aspects and advantages of these embodiments are described. Not necessarily all such aspects or advantages are achieved by any particular embodiment. Thus, for example, various embodiments may be carried out in a manner that achieves or optimizes one advantage or group of advantages as taught herein without necessarily achieving other aspects or advantages as may also be taught or suggested herein. 
       FIG. 1  depicts an example embodiment of a multi-laser system. The multi-laser system  100  depicted in  FIG. 1  may comprise a mounting mechanism, mounting system (e.g., mounting alignment system), etc. for a flow cell, a flow cell mount, a light pipe, a waveguide, an optical fiber, and/or a lab on a chip. 
     In some embodiments, the temperature across the enclosure may be stable over time and with changes in the ambient temperature. The constant temperature over time may help with long term system performance. For example, if the enclosure temperature were to change with time, then the system performance would also potentially degrade with time. This could eventually result in servicing the system, e.g., to realign the system. 
     The thermally stable enclosure  150  comprises a material with high thermal conductivity. In some embodiments, a material with thermal conductivity of at least about 5 W/(m K), (e.g., between about 5 W/(m K) and about 2000 W/(m K)) is used. In some embodiments, a material with thermal conductivity at least about 50 W/(m K) (e.g., between about 50 W/(m K) and about 2000 W/(m K)) is used. In other embodiments, a material with thermal conductivity of about 375 W/(m K) or greater is used. In other embodiments, a material with thermal conductivity of at least about 380 W/(m K) is used. In some embodiments, a material with thermal conductivity between about 125 W/(m K) and about 425 W/(m K)) is used. In some embodiments, a material with thermal conductivity between about 375 W/(m K) and about 425 W/(m K)) is used. In some embodiments, a material with thermal conductivity between about 125 W/(m K) and about 250 W/(m K)) is used. In some embodiments, a material with thermal conductivity between about 200 W/(m K) and about 250 W/(m K)) is used. In some embodiments, the material has a heat capacity corresponding to the heat capacity of the materials described herein. The use of such thermally conductive material helps ensure a relatively reduced temperature variation within the enclosure  150 , even when the ambient temperature outside of the enclosure varies relatively widely. 
     As described more fully below, a temperature controller in thermal contact with the enclosure adjusts the temperature of the enclosure in response to variations in ambient conditions. A highly thermally conductive enclosure enables the temperature controller to more quickly and effectively maintain the enclosure and system temperature without temperature gradients in response to such variations in ambient conditions. A variety of thermally conductive materials can be used (e.g., copper, aluminum, copper tungsten, ceramics, epoxy, etc.). In some embodiments, a material with a thermal conductivity of at least 5 W/(m K) may be used. In other embodiments, a material with a thermal conductivity of less than 5 W/(m K) may be used. The thermally conductive material can be used to form the entire enclosure, or merely a portion thereof. In certain embodiments, the enclosure can include, or can substantially include, highly thermally conductive material. For example, highly thermally conductive material can be used to form the top, the bottom, or any number of the sides of the enclosure  150 , or any combination thereof. In some embodiments, a majority of the enclosure  150  is made of the thermally conductive material. In some embodiments, only a relatively small portion of the enclosure  150  is made of the thermally conductive material. In some embodiments, a portion of the enclosure  150  is made of the substantially thermally conductive material. In some embodiments, multiple thermally conductive materials can be used, with some areas of the enclosure  150  being more thermally conductive than others. 
     The multi-laser system  100  includes a plurality of lasers  101 A- 101 N, enclosed within the thermally stable enclosure  150 . The plurality of lasers  101 A- 101 N may comprise diode lasers, solid-state lasers, frequency-doubled lasers, and/or other types of lasers. The plurality of lasers  101 A- 101 N output a plurality of respective laser beams  102 A- 102 N. Each of the laser beams  102 A- 102 N may have a wavelength different from the other laser beams. 
     As shown in  FIG. 1 , the multi-laser system  100  further includes a beam positioning system  1000 . To achieve a desired spatial arrangement of the laser beams  102 A- 102 N, the inherent laser beam boresight and centration errors present in lasers  101 A- 101 N, as well angular and lateral positioning errors present in the multi-laser system&#39;s opto-mechanical components can be compensated for. In some embodiments, the beam positioning/combining system  1000  may include mechanical and/or opto-mechanical provisions to perform such compensation. 
     Mechanical provisions to the laser mounting may be used to adjust the angular and/or lateral position of the lasers so that the boresight and centration errors of the lasers  101 A- 101 N as well as the angular and lateral positioning errors of the opto-mechanical components are compensated for. The aligned laser beams may then be positioned or combined by the beam positioning/combining system  1000  into a desired spatial arrangement that a specific application requires. 
     Opto-mechanical provisions to the beam positioning/alignment system may be used to allow for angular and lateral position adjustment of the laser beams. This adjustment capability may help compensate for the lasers&#39; boresight and centration errors as well as the angular and lateral positioning errors of the opto-mechanical components to achieve a desired spatial arrangement of the laser beams. 
     In embodiments in which the system is used perform testing of biological samples, flow cells are illuminated with laser beams. Fluorescent dyes absorb light at certain wavelengths and in turn emit their fluorescence energy at a different wavelength. This emission can be detected to ascertain properties of the fluid in the flow cell. Temperature variations may cause the wavelength and/or the intensity of light output by the lasers to vary. Such variations in the laser beams directed into the flow cell may cause fluctuations in output fluorescent signals, which may introduce inaccuracy in the optical measurements. Temperature variations and/or temperature gradients also may cause movement of the optical elements (e.g., due to thermal expansion) and resultant shifting of the laser beams. These pointing errors may cause the laser beams to deviate from the flow cell, such that the signal changes, or is altogether lost, again introducing inaccuracy in the test results. 
     Temperature variations can result from ambient temperature fluctuations. Accordingly, reducing the temperature variation of and the presence of temperature gradients within the laser beam system can improve the accuracy and usability of the test results. 
     Various embodiments described herein may address one or more of these problems.  FIG. 2  is a top view of another example embodiment of the multi-laser system  100 . The multi-laser system  100  depicted in  FIG. 2  comprises a thermally stable enclosure  150  configured to mechanically and/or thermally couple to a flow cell  132 . The thermally stable enclosure  150  helps to isolate the laser and optics within the enclosure  150  from the ambient environment, which may have varying temperature. In some embodiments, the enclosure  150  can achieve thermal stability through the use of a temperature controller, as discussed in relation to  FIG. 3  below. In various embodiments, the enclosure  150  helps reduce variations in the temperature of the various components of the multi-laser system  100 . By maintaining the temperature within the enclosure within a relatively small range, thermally induced laser wavelength and intensity fluctuations as well as pointing instabilities of the laser beams can be reduced or minimized and alignment of the laser beams to a target object may be maintained over a range of ambient temperatures (e.g., between about 10° C. and about 55° C.). Accordingly, the use of a thermally stable enclosure  150  may help achieve more accurate test results. 
     Some materials expand and contract when heated or cooled. Changes in the enclosure temperature or temperature variations across the enclosure can result in a change in the relative positions of lasers, mirrors, lenses, and the target object (e.g., flow cell). Some lasers exhibit beam pointing that is temperature dependent. This may be due in part to the fact that different materials are used in the construction of the laser (e.g., metals, glass, adhesives, etc). The different materials may have different thermal expansion coefficients, which may cause beam deviations when the laser system&#39;s temperature changes. Some mirror and lens systems also show some temperature dependence for the same reason. 
     The multi-laser system  100  depicted in  FIG. 2  includes a plurality of lasers  101 ,  102 ,  103  enclosed within the thermally stable enclosure  150 . Although  FIG. 2  includes three lasers, a different number of lasers can be used. The multi-laser system  100  shown in  FIG. 2  includes a 405 nm laser, a 488 nm laser and a 635 nm laser, but other wavelengths can also be used (e.g., lasers having wavelengths of 375 nm, 440 nm, 515 nm, 561 nm, 594 nm, 640 nm, etc.). 
     The plurality of lasers  101 ,  102 ,  103  output a plurality of respective laser beams  104 ,  105 ,  106 . Laser beam  104  has a first wavelength, laser beam  105  has a second wavelength, and laser beam  106  has a third wavelength. The first, second, and third wavelengths are different from one another. In  FIG. 2 , these wavelengths are 405 nm, 488 nm and 635 nm, respectively, but other wavelengths can also be used (e.g., 375 nm, 440 nm, 515 nm, 561 nm, 594 nm, 640 nm, etc.). 
     As shown in the example embodiment of  FIG. 2 , the multi-laser system  100  further includes a plurality of automatic power control (APC) modules  107 ,  108 ,  109 . In some embodiments, the APC modules  107 ,  108 ,  109  may each comprise a beamsplitter (not shown) and a photodetector (not shown) configured to sample light from the laser beams  104 ,  105 ,  106 , respectively, and to feed back the signal from the detector in communication with a laser controller (not shown) to adjust the output power of lasers  101 ,  102 ,  103 , respectively. Other approaches may also be possible. 
     Referring still to  FIG. 2 , the beam positioning system comprises a plurality of wavelength selective mirrors  110 ,  111 ,  112 ,  113 . In various embodiments, some of the wavelength selective  110 ,  111 ,  112 ,  113  mirrors have significantly different reflection or transmission properties at different wavelengths. Accordingly, the wavelength selective mirrors  110 ,  111 ,  112 ,  113  can separate or combine laser beams with different wavelengths. In some embodiments, the mirrors  110 ,  112  may be broadband, for example because light is not transmitted through the mirrors  110 ,  112 . Through the use of suitable optical coatings, wavelength selective mirrors exhibit high reflection over some range of wavelengths and high transmission over another range of wavelengths. The wavelength selective mirrors are appropriate for the wavelengths of the laser sources. For example, various of the wavelength selective mirrors will selectively reflect (or transmit) light propagating from one laser at a first wavelength and not light propagating from another laser at a second wavelength. The example embodiment of  FIG. 2  depicts four wavelength selective mirrors  110 ,  111 ,  112 ,  113 . In other embodiments, a different number of wavelength selective mirrors may be used (e.g., see  FIG. 2A ). In some embodiments, the wavelength selective mirrors may comprise dichroic mirrors. In some embodiments, the wavelength selective mirrors may comprise trichroic mirrors. In some embodiments, the wavelength selective mirrors may comprise dichroic and trichroic mirrors. Dichroic mirrors can separate or combine lasers with two different wavelengths. In various embodiments dichroic mirrors may allow at least one wavelength to substantially or totally pass through and may substantially or totally reflect at least one wavelength. Trichroic mirrors can separate or combine lasers with three different wavelengths. Trichroic mirrors may be configured and/or optimized for reflecting three wavelengths. In some embodiments, trichroic mirrors they may be configured such that the reflected radiation has three wavelength peaks. In some embodiments, trichroic mirrors may be configured to have or one broad peak that covers multiple wavelengths. In other embodiments, the wavelength selective mirrors may include mirrors configured for a selective different number of wavelengths. Alternatively, non-wavelength selective mirrors, or substantially non-wavelength selective mirrors, that do not selectively reflect (or transmit) light of one laser and not light of another laser may be inserted in the path of the beam to redirect and/or alter the beam path or the beam. Various embodiments may have additional and/or other optical elements in the optical path. 
     The wavelength selective mirrors  110 ,  111 ,  112 ,  113  are configured with highly reflective and anti-reflective coatings in accordance with the wavelengths of the plurality of laser beams  104 ,  105 ,  106 . As shown in  FIG. 2 , wavelength selective mirror  110  is configured to be highly reflective of the wavelength of the laser beam  104  (e.g., 405 nm, all wavelengths); wavelength selective mirror  111  is configured to be highly reflective of the wavelength of the laser beam  104  (e.g., 405 nm) and anti-reflective of the wavelength of the laser beam  105  (e.g., 488 nm); wavelength selective mirror  112  is configured to be highly reflective of the wavelength of the laser beam  106  (e.g., 635 nm, all wavelengths), and wavelength selective mirror  113  is configured to be highly reflective of the wavelength of the laser beam  106  (e.g., 635 nm), and anti-reflective of the wavelengths of the laser beams  104  (e.g., 405 nm) and  105  (e.g., 488 nm). In other embodiments, the wavelength selective mirrors can be configured to be highly reflective of some wavelengths and anti-reflective of some other wavelengths in order to separate or combine the wavelengths as necessary. 
     In some embodiments, this plurality of wavelength selective mirrors  110 ,  111 ,  112 ,  113  may be supported by a plurality of respective flexure mounts (not shown). Flexure mounts are less likely to move with external vibrations and thus are less likely to require adjustment. Flexure mounts reduce impact on the optics from shocks such as may be introduced by shipping of the system. Additionally, flexure mounts typically exhibit less hysteresis than rolling or sliding contacts. Flexure mounts are typically fabricated from materials which make them relatively less sensitive to temperature variations. Flexure mounts may also be smaller than conventional spring loaded mounts. In some embodiments, the flexure mounts may comprise a nickel-iron alloy material for example. Other materials may also be used. In other embodiments, the plurality of wavelength selective mirrors  110 ,  111 ,  112 ,  113  may be supported by a plurality of respective spring-loaded mirror mounts (not shown). In other embodiments, the plurality of wavelength selective mirrors  110 ,  111 ,  112 ,  113  may be supported by a plurality of respective glue-block mounts (not shown). 
     In the multi-laser system  100  shown in  FIG. 2 , three optical paths are depicted. A first optical path at a wavelength of 405 nm originates at laser  101 , passes through the APC  107 , where a portion of the signal is picked off (e.g., by a beam splitter), is then highly reflected at wavelength selective mirrors  110  and  111  and transmitted through wavelength selective mirror  113 , and then arrives at the focusing optics  117 . A second optical path at a wavelength of 488 nm originates at laser  102 , passes through the APC  108 , where a portion of the signal is picked off (e.g., by a beam splitter), is then transmitted through wavelength selective mirrors  111  and  113 , and then arrives at the focusing optics  117 . A third optical path at a wavelength of 635 nm originates at laser  103 , passes through the APC  109 , where a portion of the signal is picked off (e.g., by a beam splitter), is then reflected at wavelength selective mirrors  112  and  113 , and then arrives at the focusing optics  117 . Propagating along these paths, laser beams  104 ,  105 ,  106 , which may have originally been far from one another, are repositioned to be closer together as beams  114 ,  115 ,  116  and, after the focusing optics, beams  118 ,  119 ,  120 , respectively. In some embodiments, the beams  118 ,  119 ,  120  are parallel to one another. In other embodiments, the beams  118 ,  119 ,  120  are not parallel to one another. Other mirrors and optical components (e.g., lenses, prisms, polarization rotators, waveplates, etc.) can be included to alter the laser beams and/or optical paths. 
     Still referring to  FIG. 2 , the multi-laser system  100  further includes optional beam focusing optics  117  to provide size reduction and/or shaping to the output laser beams  118 ,  119 ,  120 . For example, the focusing optics  117  may focus a laser beam down to a smaller spot, generally referred to herein as a focus point. Due to non-ideal optical elements and configurations, the “focus point” where focusing optics focus the light the may not be an actual “point” but instead represent and area larger than a point, for example, a small spot shaped area. Additionally, the focusing optics  117  may change the shape of the laser beams. In some embodiments, for example, the laser beams  118 ,  119 ,  120  can have a generally Gaussian profile, so that when illuminating a flow cell, the intensity of the light illuminating the center of the flow cell is significantly greater than the intensity of the light illuminating the peripheral edges of the flow cell. Accordingly, the beams of light  118 ,  119 ,  120  can be elongated (e.g., elliptical) beams, so that the relatively high intensity center regions of the light beams extend across the entire width of the flow cell, while the relatively low intensity outer regions of the light beams do not strike the flow cell. By using an elongated (e.g., elliptical) beam of light, a more uniform distribution of light across the width of the flow cell or other target output can be achieved while illuminating a relatively small longitudinal area along the length of the flow cell and maintaining substantially uniform high light intensity. 
     In some embodiments, the beams  114 ,  115 ,  116  enter the beam focusing optics  117  and can have circular cross-sections with a Gaussian fall-off. In some embodiments, the beam focusing optics  117  may include an anamorphic lens system which may produce non-rotationally symmetric or elongated beam such as a beam with elliptical cross-section and spot size. In other embodiments, the beam focusing optics  117  may include cylindrical lenses. In some embodiments, the beam focusing optics  117  may include spherical lenses. In some embodiment, the beam focusing optics  117  may include Powell lenses (Gaussian to flat-top transformers). In some embodiments, the beam focusing optics  117  may include aspherical lenses. The focusing optics may be achromatic with reduced chromatic aberration thereby reducing positioning error which may otherwise result from different color laser beams. Accordingly, achromatic anamorphic optics, achromatic elliptical optics, achromatic spherical optics and achromatic aspherical optics, may be used. In some embodiments, lenses can be an anamorphic microlens array. In some embodiments, refractive and/or diffractive optics can be used to produce the elongated beams of light  118 ,  119 ,  120 . Other types of optics are possible. 
     In cases where the laser comprises a semiconductor laser, the laser beam output may already be elliptical-shaped, and optics to convert the elliptical beam into a circular beam can be excluded. In such cases, there would be no need to include anamorphic focusing optics to make the elliptical-shaped beam spherical (e.g., rotationally symmetric). Spherical or rotationally symmetric optics may be employed without anamorphic elements. 
     The output laser beams  118 ,  119  and  120  depicted in  FIG. 2  may have respective spot sizes of between about 55 μm and about 110 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have respective spot sizes of between about 70 μm and about 110 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have respective spot sizes of between about 50 μm and about 150 μm in one direction and between about 5 μm and about 20 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have spot sizes of between about 55 μm and about 100 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have spot sizes of between about 70 μm and about 100 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have respective spot sizes of between about 50 μm and about 150 μm in one direction and between about 5 μm and about 20 μm in another direction (e.g., perpendicular to the one direction). In some embodiments, the output laser beams  118 ,  119 ,  120  may have respective spot sizes of about 80 μm in one direction and about 10 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the output laser beams  118 ,  119 ,  120  may have respective spot sizes of about 100 μm in one direction and about 10 μm in another direction (e.g., perpendicular to the one direction). The directions may correspond to major and minor axes of an ellipse for a beam with an elliptical cross-section and spot shape. Other sizes and shapes are possible for the light beams. 
     Still referring to  FIG. 2 , the multi-laser system  100  includes coupling to a flow cell  132 . The multi-laser system  100  can include an output window  121  that allows the beams of light  118 ,  119 ,  120  to exit the enclosure  150 . The output window  121  can be made from, for example, fused silica, glass, acrylic, or a variety of other transparent materials (e.g., plastic). In some embodiments, the enclosure  150  includes an aperture  122  in a wall thereof and the output window  121  comprises a transparent window pane  124  positioned over the aperture  122 . The window pane  124  can be made from, for example, fused silica, glass, acrylic, or a variety of other transparent materials (e.g., plastic). The aperture  122  and window pane  124  can assume a variety of shapes, but in some embodiments they are rectangular, circular, or elliptical. The window  121  can be attached to the enclosure  150  by a plurality of fasteners such as bolts  126 . In  FIG. 2 , only two bolts  126  are shown, but in some embodiments, additional bolts can be positioned along the edges of the window  121 . In some embodiments, the window  121  can include a flange for mounting the window. The flange may have a plurality of through holes through which fasteners (e.g., bolts  126 ) can pass to secure the window  121  to the enclosure  150 . A seal  128  (e.g., an O-ring) can be positioned between the enclosure  150  and the window  121 . The bolts  126  can be tightened, causing the O-ring  128  to be compressed between the enclosure  150  and the window  121 . In some embodiments, the O-ring  128  produces a hermetic seal. Other approaches can be used to fasten the window  121  to the enclosure  150 . The window  121  can be secured to the enclosure  150  by an adhesive, epoxy, or cement. 
     In some embodiments, the seal described may produce a hermetic seal. A hermetic seal may help reduce particles and contamination from outside the enclosure. A hermetic seal may also help to prevent or reduce the flow of air currents and thus prevent or reduce the flow of ambient temperature changes into the enclosure. This in turn may help reduce temperature instability within the enclosure. In some of the embodiments discussed above, the entire enclosure  150  is hermetically sealed from the ambient air. Thus, the interior of the enclosure  150  is isolated from air currents which can cause temperature variation, and the internal optical elements are protected from external contaminants. In some embodiments a getter (not shown) is located inside the enclosure  150  which can reduce contaminant particles or chemical species. Additional, a desiccant (not shown) can be positioned inside the enclosure  150  to reduce moisture. 
     Although  FIG. 2  shows a single output window, multiple output windows can be used. For example, each beam of light  118 ,  119 ,  120  can exit the enclosure  150  via a respective output window. In some embodiments, it is desirable that as much as possible of the enclosure  150  comprise the thermally conductive material, to better achieve temperature uniformity. Accordingly, the output windows can be separated by thermally conductive material and can cover only as much area as necessary to allow light beams  118 ,  119 ,  120  to leave the enclosure  150 . However, in some embodiments, a single output window is easier and less expensive to construct. 
     The multi-laser system  100  can include a flow cell connector (not shown) that is mechanically and thermally coupled to the enclosure  150 , and the flow cell connector is configured to secure a flow cell  132  so that it intersects and maintains the alignment of the beams of light  118 ,  119 ,  120 . In some embodiments, the flow cell connector can permanently attach the flow cell  132  to the enclosure  150 . However, in some embodiments, the flow cell connector can allow the flow cell  132  to be removably attached to the enclosure  150 . In some embodiments, the flow cell connector can be compatible with multiple types and/or sizes of flow cells. For example, the flow cell connector can include a clip, a friction or pressure fit coupling, a threaded portion configured to receive a corresponding threaded portion of the flow cell  132 , or a variety of other connectors known in the art or yet to be devised. The flow cell  132  can be a capillary flow cell, and at least part of the flow cell can comprise a transparent material (e.g., fused silica or glass) that allows the light beams  118 ,  119 ,  120  to enter the flow cell  132  and interact with a sample fluid contained within the flow cell  132 . The flow cell  132  can be a thin hollow tube, forming a flow path that has a diameter of about 10 μm. Other flow cell types and/or sizes can be used, and the flow cell  132  can be oriented differently than as shown in  FIG. 1 . In some embodiments, the beams of light  118 ,  119 ,  120  strike the flow cell over areas centered about 110 μm to about 140 μm apart from each other, and in some embodiments, about 125 μm apart from each other. In some embodiments, the beams of light  118 ,  119 ,  120  strike the flow cell over areas centered about 100 μm to about 150 μm apart from each other. In some embodiments, the beams of light  118 ,  119 ,  120  strike the flow cell over areas centered about 100 μm to about 500 μm apart from each other. In some embodiments, the beams of light  118 ,  119 ,  120  strike the flow cell over areas centered up to about 500 μm apart from each other. In some embodiments, the thermal expansion coefficient of the thermally stable enclosure  150  matches the thermal expansion coefficient of the flow cell  132 . Matching of thermal expansion coefficients may help reduce overall stress on the flow cell. For some forms of optical measurements, it may be desirable for the different laser beams to be focused to different locations in the flow cell  132  at specific locations (e.g., areas spaced about 125 μm apart). 
       FIG. 2A  depicts another example embodiment of a multi-laser system in which the beam positioning/combining system comprises mirrors. As shown in  FIG. 2A , a beam positioning combiner system that employs mirrors mounted onto a frame may be used. In various embodiments, the frames on which the mirrors are mountable may be adjustable, e.g., translatable, tiltable, etc. In various embodiments, the wavelength selective mirrors have significantly different reflection or transmission properties at different wavelengths. Accordingly, the wavelength selective mirrors can separate or combine laser beams with different wavelengths. 
     Through the use of suitable optical coatings, wavelength selective mirrors will selectively reflect (or transmit) light of at least one wavelength and not light of at least one other wavelength. In other embodiments, the wavelength selective mirrors may comprise mirrors with selectivity for a different number of wavelengths. The example embodiment of  FIG. 2A  depicts a plurality of wavelength-selective mirrors. The mirrors can be used to separate or combine lasers with different wavelengths. Alternatively, non-wavelength selective mirrors that do not selectively reflect (or transmit) light of one laser and not light of another laser may be inserted in the path of the beam to redirect and/or alter the beam path or the beam. Other optical elements can also be inserted into the optical path. 
     The wavelength-selective mirrors  221 A,  221 B . . .  221 N are configured with highly reflective and anti-reflective coatings in accordance with the wavelengths of the plurality of laser beams  102 A,  102 B . . .  102 N. As shown in  FIG. 2A , wavelength selective mirror  221 A is configured to be highly reflective of the wavelength of the laser beams  102 B through  102 N and anti-reflective of the wavelength of laser beam  102 A; wavelength-selective mirror  221 B is configured to be highly reflective of the wavelength of the laser beam  102 B and anti-reflective of the wavelength of the laser beam  102 N; and wavelength selective mirror  221 N is configured to be highly reflective of the wavelength of the laser beam  102 N. Other configurations are possible. 
     In the multi-laser system  100  shown in  FIG. 2A , a plurality of optical paths are depicted. A first optical path originates at laser  101 A and is transmitted through wavelength selective mirror  221 A and transmitted toward the target object  1100 . A second optical path originates at laser  101 B, is then reflected at wavelength selective mirrors  221 B and  221 A, and transmitted toward the target object  1100 . An n-th optical path originates at laser  101 N, is then reflected at wavelength selective mirror  221 N, transmitted at wavelength selective mirror  221 B, reflected at wavelength selective mirror  221 A, and transmitted toward the target object  1100 . Propagating along these paths, laser beams  102 A- 102 N, which may have originally been far from one another, are repositioned to be closer together as beams  2001 A- 2001 N. 
     The mirrors may be configured to adjust the position of the plurality of laser beams to be at a certain distance of one another, for example in addition to the spacing adjustment that may be provided by placing the lasers at different heights within the enclosure. In some embodiments, the laser beams can be positioned to be coaxial, slightly offset but parallel to each other, or slightly offset but not parallel to each other. 
       FIG. 2B  depicts an embodiment of a triangular prism. The prism is a transparent optical element comprising a substantially transparent optical material. The prism has flat, polished surfaces that reflect and/or refract light. One or more of these surfaces may be coated with an optical coating such as an interference coating that is reflective and/or anti-reflective. In some embodiments the coating is wavelength selective. For example, the prism may be configured to be highly reflective for certain wavelengths (e.g., of a first laser), and highly anti-reflective for other wavelengths (e.g., of a second laser). The exact angles between the surfaces depend on the application. As shown, the triangular prism generally has a triangular base and rectangular sides. Prisms may be made out of glass, or any material that is transparent to the wavelengths for which they are designed. In some embodiments, the material may include one of polymer, polycarbonate, polyethylene terephthalate, glycol-modified polyethylene terephthalate, amorphous thermoplastic, and/or other substrates. Prisms can be used to reflect light, and to split light into components with different, e.g., wavelength, polarizations. As illustrated in  FIG. 2B , a triangular prism includes a glass surface configured to allow transmission of a laser beam of a given wavelength. The surface may be coated with a reflective coating to allow for the reflection of the laser beam of a different wavelength. In some embodiments, each of the wavelength selective mirrors illustrated in  FIGS. 2 and 2A  may be replaced with a triangular prism as the one illustrated in  FIG. 2B . Triangular prisms may also be used that reflect a plurality of wavelength, for example, using total internal reflection. Accordingly, the prisms may be used to redirect laser beams and not for wavelength selection in various cases. 
       FIG. 2C  depicts an embodiment of a rectangular prism. This rectangular prism comprises two triangular prisms contacted together. As illustrated in  FIG. 2C , a rectangular prism may be used to deflect a beam of light, for example, by 90 degrees, although other angles are also possible. As described above, in some embodiments, prisms employ total internal reflection at the surfaces rather than for dispersion. If light inside the prism hits one of the surfaces at a sufficiently steep angle (greater than the critical angle), total internal reflection occurs and all of the light is reflected. This makes a prism a useful substitute for a mirror in some situations. As described above, triangular prisms or prisms having other shapes can also be used for this purpose. In some embodiments, rectangular prisms can be wavelength selective. For example, the interface between the two triangular prisms or prism portions that make up the rectangular prism shown in  FIG. 2C  can include an optical coating such as an interference coating that is wavelength selective. In some embodiments, for example, the rectangular prism selectively reflects one laser wavelength and selectively transmits another wavelength. Accordingly, the rectangular prism may include one or more coatings that are highly reflective for one or more laser wavelength. The rectangular prism may include one or more coatings that are anti-reflective for one or more laser wavelength. In some embodiments, each of the wavelength selective mirrors illustrated in  FIGS. 2 and 2A  may be replaced with a rectangular prism such as the one illustrated in  FIG. 2C . Other arrangements and configurations are also possible. For example, a prism (e.g., a rectangular prism) may comprise two or more triangular or other shape prisms that are contacted together. 
       FIG. 2D  depicts an embodiment of the multi-laser system including a prism or prism bar beam positioning/combining system  1000 C. As shown in  FIG. 2D , a prism-based beam positioning combiner system is used to allow the lasers to be arranged in a row at one end of the temperature controlled enclosure. In some embodiments, the prism beam positioning/combining system may include optically contacted prisms having one or more surfaces coated to allow for the selective transmission or reflection of the laser beams. By proper selection of the surface coatings (such as for example wavelength selective reflective interference coatings), various lasers of different wavelength may be combined and output from the prism beam positioning/combining system. The prism beam positioning/combining system may also be configured and arranged with respect to the lasers and the respective laser beam paths such that the laser beams can be positioned such that they are, for example, closely spaced and/or parallel or co-linear on the output side of the prism-based beam positioning combiner system. In other embodiments, the prism beam positioning/combining system can be configured to position the beams in converging or diverging with respect to one another. 
     The prism illustrated in  FIG. 2D  may comprise a plurality of prisms or prism portions contacted or adhered together (e.g., using optical contact bonding, or optical adhesive at optical interfaces, and the like) to make a monolithic multi-prism beam combiner, or an aggregated prism. In some embodiments, a monolithic multi-prism may comprise 2, 3, 4, 5, or more prism portions. For example, a monolithic multi-prism may comprise N+1 or N+2 prism portions, where N is the number of lasers. In some embodiments, a monolithic multi-prism may comprise 1, 2, 3, 4, or more optical interfaces. For example, a monolithic prism may comprise N or N+1 optical interfaces, where N is the number of lasers. In various embodiments, one or more interface between the prism portions may be wavelength selective. For example, various of the prism portions may be configured to have one or more wavelength selective surfaces with one or more highly reflective and/or an anti-reflective (e.g., interference) coatings in accordance with the wavelengths of the plurality of laser beams  102 A- 102 N. As shown in  FIG. 2D , the wavelength selective internal surface  3001 A may be configured to be highly anti-reflective of the wavelength of the laser beam  102 A and highly reflective of the wavelengths of laser beams  102 B- 102 N. The wavelength selective internal surface  3001 B may be configured to be highly reflective of the wavelength of the laser beam  102 B. The wavelength selective surface internal surface  3001 N may be configured to be highly reflective of the wavelength of the laser beam  102 N. 
     In the embodiment shown in  FIG. 2D , various prisms are contacted together (e.g., using cement, adhesive (e.g., optical adhesive), optical contact bonding) to form a monolithic multi-prism beam combiner or an integrated or aggregated prism in the shape of a rectangular structure or bar having a rectangular base and rectangular sides. The different prisms that are contacted together may have different shapes. Some of the prisms, for example, may have a base in the shape of a parallelogram and rectangular sides. Some of the other prisms may have different shaped bases and rectangular sides. For example, at least one triangular prism is shown. Other shapes and configurations are also possible. 
     In the multi-laser system  100  shown in  FIG. 2D , a plurality of optical paths are depicted. A first optical path originates at laser  101 A, is transmitted through a prism portion to the internal surface  3001 A, and then is transmitted toward the target object  1100 . A second optical path originates at laser  101 B, then is reflected at internal surfaces  3001 A and  3001 B, and then is transmitted toward the target object  1100 . An n-th optical path originates at laser  101 N, is transmitted through internal surfaces  101 B through  101 N−1, then is reflected at internal surface  3001 A, and then is transmitted toward the target object  1100 . Propagating along these paths, laser beams  102 A- 102 N, which may have originally been far from one another, are repositioned to be closer together as beams  3201 A- 3201 N. 
     The prisms and interfaces therebetween within the prism-based beam positioning/combining system are configured to adjust the position of the plurality of laser beams to be at a certain distance from one another, in addition to the spacing adjustment that may be provided by placing the lasers at different heights within the enclosure. In some embodiments, the laser beams can be positioned to be coaxial, slightly offset but parallel to each other, or slightly offset but not parallel to each other. 
       FIG. 2E  depicts another embodiment of a prism beam positioning/combining system. As shown in  FIG. 2E , a prism-based beam positioning combiner system is used to allow the lasers to be spread out over the surface of the temperature controlled enclosure&#39;s base plate. The surfaces of the prisms may be coated to allow for the transmission or reflection of the laser beams. The prism illustrated in  FIG. 2E  may comprise a plurality of prisms or prism portions contacted or adhered together to make an aggregated prism or a monolithic multi-prism beam combiner. In various embodiments, one or more interface between the prism portions may be wavelength selective. For example, various of the prism portions may be configured to have one or more wavelength selective surfaces with one or more highly reflective and/or an anti-reflective (e.g., interference) coatings in accordance with the wavelengths of the plurality of laser beams  102 A- 102 N. As shown in  FIG. 2E , the wavelength selective internal surface  3601 A may be configured to be highly anti-reflective of the wavelength of the laser beam  102 A and highly reflective of the wavelength of laser beam  102 B. The wavelength selective internal surface  3601 B may be configured to be highly anti-reflective of the wavelength of the laser beams  102 A and  102 B and highly reflective of the wavelength of laser beam  102 C. The wavelength selective surface internal surface  3601 C may be configured to be highly anti-reflective of the wavelength of the laser beams  102 A,  102 B, and  102 C, and highly reflective of the wavelength of the laser beam  102 D. The wavelength selective surface internal surface  3601 N may be configured to be highly anti-reflective of the wavelength of the laser beams  102 A,  102 B,  102 C, through  102 N−1, and highly reflective of the wavelength of the laser beam  102 N. 
     In the embodiment shown in  FIG. 2E , various prisms are contacted together (e.g., using cement, adhesive (e.g., optical adhesive), optical contact bonding) to form an integrated or aggregated prism in the shape of a rectangular structure or bar having a rectangular base and rectangular sides, or a monolithic multi-prism beam combiner. The different prisms that are contacted together have different shapes. For example, different triangular prisms are shown. Some of the prisms, for example, may have a base in the shape of a right angle triangle and rectangular sides while other prisms may have a base in the shape of an equilateral triangle and have rectangular sides. Other shapes and configurations are also possible. 
     In the multi-laser system  100  shown in  FIG. 2E , a plurality of optical paths are depicted. A first optical path originates at laser  101 A, is transmitted through prism portions and internal surfaces  3601 A,  3601 B,  3601 C through  3601 N, and is transmitted toward the target object  1100 . A second optical path originates at laser  101 B, is then reflected at internal surface  3601 A, transmitted through prism portions and internal surfaces  3601 B,  3601 C through  3601 N, and toward the target object  1100 . A third optical path originates at laser  101 C, is then reflected at internal surface  3601 B, transmitted through prism portions and internal surfaces  3601 C through  3601 N, and toward the target object  1100 . A fourth optical path originates at laser  101 D, is reflected at internal surface  3601 C, transmitted through prism portions and internal surfaces  3601 D through  3601 N, and toward the target object  1100 . An n-th optical path originates at laser  101 N, is reflected at internal surface  3601 N, and transmitted toward the target object  1100 . Propagating along these paths, laser beams  102 A- 102 N, which may have originally been coming from different directions and far from one another, are repositioned to be closer together as beams  3701 A- 3701 N. As described herein, the laser beams  102 A- 102 N may also be repositioned to be parallel to each other as beams  3701 A- 3701 N. 
     An embodiment of a beam combiner can include an arrangement of optical elements, for example, one or more beam splitters and light directing elements. A beam splitter may divide the incident light into two paths, for example, one by transmission and another by reflection. Examples of beam splitters may be coated with a material that enables optical elements to reflect monochromatic light and transmit light of other wavelengths. In various embodiments of beam combiners, a beam combiner may include a wide range of aggregated prisms (or monolithic multi-prism beam combiners). For example, a plurality of prism portions contacted or coupled together. Aggregated prisms (or monolithic multi-prism beam combiners) may include optical coating for example at interfaces between prism portions or prisms that make up the aggregated prism. These optical coatings may be wavelength selective reflective coating or may be anti-reflective (AR) coatings. One example of such an aggregated prism comprising a plurality or prisms or prism portions contacted together is the X-prism. Other aggregated prisms, however, may also be used. 
     A multi-prism beam combiner may be more advantageous than beam combiners using separate dichroic mirrors mounted in individual flexure mounts, mounted using a glue-block approach, or all mounted in a common mount. In a multi-prism beam combiner, all of the reflective surfaces are tied together so that the number of opto-mechanical components that can contribute to the relative movement of the laser beams with respect to each other is greatly reduced thereby improving the system performance. Additionally, the reduced parts count and reduced complexity make for increased ease of manufacturing and should allow for a decrease in system size. Furthermore, the number of surfaces exposed to possible contamination is reduced. Also, the relatively large size of the prism combiner compared to an individual dichroic mirror reduces the impact that the coefficient of thermal expansion (CTE) mismatch between most adhesives, the optics and the metal used in the optical mounts has on beam position. 
       FIG. 3  depicts the front view of the multi-laser system  100  depicted in  FIG. 2 . As described above, in some embodiments, the thermally stable enclosure  250  is hermetically sealed. The hermetic sealing may be provided by o-rings  233 . Again, hermetically sealing can reduce particles and contamination from outside the enclosure. Moreover, as described above, a hermetic seal may also reduce or prevent the flow of air currents and thus prevent or reduce the flow of ambient temperature changes into the enclosure. This in turn may reduce temperature instability within the enclosure. In some embodiments, the top of enclosure  250  may be thermally coupled, possibly with a copper braid, to the main body of the enclosure  250  to reduce thermal effects. 
     As shown in  FIG. 3 , the multi-laser system may further comprise a temperature controller  252 . In some embodiments, the temperature controller  252  may comprise a thermo electric cooler (TEC), a temperature sensor and control electronics. The TEC may pump heat from one side to the other depending on the direction of current flow through the TEC. The direction of current flow may be determined by the control electronics. In some embodiments, for example, if the ambient temperature were higher than the enclosure  250 &#39;s set point temperature then the control electronics may direct current flow through the TEC so that heat was pumped out of the enclosure  250  thereby helping maintain the enclosure&#39;s set point temperature. In other embodiments, if the ambient temperature were lower than the enclosure  250 &#39;s set point temperature, then the control electronics may reverse the current flow through the TEC so that heat was pumped into the enclosure  250  again helping maintain the enclosure&#39;s set point temperature. A temperature controller  252  can be thermally coupled to the thermally stable enclosure  250 . The temperature controller  252  can include a temperature sensor (not shown) to measure the temperature of the thermally stable enclosure  250 , and to provide feedback to the control electronics. In some embodiments, the temperature sensor may comprise a thermistor. The temperature controller  252  may remove heat from or add heat to the thermally stable enclosure  250  in order to maintain a substantially constant temperature in the thermally stable enclosure  250 . The high thermal conductivity of the material of the enclosure  250  helps the temperature controller to relatively quickly adjust the temperature within the enclosure  250  in response to temperature variations outside of the enclosure  250  and also reduce the presence of temperature variations across the enclosure  250 . 
     As shown in  FIG. 3 , the multi-laser system may also comprise a baseplate  260 . The baseplate  260  may act as a thermal heat sink for the temperature controller  252 . 
     In some embodiments, the temperature within the thermally stable enclosure  250  can be held stable to within ±1° C., ±2° C., ±3° C., ±5° C., etc., for example, of a target temperature. In some embodiments, the temperatures of the wavelength selective mirrors and the focusing optics can be held to be within ±1° C., ±2° C., ±3° C., ±5° C., etc. of one another. In some embodiments, the temperature over a substantial portion of the enclosure can be held to be within ±1° C., ±2° C., ±3° C., ±5° C., etc. In some embodiments, the temperature over the entire enclosure can be held to be within ±1° C., ±2° C., ±3° C., ±5° C., etc., for example, of a target temperature. In some embodiments, the temperature within the enclosure can be held to be within ±1° C., ±2° C., ±3° C., ±5° C., etc., for example, of a target temperature. In some embodiments, the temperature within the thermally stable enclosure  250  can be held within ±1° C. of the target temperature. In some embodiments, the target temperature can be between 10° C. and 50° C. In some embodiments, the target temperature can be between about 15° C. and about 45° C. In other embodiments, the target temperature can be between about 15° C. and about 35° C. In other embodiments, the target temperature can be between about 10° C. and about 40° C. The temperature controller  252  also maintains the focused laser beams aligned with respect to the flow cell over a wide range of ambient temperatures. In some embodiments, the range of ambient temperatures can be between about 10° C. and about 55° C. In some embodiments, the range of ambient temperatures can be between about 10° C. and about 50° C. In some embodiments, the range of ambient temperatures can be between about 15° C. and about 45° C. In other embodiments, the range of ambient temperatures can be between about 15° C. and about 35° C. In other embodiments, the range of ambient temperatures can be between about 10° C. and about 40° C. 
       FIG. 3  also depicts that the three lasers  201 ,  202 , and  203  may be placed at different heights within the enclosure  250 . The placement at different heights may assist in positioning the focused laser beams at a desired spacing from one another at the flow cell. By disposing the lasers at different heights, the focused beams at the flow cell may be separated by between about 110 μm and about 140 μm of one another. In some embodiments, the focused beams may be separated by between about 100 μm to about 150 μm of one another. In some embodiments, the focused beams may be separated by between about 100 μm to about 500 μm of one another. In some embodiments, the focused beams may be separated by up to about 500 μm of one another. The wavelength selective mirrors, however, can additionally be adjusted to account for the imperfection in laser positions that may result, for example, from manufacturing tolerances. Accordingly, the wavelength selective mirrors may establish better positioning of the beams directed onto the flow cell. 
       FIG. 4  depicts the side view of the multi-laser system  100  depicted in  FIG. 2 .  FIG. 4  also shows the placement of the lasers at different heights. The thermally stable enclosure  350  comprises wavelength selective mirrors  310 ,  311 ,  312 ,  313  that are configured to adjust the position of the plurality of laser beams  314 ,  315 ,  316  to be at a certain distance of one another, in addition to the spacing adjustment that may be provided by placing the lasers at different heights within the enclosure  350 . In some embodiments, the laser beams can be positioned to be coaxial, slightly offset but parallel to each other, or slightly offset but not parallel to each other. In some embodiments, the plurality of focused laser beams  318 ,  319 ,  320  may be separated by about 110 μm and about 140 μm of one another. In some embodiments, the plurality of focused laser beams  318 ,  319 ,  320  may be separated by about 100 μm and about 150 μm of one another. In some embodiments, the plurality of focused laser beams  318 ,  319 ,  320  may be separated by about 100 μm and about 500 μm of one another. In some embodiments, the plurality of focused laser beams  318 ,  319 ,  320  may be separated by up to about 500 μm of one another. In some embodiments, the plurality of focused laser beams  318 ,  319 ,  320  may be positioned to be at a distance of about 125 μm of one another. 
     As can be seen in  FIG. 4 , the thermally stable enclosure  350  comprises a top, a bottom, and four sides. In some embodiments, the thermally stable enclosure  350  has a width of about 3 inches or less, a length of about 6 inches or less, and/or a height of about 2 inches or less. In other embodiments, the length, the width, and the height of the thermally stable enclosure  350  may be relatively larger or smaller. In some embodiments, the thermally stable enclosure  350  has a width of about 6 inches or less, a length of about 12 inches or less, and/or a height of about 3 inches or less. In some embodiments, the thermally stable enclosure  350  has a volume of 36 cubic inches (in 3 ) or less. With a relatively small volume, the temperature controller is better able to adjust the temperature of the enclosure and system in response to variations in ambient temperature. The temperature controller is thus able to avoid temporal variations in temperature induced by fluctuation in ambient conditions. The relatively small volume may reduce temperature instabilities within the enclosure  350  by reducing temperature gradients across the enclosure  350 . In other embodiments, the volume of the thermally stable enclosure  350  may be relatively larger or smaller. Also shown in  FIG. 4  is the flow cell connection  330 , described above. 
       FIG. 5  depicts an example embodiment of a multi-laser system further including an optional plurality of beam adjusters  504 A- 504 N. In various embodiments, the boresight and centration errors of the n laser beams and/or the angular and lateral positioning errors of the opto-mechanical components may be compensated for by using the separate beam position adjusters  504 A- 504 N. The adjusted laser beams may then be positioned and/or combined into a desired spatial arrangement by the beam positioning/combining system that a specific application requires. 
       FIG. 6  depicts the embodiment of the multi-laser system of  FIG. 5  further including optional focusing or beam shaping optics  117 . As described in relation to  FIG. 2  above, beam focusing optics or beam shaping optics may be used to provide size reduction and/or shaping to the output laser beams. For example, the focusing/beam shaping optics may focus a laser beam down to a smaller spot. The focusing/beam shaping optics may also be used to change the shape of the laser beams. 
     The output laser beams depicted in  FIG. 6  may have respective spot sizes of between about 55 μm and about 110 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have respective spot sizes of between about 70 μm and about 110 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have respective spot sizes of between about 50 μm and about 150 μm in one direction and between about 5 μm and about 20 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have spot sizes of between about 55 μm and about 100 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have spot sizes of between about 70 μm and about 100 μm in one direction and between about 5 μm and about 15 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the laser beams may have respective spot sizes of between about 50 μm and about 150 μm in one direction and between about 5 μm and about 20 μm in another direction (e.g., perpendicular to the one direction). In some embodiments, the output laser beams  118 ,  119 ,  120  may have respective spot sizes of about 80 μm in one direction and about 10 μm in another direction (e.g., perpendicular to the one direction). In other embodiments, the output laser beams  118 ,  119 ,  120  may have respective spot sizes of about 100 μm in one direction and about 10 μm in another direction (e.g., perpendicular to the one direction). These may correspond to major and minor axes of an ellipse for a beam with an elliptical cross-section and spot shape. Other sizes and shapes are possible for the light beams. 
       FIG. 7  depicts an example embodiment of a multi-laser system in which the beam adjusters  504 A- 504 N comprise Risley prism pairs  705 A- 705 N. In other embodiments, other systems may be used as the separate beam position adjusters  504 A- 504 N. In various embodiments, the laser boresight and opto-mechanical angular errors may be compensated for by rotating the Risley prisms while the laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the Risley prism assembly pitch, yaw, and/or separation between the individual prisms (e.g., by adjusting one or both of the individual prisms). The aligned laser beams may then be positioned or combined into a desired spatial arrangement that a specific application requires by the beam positioning/combining system. 
       FIG. 7  depicts a Risley prism pair used with each laser beam. In other embodiments, a different number of Risley prisms may be used. Other optical elements can also be inserted into the optical path. 
     In various embodiments, Risley prisms comprising wedged optics, usually used in pairs, to redirect optical beams are used. In various embodiments, an incoming light beam enters a Risley prism pair, experiences refraction and redirection under Snell&#39;s Law, and exits the Risley prism pair. In some configuration of the Risley prisms, there is just a translation of the output beam with respect to the input beam. If the arrangement of the Risley prisms with respect to each other is changes, the output beam may experience an elevation deviation. The ability to control azimuth may be provided by rotating the prism pair together. Therefore, the Risley prism pair can be used to direct a light beam at a variety of elevation angles and azimuthal angles. 
     The Risley prism pairs  705 A- 705 N wedge angles and the azimuthal rotation between the prisms are determined in accordance with the respective laser beam  102 A- 102 N. As shown in  FIG. 6 , Risley prism pair  705 A is configured to adjust the laser beam  102 A, Risley prism pair  705 B is configured to adjust the laser beam  102 B, and Risley prism pair  705 N is configured to adjust the laser beam  102 N. 
     In the multi-laser system  100  shown in  FIG. 7 , a plurality of optical paths are depicted. A first optical path originates at laser  101 A, passes through the Risley prism pair  705 A, where laser boresight, centration and opto-mechanical angular and lateral positioning errors may be compensated through adjustment of the wedge angles of and the azimuthal rotation between the prism pair  705 A, and then arrives at the beam combining/positioning system  1000 . A second optical path originates at laser  101 B, passes through the Risley prism pair  705 B, where laser boresight, centration and opto-mechanical angular and lateral positioning errors may be compensated through adjustment of the wedge angles of and the azimuthal rotation between the prism pair  705 B, and then arrives at the beam combining/positioning system  1000 . An N-th optical path originates at laser  101 N, passes through the Risley prism pair  705 N, where laser boresight, centration and opto-mechanical angular and lateral positioning errors may be compensated through adjustment of the wedge angles of and the azimuthal rotation between the prism pair  705 N, and then arrives at the beam combining/positioning system  1000 . 
     Propagating along these paths, laser beams  102 A- 102 N, which may have originally been far from one another, are repositioned to be closer together as beams  1001 A- 1001 N. In some embodiments, the beams  1001 A- 1001 N are parallel to one another. In other embodiments, the beams  1001 A- 1001 N are not parallel to one another. Other optical components (e.g., lenses, prisms, polarization rotators, waveplates, etc.) can be included to alter the laser beams and/or optical paths. 
       FIGS. 8A-8B  depict example embodiments of a multi-laser system in which the beam adjusters comprise Risley prisms and plane parallel plates. In the embodiment of  FIG. 8A , a combination of Risley prism pairs  705 A- 705 N and glass etalon plates  707 A- 707 N are used for the separate beam position adjusters  504 A- 504 N illustrated in  FIG. 5 . In other embodiments, the etalon plates may be comprised of material other than glass. In some embodiments, the plane parallel plates may be made out of glass, or any material that is transparent to the wavelengths for which they are designed. In some embodiments, the material may include one of polymer, polycarbonate, polyethylene terephthalate, glycol-modified polyethylene terephthalate, amorphous thermoplastic, and/or other substrates. The etalon plates comprise plane parallel plates. Other optical elements may however be used in different embodiments. Adjustment of the beams may be provided for by using the combination of Risley prism pairs as described in relation to  FIG. 7  above, and glass etalon plates  707 A- 707 N. In the embodiment of  FIG. 8A , a single glass etalon plate may be used for providing correction to lateral positioning errors in both x and y planes. In the embodiment of  FIG. 8B , a separate glass etalon plate is used for correcting later positioning errors in each (e.g., by being tiltable along one axis) of the x and y planes or in both (e.g., by being tiltable along multiple axes) of the x and y planes. 
     In various embodiments, the laser boresight and opto-mechanical angular errors may be compensated for by rotating the prisms while the laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the pitch and/or yaw of the parallel optical plate. The aligned laser beams may then be positioned or combined into a desired spatial arrangement by the beam positioning/combining system that a specific application requires. 
     In the multi-laser system  100  shown in  FIG. 8A , a plurality of optical paths are depicted. A first optical path originates at laser  101 A, passes through the Risley prism pair  705 A, where laser boresight and opto-mechanical angular errors may be compensated through adjustment of the wedge angles of the prism pair  705 A, passes through the glass etalon plate  707 A, where laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the pitch and/or yaw of the glass etalon plate  707 A, and then arrives at the beam combining/positioning system  1000 . A second optical path originates at laser  101 B, passes through the Risley prism pair  705 B, where laser boresight and opto-mechanical angular errors may be compensated through adjustment of the wedge angles of the prism pair  705 B, passes through the glass etalon plate  707 B, where laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the pitch and/or yaw of the glass etalon plate  707 B, and then arrives at the beam combining/positioning system  1000 . An N-th optical path originates at laser  101 N, passes through the Risley prism pair  705 N, where laser boresight, and opto-mechanical angular errors may be compensated through adjustment of the wedge angles of the prism pair  705 N, passes through the glass etalon plate  707 N, where laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the pitch and/or yaw of the glass etalon plate  707 N, and then arrives at the beam combining/positioning system  1000 . 
     In the multi-laser system  100  shown in  FIG. 8B , a plurality of optical paths are depicted. A first optical path originates at laser  101 A, passes through the Risley prism pair  705 A, where laser boresight and opto-mechanical angular errors may be compensated through adjustment of the wedge angles of the prism pair  705 A, passes through glass etalon plates  707 A,  708 A, where laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the pitch and/or yaw of the glass etalon plates  707 A and/or  708 A, and then arrives at the beam combining/positioning system  1000 . A second optical path originates at laser  101 B, passes through the Risley prism pair  705 B, where laser boresight and opto-mechanical angular errors may be compensated through adjustment of the wedge angles of the prism pair  705 B, passes through glass etalon plates  707 B,  708 B, where laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the pitch and/or yaw of the glass etalon plates  707 B and/or  708 B, and then arrives at the beam combining/positioning system  1000 . An N-th optical path originates at laser  101 N, passes through the Risley prism pair  705 N, where laser boresight, and opto-mechanical angular errors may be compensated through adjustment of the wedge angles of the prism pair  705 N, passes through glass etalon plates  707 N,  708 N, where laser centration and opto-mechanical lateral positioning errors may be compensated for by adjusting the pitch and/or yaw of the glass etalon plates  707 N and/or  708 N, and then arrives at the beam combining/positioning system  1000 . 
     Propagating along these paths, laser beams  102 A- 102 N, which may have originally been far from one another, are repositioned to be closer together as beams  1001 A- 1001 N. In some embodiments, the beams  1001 A- 1001 N are parallel to one another. In other embodiments, the beams  1001 A- 1001 N are not parallel to one another. Other optical components (e.g., lenses, prisms, polarization rotators, waveplates, etc.) can be included to alter the laser beams and/or optical paths. 
       FIG. 9  depicts an example embodiment of a multi-laser system in which the target object  1100  comprises an optical fiber or waveguide. An optional lens  902  may be used to couple the beams into the optical fiber  900 . As shown in  FIG. 9 , the n laser beams may be combined, for example, by one of the embodiments for beam positioning and combining described above, or any combination of the embodiments described above and coupled into an optical fiber or waveguide. Both the coupling optics and fiber or waveguide may be located inside the temperature controlled enclosure and hard-mounted to the enclosure&#39;s temperature controlled base plate  901 . 
       FIG. 10  depicts an example embodiment of a multi-laser system in which the target object  1100  comprises an adjuster mount  1010 . This adjuster mount may be configured to receive an optical fiber  900 . Fiber optic coupling mounts are commercially available. In various embodiments, the fiber optic coupling mounts may comprise coupling optics mounted one focal length away from the optical fiber input with the optical axis of the coupling optics co-linear with a beam that would be emitted from the optical fiber. The coupling optics and optical fiber are mounted in a metal housing (e.g., a cylindrical housing) so that the alignment between the coupling optics and optical fiber input is maintained. This component may be a coupler/collimator assembly. In some embodiments, the mounts may comprise coupling optics and fiber in a metal housing. The coupler/collimator assembly is inserted into a positioning mount which is attached to the temperature controlled enclosure. For polarization maintaining fibers the coupler/collimator assembly and positioning mounts may be keyed so as to provide registration between the polarization axis of the laser beams and the polarization axis of the optical fiber. The positioning mount may be made of metal. The mount has mechanical adjusters that allow the pitch, yaw and lateral position of the coupler/collimator assembly to be moved relative to the input laser beams to optimize the amount of light coupled into the optical fiber. As shown in  FIG. 10 , the n laser beams may be combined, for example, by one of the embodiments for beam positioning and combining described above, or any combination of the embodiments described above and coupled into the adjustor mount or an optical element such as an optical fiber coupled to the adjuster mount. The optical fiber, coupling optics and coupling optimization hardware may be mounted at least partially on the outside of the temperature controlled enclosure. 
       FIGS. 11A-11N  depict example types and spatial arrangements of laser beams in multi-laser systems. The specific desired type and spatial arrangement of the laser beams may be application specific. The laser beams themselves may be collimated or focused. In some applications, however, it may be desirable to focus the laser beam in order to create small spot sizes at the target object and, hence, to increase power density or brightness on the target object. Accordingly, laser beams that are collimated or focused beams may be used. A plurality of collimated or a plurality of focused beams may be substantially co-linear to one another at the target object. The plurality of beams may alternatively be substantially parallel to one another but spaced apart from each other, or converging towards each other, or diverging away from one another at the target object. In some embodiments, the plurality of parallel beams may have identical beam separations (such as a substantially constant separation d 0 ) at the target object, or different beam separations (such as separations d 1 , d 2 , . . . ) at the target object. In some embodiments, the plurality of converging or diverging beams may have identical angular separations (such as a substantially constant separation θ 0 ) at the target object, or different angular separations (such as separations θ 1 , θ 2 , . . . ) at the target object. In some embodiments, the angular separation may be less than about 5°. 
     Some examples of spatial arrangements of laser beams are depicted in  FIGS. 11A-11N . While these examples illustrate spatial arrangements of two or three laser beams, arrangements with more than two or three laser beams are also contemplated, having similar characteristics of the illustrated arrangements. In a first example,  FIG. 11A  depicts an example of parallel, or nearly parallel, collimated beams with identical, or nearly identical, beam separations, d 0 . As used herein, the term “identical” is generally used to indicate that two things (e.g., a distance, angle, and the like) are within 3% of the measured characteristic of each other, unless the context of use of the term indicates otherwise. As used herein, the term “nearly identical” is generally used to indicate that two things (e.g., a distance, angle, and the like) are the within 10% of the measured characteristic of each other, unless the context of use of the term indicates otherwise.  FIG. 11B  depicts an example of parallel collimated beams with different beam separations, d 1  and d 2 .  FIG. 11C  depicts an example of converging collimated beams with identical angular separations, θ 0 .  FIG. 11D  depicts an example of converging collimated beams with different angular separations, θ 1  and θ 2 .  FIG. 11E  depicts an example of diverging collimated beams with identical angular separations, θ 0 .  FIG. 11F  depicts an example of diverging collimated beams with different angular separations, θ 1  and θ 2 .  FIG. 11G  depicts an example of co-linear collimated beams.  FIG. 11H  depicts an example of parallel focused beams with identical beam separations, d 0 .  FIG. 11I  depicts an example of parallel focused beams with different beam separations, d 1  and d 2 .  FIG. 11J  depicts an example of converging focused beams with identical angular separations, θ 0 .  FIG. 11K  depicts an example of converging focused beams with different angular separations, θ 1  and θ 2 .  FIG. 11L  depicts an example of diverging focused beams with identical angular separations, θ 0 .  FIG. 11M  depicts an example of diverging focused beams with different angular separations, θ 1  and θ 2 .  FIG. 11N  depicts an example of co-linear focused beams. 
       FIG. 12  schematically shows an optical system  5100  that can be used to direct light to a sample for performing optical measurements such as laser-induced fluorescence and spectroscopic analysis. The optical system  5100  can include a housing  5102  enclosing an interior chamber  5104 . The housing  5102  can be made of a thermally conductive material. The thermally conductive material can have a thermal conductivity between about 50 W/(m-K) and about 2000 W/(m-K). For example, the thermally conductive material may be copper which has a thermal conductivity of about 380 W/(m-K). A variety of thermally conductive metals can be used (e.g., copper or aluminum), as well as thermally conductive non-metals (e.g., ceramics or epoxy). The thermally conductive material can be used to form the entire housing, or merely a portion thereof. For example, substantially thermally conductive material can be used to form the top, the bottom, or any number of the sides of the housing  5102 , or any combination thereof. In some embodiments, a majority of the housing  5102  is made of the substantially thermally conductive material. In some embodiments, only a relatively small portion of the housing  5102  is made of the substantially thermally conductive material. In some embodiments, a substantial portion of the housing  5102  is made of the substantially thermally conductive material. In some embodiments, multiple substantially thermally conductive materials can be used, with some areas of the housing  5102  being more thermally conductive than others. 
     In some of the embodiments discussed above, the housing is hermetically sealed from the ambient air. Thus, the interior chamber  5104  is isolated from air currents which can cause temperature variation, and the internal optical elements are protected from external contaminants. In some embodiments a getter (not shown) is located inside interior chamber  5104  which can reduce contaminant particles or chemical species. Additional, a desiccant (not shown) can be positioned inside the interior chamber  5104  to reduce moisture. 
     A thermoelectric controller  5106  can be thermally coupled to the housing  5102 . The thermoelectric controller  5106  can include one or more temperature sensors (not shown) (e.g., thermistors) to measure the temperature of the housing  5102  and/or the temperature of the interior chamber  5104 , and a heat transfer system (not shown) for removing heat from or adding heat to the housing  5102  in order to maintain a substantially constant temperature in the housing or in the interior chamber. In some embodiments, the thermoelectric controller  5106  can include a cooler for removing heat (e.g., heat resulting from operation of the optical system). In some embodiments, the thermoelectric controller  106  can include a heater for heating the housing  5102  and internal chamber  5104 . In some embodiments, the heater can be used to maintain the internal chamber  5104  at a temperature above the anticipated highest ambient temperature. In some embodiments, the thermoelectric controller  5106  can include a thermoelectric cooler (TEC). The heat transfer system can be coupled directly to the housing  5102  and to the cooler and/or heater (e.g. TEC). In some embodiments, the temperature can be held within held within ±1° C., ±2° C., ±3° C., ±5° C., etc. of the target temperature. In some embodiments, the temperature of the interior chamber  5104  is between 15° C. and 45° C. 
     In some embodiments, the housing is compact. For example, the housing may be a size of less than 10 cubic inches. The relatively small size of the volume allows for rapid adjustment of temperature in response to variations in the ambient temperature and thus more precise control of the temperature in the internal chamber  5104 . 
     The optical system  5100  can include a number of optical input ports  5108 A- 5108 D. Although the embodiment shown in  FIG. 12  includes four optical input ports, a different number of optical input ports can be used. In some embodiments, the optical input ports  5108 A- 5108 D can be secured and hermetically sealed into respective apertures formed in the housing  5102 , and can engage optical fibers  5110 A- 5110 D. A variety of fiber connectors can be used, such as screw-type optical fiber connectors (e.g., an FC connector), snap-type fiber connectors, or other fiber connectors known in the art or yet to be devised. In some embodiments, the optical input ports  5108 A- 5108 D include an angle-polished fiber connector (e.g., an FC/APC connector). In some embodiments, at least a portion of the optical input ports  5108 A- 5108 D, such as the threading of a screw-type connector, can be integrally formed as part of the housing  5102 . The optical fibers  5110 A- 5110 D include fiber connectors (not shown) configured to securely and precisely mate with the optical input ports  5108 A- 5108 D so that light can be efficiently transferred from the optical fibers  5110 A- 5110 D to a plurality of optical fibers  5114 A- 5114 D within the internal chamber  5104 . In some embodiments, the optical fibers  5110 A- 5110 D are single mode optical fibers. Highly polarized light can be injected into the optical fibers  5110 A- 5110 D (e.g., from a diode laser), and in some applications it can be advantageous to preserve the polarization of the light. Accordingly, polarization-maintaining optical fibers can be used. In some embodiments different types of optical fibers can be connected to different optical input ports  5108 A- 5108 D Likewise, in some embodiments, the different optical input ports  5108 A- 5108 D can comprise different types of optical connectors. 
     The optical fibers  5110 A- 5110 D can be coupled to laser light sources  5112 A- 5112 D. Although the embodiment shown in  FIG. 12  includes four lasers, a different number of lasers can be used. The lasers  5112 A- 5112 D can include a variety of different laser types and can provide light of variety of different wavelengths. The optical system  5100  shown in  FIG. 12  includes a 405 nm laser, a 488 nm laser, a 561 nm laser, and a 640 nm laser, but other common wavelengths of laser light can be used (e.g., light having a wavelength of 440 nm, 635 nm, or 375 nm). The lasers  5112 A- 5112 D can be diode lasers, diode-pumped solid state lasers, frequency doubled lasers, or other laser types that produce light useful for example in laser-induced fluorescence and spectroscopic analysis. Although  FIG. 12  shows the lasers  5112 A- 5112 D connected to the optical input ports  5108 A- 5108 D via the optical fibers  5110 A- 5110 D, in some embodiments the optical fibers  5110 A- 5110 D and the lasers  5112 A- 5112 D can be disconnected from the optical input ports  5108 A- 5108 D by the user so that other lasers can be interchangeably connected to the optical system  5100 . Thus, the optical system  5100  is a versatile tool which a user can easily modify to utilize a wide variety of lasers without difficult and time consuming adjustments. 
     The optical system  5100  can include a plurality of optical fibers  5114 A- 5114 D contained within the internal chamber  5104 . The optical fibers  5114 A- 5114 D can be optically coupled to the optical input ports  5108 A- 5108 D so that they receive light from the optical input ports  5108 A- 5108 D and direct the light into the internal chamber  5104 . In some embodiments, the cores of the optical fibers  5114 A- 5114 D can be exposed by optical input ports  5108 A- 5108 D so that the cores of the optical fibers  5110 A- 5110 D can contact the cores of the optical fibers  5114 A- 5114 D directly or come in substantial proximity to the cores of optical fibers  5114 A- 5114 D. As with the optical fibers  5110 A- 5110 D discussed above, the optical fibers  5114 A- 5114 D can be single mode optical fibers and can be polarization-maintaining optical fibers. 
     In some embodiments, the optical system can include a fiber support structure  5116  that is configured to change the pitch of the optical fibers  5114 A- 5114 D, bringing the output ends closer together than the input ends. For example, the optical input ports  5108 A- 5108 D can be spaced about 10 to 20 millimeters or more apart from each other, so that the user can conveniently connect and disconnect optical fibers. The input ends of the optical fibers  5114 A- 5114 D, which are coupled to the optical input ports  5108 A- 5108 D, can be similarly distributed for example about 10 to 20 millimeters or more apart. The fiber support structure  5116  can have grooves (e.g., V-grooves) defining generally converging pathways, and the optical fibers  5114 A- 5114 D can be secured in the grooves by a top-plate positioned over the grooves or by an adhesive. In some embodiments, the V-grooves can be configured to precisely hold the fibers. In some embodiments, silicon V-grooves manufactured using silicon processing techniques (e.g., etching, photoresists, etc.) can be used to secure the optical fibers  5114 A- 5114 D. Grooves, holes, or slots for supporting the optical fibers  5114 A- 5114 D may be formed in a support material (e.g., aluminum) by a machining process, such as electrical discharge machining (EDM). The fiber support structure  5116  can be configured to bring the optical fibers  5114 A- 5114 D closer together so that when the light is output from the optical fibers  5114 A- 5114 D the light is emitted from nearby locations (e.g., about 110 to 140 microns apart, and more specifically, about 125 microns apart, although other distances are possible). 
       FIG. 13  is a cross-sectional view (shown from the position indicated by line  2 - 2  in  FIG. 12 ) of an embodiment of optical fibers  5214 A- 5214 D. As shown in  FIG. 13 , the optical fibers  5214 A- 5214 D can be single mode optical fibers that have output ends measuring about 125 microns in total diameter, with the core measuring about 3-4 microns in diameter. Other sizes can be used. In the embodiment shown in  FIG. 13 , the output ends of the optical fibers  5214 A- 5214 D are brought close together so that the cladding of one optical fiber is adjacent to the cladding of the next optical fiber, and light is emitted by the cores of optical fibers  5214 A- 5214 D at locations which have centers positioned about 125 microns apart. Other arrangements are possible. It should be noted that the drawings herein are not drawn to scale (unless otherwise indicated), and in some embodiments the tapering of the optical fibers provided by the fiber support structure  5116  can be much more pronounced than is indicated in  FIG. 12 . 
     In some embodiments, the fiber support structure  5116  does not bring the optical fibers  5114 A- 5114 D significantly closer together, but merely orients the optical fibers  5114 A- 5114 D so that light is emitted in a direction that causes the light to contact the optical elements  5118 A- 5118 D at a suitable angle. Other variations are possible. 
     Although the embodiment illustrated by  FIG. 12  includes optical fibers  5114 A- 5114 D, other types of waveguides can be used (e.g., planar waveguides). In some embodiments, the waveguides can be rigid waveguides. The waveguides can include curved and/or linear paths. The waveguides can include a taper to otherwise have an output end with outputs closer together than inputs at an input end, similar to the embodiment shown in  FIG. 12 . In some embodiments, an integrated waveguide chip is used. 
     Although the embodiment illustrated in  FIG. 12  shows the optical fibers  5110 A- 5110 D and the optical fibers  5114 A- 5114 D as being different sets of optical fibers, in some embodiments, the optical system can include a single set of optical fibers that extend through the housing and couple to the laser light sources. In these embodiments, the optical input ports  5108 A- 5108 D can be apertures in the housing  5102  through which the optical fibers can pass. In some embodiments, the apertures can include seals formed around the optical fibers to hermetically seal the interior chamber. Epoxy may be used to provide such a hermetic seal, although other approaches can be used. The optical fibers can include optical connectors (e.g., FC/APC connectors) configured to removably couple with the laser light sources  5112 A- 5112 D. 
     The optical fibers  5114 A- 5114 D (or waveguides) emit light toward a plurality of optical elements  5118 A- 5118 D, which convert the light into beams of light  5120 A- 5120 D having a suitable shape and/or size. The optical elements  5118 A- 5118 D can be lenses, and can be separate individual lenses, or they can be conjoined forming a lens array. In some embodiments, optical elements  5118 A- 5118 D can be compact microlenses. In some embodiments, a single lens can be used to produce each of the light beams  5120 A- 5120 D. In some applications, it can be advantageous to produce elongated beams of light, such as beams of light having a generally elliptical cross-sectional shape (shown schematically in  FIG. 12 ). For example, the beams of light  5120 A- 5120 D can have a generally Gaussian profile, so that when illuminating a flow cell, the intensity of the light illuminating the center of the flow cell is significantly greater than the intensity of the light illuminating the peripheral edges of the flow cell. Accordingly, the beams of light  5120 A- 5120 D can be elongated (e.g., elliptical) beams, so that the relatively high intensity center regions of the light beams extend across the entire width of the flow cell, while the relatively low intensity outer regions of the light beams do not strike the flow cell. By using an elongated (e.g., elliptical) beam of light, a more uniform lateral distribution of light across the narrow width of the flow cell can be achieved while illuminating a relatively small longitudinal area along the length of the flow cell and maintaining high light intensity. In some embodiments, the elliptical light beams can have a substantially elliptical cross sectional shape that measure about 5 to 15 microns in one direction and 55 to 100 microns in the other direction, or more specifically about 10 microns in one direction and about 70 microns in the other direction. Light beams of other shapes and sizes can be used. To produce elongated (e.g., elliptical) beams of light  5120 A- 5120 D, optical elements  5118 A- 5118 D can be anamorphic lenses (e.g., cylindrical lenses) or Powell lenses (Gaussian to flat-top transformers). In one embodiment, optical elements  5118 A- 5118 D can be an anamorphic microlens array. In some embodiments, the optical elements  5118 A- 5118 D can be achromatic lenses. In some embodiments, optical elements  5118 A- 5118 D can be refractive and/or diffractive optical elements used to produce the elongated beams of light  5120 A- 5120 D. In some embodiments, the optical elements  5118 A- 5119 D can be located adjacent to the output ends of the optical fibers  5114 A- 5114 D. 
     The optical system  5100  can include an output window  5121  that allows the beams of light  5120 A- 5120 D to exit the internal chamber  5104 . In some embodiments, the housing  5102  includes an aperture  5122  in a wall thereof and the output window  5121  comprises a transparent window pane  5124 , positioned over the aperture  5122 . The window pane  5124  can be made from glass or acrylic or a variety of other transparent materials (e.g., plastic). The aperture  5122  and window pane  5124  can assume a variety of shapes, but in some embodiments they are circular or elliptical. The window  5121  can be attached to the housing  5102  by a plurality of fasteners such as bolts  5126 . In  FIG. 12 , only two bolts  5126  are shown in the cross-sectional view, but in some embodiments, additional bolts can be positioned along the edges of the window  5121 . In some embodiments, the window  5121  can include a flange  5123  for mounting the window. The flange  5123  may have a plurality of through holes through which fasteners (e.g., bolts  5126 ) can pass to secure the window  5121  to the housing  5102 . A seal  5128  (e.g., an O-ring) can be positioned between the housing  5102  and the window  5121  (e.g., the flange  5123 ). The bolts  5126  can be tightened, causing the O-ring  5128  to be compressed between the housing  5102  and the window  5121 . In some embodiments, the O-ring  5128  produces a hermetic seal. Other approaches can be used to fasten the window  5121  to the housing  5102 . For example, the window  5121  can be disposed in recess on the outer or inner surface of the housing  5102 , or can be embedded into the housing  5102 , or can be mounted onto the inside of the housing  5102 . The window  5121  can be secured to the housing  5102  by an adhesive, epoxy, or cement. 
     Although the embodiment shown in  FIG. 12  shows a single output window, multiple output windows can be used. For example, each beam of light  5120 A- 5120 D can exit the interior chamber  5304  via a respective output window. In some embodiments, it is desirable that as much as possible of at least the inner surface area of the housing  5102  comprise the thermally conductive material, to better achieve temperature uniformity. Accordingly, the output windows can be separated by thermally conductive material and can cover only as much area as necessary to allow light beams  5120 A- 5120 D to leave the interior chamber  5104 . However, in some embodiments a single output window is easier and less expensive to construct. 
     In some embodiments, the optical elements (e.g., lenses or lens) that produce the light beams  5120 A- 5120 D can be formed as part of the output window (or windows). For example, the window pane  5124  can include at least one curved surface to produce optical power, which can be configured to produce the plurality of light beams  5120 A- 5120 D having a desired shape and/or size. The window pane  5124  can comprise a lens array such as a microlens array, and can be anamorphic as discussed above. 
     The optical system  5100  can include a flow cell connector  5130  that is attached to the housing, and the flow cell connector  5130  is configured to secure a flow cell  5132  so that it intersects the beams of light  5120 A- 5120 D. In some embodiments, the flow cell connector  5130  can permanently attach the flow cell  5132  to the housing  5102 . However, in some embodiments, the flow cell connector  5130  can allow the flow cell  5132  to be removably attached to the housing  5102 . In some embodiments, the flow cell connector  5130  can be compatible with multiple types and/or sizes of flow cells. For example, the flow cell connector can include a clip, a friction or pressure fit coupling, a threaded portion configured to receive a corresponding threaded portion of the flow cell  5132 , or a variety of other connectors known in the art or yet to be devised. The flow cell  5132  can be a capillary flow cell, and at least part of the flow cell can comprise a transparent material (e.g., glass) that allows the light beams  5120 A- 5120 D to enter the flow cell  5132  and interact with a sample fluid contained within the flow cell  5132 . In one embodiment, the flow cell  5132  can be a thin hollow tube, forming a flow path that has a diameter of about 10 microns. Other flow cell types and/or sizes can be used, and the flow cell  5132  can be oriented differently than as shown in  FIG. 12 . In some embodiments, the beams of light  5120 A- 5120 D strike the flow cell over areas centered about 110 to 140 microns apart from each other, and in some embodiments, 125 microns apart from each other. For some forms of optical measurements, it is desirable for the laser light to strike the flow cell at specific locations (e.g., areas spaced about 125 microns apart). In some embodiments, the optical system  5100  mounts the optical fibers to automatically direct the light from the laser light sources  5112 A- 5112 D to the desired locations of the flow cell  5132  without requiring the user to manipulate any mirrors or wavelength selective elements such as dichroic mirrors or optical elements. 
     The optical system  5100  can be compatible with various types of optical (e.g., spectroscopic) analysis. For example, for laser-induced fluorescence spectroscopy, a fluorescent dye designed to bond with an analyte can be introduced into the fluid sample. When the fluid sample passes through the beams of light  5120 A- 5120 D, the fluorescent dye absorbs photons and emits photons that have a longer wavelength (less energy). By using photodetectors such as a photomultiplier tube (PMT) (not shown) to measure the amount of light that is emitted, the presence or concentration of the analyte in the sample fluid can be measured. For absorption spectroscopy, photodetectors (not shown) can be positioned on the side of the flow cell  5132  opposite the housing  5102  to determining the amount of light that is absorbed by the fluid sample. The optical system  5100  can also be compatible with other types of optical measurements or spectroscopic analysis. 
       FIG. 14  schematically shows an embodiment of an optical system  5300  that can be used to direct light for optical measurements (e.g., laser-induced fluorescence and spectroscopic analysis). The optical system  5300  is similar to optical system  5100  in some aspects, and similar elements are labeled with the same reference numerals used in  FIG. 12  except that the numbers are increased by  200 . The optical system  5300  can include a flow cell connector  5330  that comprises a thermally conductive auxiliary sample housing  5350  which encloses an interior chamber  5352 . The flow cell connector  5330  can be configured to secure a flow cell  5332  so that it passes through the interior chamber  5352 . For example, the sample housing  5350  can include two apertures  5354 ,  5356  and two flexible seals  5358 ,  5360 , so that the flow cell  5332  can be slidably inserted through the apertures  5354 ,  5356  and held in place by friction against the flexible seals  5358 ,  5360 . Alternatively, the sample housing  5350  can include a door allowing the sample housing  5350  to be opened and the flow cell  5332  to be placed inside. In various embodiments where the interior chamber  5352  of sample housing  5350  is hermetically sealed with respect to interior chamber  5304  of the main housing  5302 , the interior chamber  5352  of the sample housing  5350  can be exposed to ambient air without exposing the components contained within interior chamber  5304  of the main housing  5302 . Accordingly, the interior chamber  5352  of the sample housing  5350  can be exposed to ambient air when flow cell  5332  is removed and the seals  5358 ,  5360  may be excluded in some embodiments. 
     In some embodiments, the sample housing  5350  can be integrally formed as part of the main housing  5302  or can be thermally coupled to the main housing  5302  so that the thermoelectric controller  5306  regulates the temperature within the interior chamber  5352  of the sample housing  5350  as well as the interior chamber  5304  of the main housing  5302 . In some applications it may be desirable to maintain the internal chamber  5352  of the sample housing  5352  enclosing the flow cell at a different temperature than the internal chamber  5304  of the main housing  5302 , such as when a fluid sample is used that should be maintained at a different temperature than the interior chamber  5304  of the main housing  5302 . Accordingly, in some embodiments, a second thermoelectric controller (not shown) can be thermally coupled to the sample housing  5350  and an insulating layer (not shown) can be positioned at the transition between the main housing  5302  and the sample housing  5350  so that the internal chamber  5352  of the sample housing  5350  can be maintained at a different temperature than the interior chamber  5304  of the main housing  5302 . 
     The optical system  5300  can include a second output window for transmitting light out of the internal chamber  5352  of the sample housing  5350 . The second output window can be similar to the output window described above, and cover an aperture  5362  covered with a transparent window pane  5364 . The transparent window pane  5364  can be attached to the housing  5350  by bolts  5366  and sealed by a seal  5368 . In some embodiments, the interior chamber  5352  of the sample housing  5350  is not hermetically sealed and the seal  5368  can therefore be a non-hermetic seal or can be omitted altogether. 
       FIG. 15  schematically shows an embodiment of an optical system  5400  that can be used to direct light for optical measurements such as laser-induce fluorescence and spectroscopic analysis. The optical system  5400  is similar to optical systems  5100  and  5300  in some aspects, and similar elements are labeled with the same reference numerals used in  FIGS. 12 and 14  except that the numbers are increased by  200  and  100  respectively. Optical system  5400  can include a flow cell connector  5430  that attaches a flow cell  5432  to the housing  5402  so that the flow cell  5432  passes through the housing  5402 . For example, the housing  5402  can comprise two apertures  5454 ,  5456  and two flexible seals  5458 ,  5460 , so that the flow cell  5432  can be slidably inserted through the apertures  5454 ,  5456  and held in place by friction against the flexible seals  5458 ,  5460 . Alternatively, the housing  5402  can include a door allowing the housing  5402  to be opened and the flow cell  5432  to be placed inside. In some embodiments, the interior chamber  5404  can be exposed to ambient air when flow cell  5432  is removed and the seals  5458 ,  5460  can be non-hermetic seals. Also, the seal  468  can be a non-hermetic seal or can be omitted altogether. 
     As discussed above, various embodiments of the optical systems described herein can be used to perform a variety of optical measurements, such as, for example laser-induced fluorescence (LIF) measurements. Embodiments disclosed herein, such as those using LIF, can be useful in biological and/or chemical analysis. For example, LIF can be used in DNA sequencing applications, molecular diagnostic applications, confocal microscopy, or flow cytometry.  FIG. 16  illustrates an embodiment of an optical system  1600  configured to analyze a sample  1613 , for example using laser induced fluorescence. The optical system comprises a light source  1601  configured to direct light at one or more incident wavelengths towards the sample  1613  along an incident path. Light from the light source  1601  can be focused onto a portion of the sample  1613  using a lens  1611 . In various implementations, the lens  1611  can comprise a microscope objective lens. In some implementations, the lens  1611  can comprise an infinity corrected objective lens. Other types of focusing lenses can also be used as the lens  1611 . In some embodiments, the lens  1611  can include multiple lens elements. The light source  1601  can comprise one or more lasers and/or one or more light emitting diodes (LEDs). The light source  1601  can be configured to emit light at one or more incident wavelengths in a wavelength range between about 250 nm and about 980 nm, or an values or ranges therebetween, in some examples. The optical power of the one or more incident wavelengths emitted from the light source  1601  can be between about 1 mW and about 10,000 mW, or any values or ranges there between, in some example. Various types of lasers can be used, including continuous-wave (CW) lasers, quasi CW lasers, pulsed lasers, laser diodes, multi-mode lasers, etc. The sample  1613  may be a biological or a chemical sample, which can be tagged with one or more fluorescent dyes that absorb the light at the one or more incident wavelengths and emit fluorescence radiation at one or more fluorescent wavelengths. The fluorescence radiation at the one more fluorescent wavelengths emitted by the sample  1613  is directed along an emission path and imaged by an imaging device  1603 , such as, for example, a camera. 
     In various implementations, a portion of the incident path and the emission path can be combined using a beam combiner  1609 , such as, for example a dichroic mirror. The beam combiner  1609  can be configured to reflect incident light from the light source  1601  towards the sample  1613  and can transmit fluorescence radiation at the one or more fluorescent wavelengths towards the imaging device  1603 . In various implementations, a wavelength selective filter  1602  can be disposed in the incident path to transmit light at one or more selected wavelengths. The wavelength filter  1602  can be disposed in a filter wheel or other filter switcher comprising a plurality of wavelength selective filters configured to transmit light at one or more different wavelengths. The filter  1602  can be used to control the wavelength of light that illuminates the sample. For example, the light source  1601  can output blue, green, and red light, and the filter  1602  can attenuate the red and green light while permitting the blue light to be directed to the sample. The filter  1602  can be selectively change (e.g., using the filter wheel or other filter selector) in order to change the wavelength of light that is directed to the sample  1613  (while using the same light source  1601 ). Various different colors of lasers and filters can be used, such as depending on the florescent dyes that are used. A second wavelength selective filter  1607  can be disposed in the emission path to transmit fluorescence radiation at one or more selected fluorescent wavelengths. The second wavelength filter  1607  can also be disposed in a filter wheel or other filter selector comprising a plurality of wavelength selective filters configured to transmit light at one or more different wavelengths. The filter  1607  can be selectively changed in order to control the wavelength of light that reaches the camera  1603 . The emission path can comprise one or more optical lenses  1605 . In some implementations, the one or more optical lenses  1605  can be a tube lens. The one or more optical lenses  1605  can focus the light onto the camera  1603 . 
       FIG. 17  illustrates another embodiment of an optical system  1700  configured to analyze biological and/or chemical samples using laser-induced fluorescence. Various aspects of the optical system depicted in  FIG. 17  can be similar to the optical system  1600  depicted in  FIG. 16 . The optical system comprises a light source  1701  (e.g., a 4-channel light source) configured to emit incident light that is focused onto a sample using a lens  1711  (e.g., a microscope objective lens, an infinity-corrected objective lens, etc.). The lens  1711  can be mounted on a translational stage  1719  configured to adjust the position of the focus with respect to the sample. The optical system can comprise an autofocus system  1717  configured to focus the incident light onto the sample. Fluorescence radiation emitted from the sample is split along two imaging paths and imaged by two imaging devices  1803  (e.g., camera). A filter wheel  1707  or other filter switcher can be disposed in one of the two imaging paths to select one or more fluorescent wavelengths. Many variations are possible. For example, the filter  1707  can be omitted in some embodiments. Multiple cameras can be used, and multiple dichroic mirrors can be used to direct particular wavelengths of light to the cameras. 
     Referring to  FIG. 16 , the sample  1613  can be contained in a flow cell. An example flow cell  1830  is depicted in  FIG. 18 . The flow cell  1830  can comprise an array of tiles  1833 . Different tiles in the array can contain different samples to be analyzed. The samples can include DNA, DNA clusters, bacteria, chemical formulations, etc. The optical system  1600  (and/or the optical system  1700 ) can be configured to analyze the different samples contained in the array of tiles by causing relative movement between the flow cell  1830  and the optical system  1600 . For example, the lens  1611  (or the lens  1711 ) or the flow cell  1830  can be moved in a plane normal to the optical axis of the lens  1611  (or the lens  1711 ) such that light from the light source  1601  (or the light source  1701 ) at the one or more incident wavelengths is focused onto different tiles of the tile array at different times. An actuator can move the flow cell and/or optical system relative to each other, such as in two dimensions, such as using an XY stage. To efficiently excite only the sample contained in the tile onto which the light from the light source  1601  (or the light source  1701 ) at the one or more incident wavelengths is focused, it is desirable that the spot size of the focused light is matched to the size of the tile and that the intensity of light is substantially uniform across the area of the tile. For example, as shown in the inset of  FIG. 18 , the illumination profile is substantially uniform across the surface of the tile  1833 . As used herein, intensity variation less than or equal to about 20% from an average intensity can be considered to be substantially uniform. As illustrated in  FIG. 18 , the illumination profile can be substantially uniform across a substantial portion (e.g., greater than or equal to about 50%) of the length and the breadth of tile  1833 . For example, light intensity along the axis  1835  parallel to the breadth of the tile  1833  can be substantially uniform (e.g., intensity variation less than or equal to about 20% from an average intensity) over at least 50% of the breadth of the tile  1833 . The light intensity along the axis  1837  parallel to the length of the tile  1833  can be substantially uniform (e.g., intensity variation less than or equal to about 20% from an average intensity) over at least 50% of the length of the tile  1833 . The light intensity across a substantial portion of the breadth of the tile  1833  can be approximately equal to the light intensity across a substantial portion of the length of the tile  1833 . Without any loss of generality, the variation of light intensity across the length and the breadth can be substantially flat for a substantial portion of the length and breadth and rapidly fall off near the edges of the tile  1833  to advantageously allow uniform illumination across the surface of the tile  1833  without exciting the samples in adjacent tiles. For example, the intensity of any side lobes can be less than or equal to 1%. In this manner, it can be accomplished that only the fluorescent dyes tagged to the sample contained in the tile  1833  are excited by the incident light and fluorescent dyes tagged to different samples in adjacent tiles are not excited by the incident light. Systems and methods of generating light with uniform intensity profile for laser-induced fluorescence are discussed below. Many variations are possible. The light intensity can vary by less than or equal to about 2%, about 3%, about 5%, about 7%, about 10%, about 15%, about 20%, about 25%, about 30%, or any values or ranges therebetween, across at least about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, or about 90% of the area of the tile, or of the length and/or breadth of the tile, or any values or ranges therebetween. In some embodiments, a flat-top distribution of light can be produced, as discussed herein. The light delivered to the flow cell can have a light profile shape that generally conforms to the shape of the flow cell or frame  1833 . In the illustrated embodiment, the frame  1833  has a square shape, and the light delivered to the frame  1833  can have a generally square shaped distribution (e.g., square with rounded edges flat-top distribution). Other shapes of light distribution can be used, such as rectangular, circular, triangle-shaped, etc. The more light intensity and/or covered area that is put into the sample, the shorter the exposure time can be for the camera, which can result in faster measurement times and more throughput. The improved illumination embodiments disclosed herein can also provide improved image quality and measurement accuracy. 
     Without any loss of generality, intensity light from the light source  1601  (or the light source  1701 ) comprising one or more lasers or LEDs need not be uniform across the length and the breadth or area of the tile. For example, the variation in the intensity across the length and/or the breadth of the tile can be greater than or equal to about 20% of the average light intensity for the substantial portion of the light area.  FIG. 19A  depicts the intensity across the length extending along axis  1937  and across the breadth extending along axis  1935 , for light output by an example light source. The intensity profile on the left of  FIG. 19A  corresponds to the variation of intensity across the breadth extending along axis  1935  and the intensity profile on the right of  FIG. 19A  corresponds to the variation of intensity across the length extending along axis  1937 . As noted from  FIG. 19A , the variation of intensity across the breadth extending along axis  1935  and across the length extending along axis  1937  is not uniform and exhibits many peaks valleys. In some embodiments, the light source  1601  or  1701  can use one or more multi-mode lasers (e.g., laser diodes), which in some cases can contribute to the non-uniformity of the light distribution. Multi-mode laser diodes can be advantageous for availability and cost reasons, and the optical system can be configured to modify the light to increase uniformity. 
     Using optical systems and methods described herein, the variation of intensity across the breadth extending along axis  1935  and across the length extending along axis  1937  can be configured to be substantially uniform as shown in  FIG. 19B . For example, using optical systems and methods described herein, the variation of intensity across the breadth extending along axis  1935  can be made substantially uniform across a substantial portion of the breadth of the tile as shown in the intensity profile on the left of  FIG. 19B . Similarly, the variation of intensity across the length extending along axis  1937  can be made substantially uniform across a substantial portion of the length of the tile as shown in the intensity profile on the right of  FIG. 19B . As noted from the intensity profiles on the left and the right of  FIG. 19B , the intensity profile has a smooth flat top with steep sides to provide uniform illumination across the length and the breadth or area of tile while dropping of quickly at the edges of the tile to reduce the chance of exciting samples in neighboring tiles. 
     To achieve an intensity profile with a smooth flat top that falls off rapidly near the edges of the tile as shown in  FIG. 19B , a beam shaping system can be disposed in the incident path. The beam shaping system can comprise a focusing lens, a dynamic diffuser, and a micro-lens array, in some embodiments.  FIG. 20  depicts the incident path of an embodiment of an optical system  2000  configured to analyze samples (e.g., biological and/or chemical samples), such as using laser-induced fluorescence. The optical system  2000  can be an illumination system, such as for illuminating a sample (e.g., to induce fluorescence). The incident path of the optical system  2000  comprises a plurality of laser diodes  2001   a ,  2001   b  and  2001   c . The plurality of laser diodes  2000   a - 2000   c  can be configured to output laser light at red, green and blue wavelengths, although any suitable wavelengths, or any suitable number of light sources (e.g., lasers) can be used. In various embodiments, the plurality of laser diodes  2001   a - 2001   c  can be further configured to output amplified spontaneous emission (ASE) along with laser light (e.g., at red, green and blue wavelengths). The optical system can include one or more lenses to modify light emitted by the one or more lasers  2001   a - c . For example, collimating lenses (e.g., aspheric lenses) can be used to collimate light from the lasers  2001   a - c . The optical system can include one or more filters to modify light emitted by the one or more lasers  2001   a - c . For example, clean-up filters can be used to attenuate some frequencies of light from the lasers. For example, the filters can attenuate light at portions of the tails of laser light, while permitting light at the peaks of the laser light to pass substantially unattenuated. 
     The laser light (e.g., at red, green and blue wavelengths) can be combined using beam combiners  2003  (e.g., which can include dichroic mirrors). The combined beam (e.g., having light at red, green and blue wavelengths) can be focused onto a dynamic diffuser  2007  using a focusing optical element (e.g., lens)  2005 . In various implementations, the focusing lens  2005  can be either be a plano-convex or a focusing aspheric lens. Light output from the dynamic diffuser  2007  can be collimated using a collimating optical element (e.g., lens)  2009  and incident on a micro-lens array  2011 . 
     Light output from the micro-lens array can be incident on the sample contained in a flow cell  2030  via a dichroic mirror (e.g., a beam combiner)  2013  and a focusing lens  2015 . The dichroic mirror  2013  can operate similar to the dichroic mirror  1609  of FIG.  16 . The dichroic mirror  2013  can reflect light from the light source (e.g., lasers  2001   a - c ) for illuminating a sample, and the dichroic mirror  2013  can transmit light emitted from the sample (e.g., by fluorescence) for imaging. The flow cell  2030  can comprise an array of tiles as shown in  FIG. 18 . The focusing lens  2015  can be a microscope objective (e.g., which can have multiple lens elements, as shown). For example, the focusing lens  2015  can be an objective lens having an effective focal length (EFL) of about 14.43 mm and a numerical aperture (NA) of 0.68, although various other configurations are possible (e.g., focal length between about 5 mm and about 25 mm, or values outside this range). 
     In various implementations, light at amber wavelength, for example, can be combined with the laser light (e.g., of red, green and blue wavelengths) either before the focusing lens  2005  of the beam shaping system or collimating lens  2009  using another beam combiner. In some embodiments, one or more LED light sources  2001   d  can be used. A collimating optical element, such as a collimating lens (e.g., aspherical lens) can collimate light from the LED. In some cases a filter  2017 , such as a band pass filter, can attenuate some wavelengths of light, while passing at least some wavelengths of light output by the LED. Light from the one or more LEDs can be combined (e.g., with the laser light) using one or more beam combiners  2019  (e.g., one or more dichroic mirrors, as shown in  FIG. 20 ). In some embodiments, the LED  2001   d , filter  2017 , and/or dichroic mirror  2019  can be omitted. In some embodiments, light from the diffuser  2007  can be reflected by the dichroic mirror  2019  to the micro-lens array  2013 . In some embodiments, LED light sources similar to  2001   d  can be used in place of lasers  2001   a - c . Many variations are possible. 
     The micro-lens array can modify the distribution of light, such as to increase uniformity. By way of example, various lenslets (e.g., each of a plurality of lenslets) of the micro-lens array  2011  can sample the incident illumination profile. Each sample can be imaged onto the field of view (FOV) at the plane of the flow cell  2030  with the focusing lens  2015 . The samples from the various lenslets (e.g., each lenslet) of micro-lens array  2011  can add together to generate a flat-top profile in the plane of the flow cell  2030 , e.g., similar to the intensity profiles depicted in  FIG. 19B . 
     The distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted to achieve a spot size sufficiently small to illuminate a target (e.g., a desired region of the flow cell  2030 ) and have sufficiently high intensity to excite fluorescence in the sample. For example, the distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted such that a size of the focused spot on the desired region of the flow cell  2030  is less than or equal to the size of the desired region of the flow cell  2030  and the focused spot has a sufficiently high intensity to excite fluorescence in the sample. As another example, consider that the desired region of the flow cell  2030  is a square or a rectangle shaped region having a length ‘l’ and a breadth ‘b’. The distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted such that focused spot has a square or a rectangle shape having a length and breadth less than or equal to the length ‘l’ and breadth ‘b’ of the selected region of the flow cell  2030  and has a sufficiently high intensity to excite fluorescence in the sample. In some implementations, the distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted such that focused spot has a circular shape having a diameter less than or equal to the length ‘l’ and/or breadth ‘b’ of the selected region of the flow cell  2030  and has a sufficiently high intensity to excite fluorescence in the sample. In some implementations, the distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted such that focused spot has an elliptical shape wherein a length of the major axis and the minor axis is less than or equal to the length ‘l’ and/or breadth ‘b’ of the selected region of the flow cell  2030  and has a sufficiently high intensity to excite fluorescence in the sample. Various other shapes for the focused spot are contemplated herein. 
     The dynamic diffuser  2007  can comprise an optical diffuser coupled to a mechanical actuator. The dynamic diffuser  2007  can move (e.g., vibrate). The mechanical actuator can be configured to move the optical diffuser along one or more directions in the plane of the diffuser. For example, the diffuser  2007  can move (e.g., vibrate) in one dimension (e.g., a back and forth motion). The diffuser  2007  can move in two-dimensions (e.g., a circular motion) while the distance between the diffuser  2007  and the focusing optical element  2005  remains substantially constant. In some cases, the diffuser can be configured to move along one or more directions that are substantially orthogonal to a normal to the plane of the diffuser. Additionally, the diffuser can be configured to move in a direction substantially orthogonal to the beam such that the beam can sample different regions of the diffuser at different times. The diffuser can be configured to move at a frequency of a few 100 Hz. In various implementations, the mechanical actuator can be configured to vibrate the optical diffuser e.g., along one or more directions in the plane of the diffuser. For the laser beam having a generally elliptical spot (e.g., having a width along a major axis that is longer than a width along a minor axis), the mechanical actuator can be configured to move/vibrate the optical diffuser along a direction that is substantially parallel (e.g., within about 1 degree, about 2 degrees, about 5 degrees, about 10 degrees, or any values or ranges therebetween, although other values can be used) to the direction of the major axis of the generally elliptical laser beam. The diffuser can move more in the direction of the major axis than in the direction of the minor axis (e.g., which can be orthogonal to the major axis). Movement along the major axis can decrease the area of the diffuser that is illuminated at only sometimes as the diffuser moves, as compared to movement along the minor axis. This can promote uniformity of the light, because movement along the major axis causes more of the light to merely move around on the portions of the diffuser that were already illuminated. Moving (e.g., vibrating) the diffuser can advantageously reduce the speckle (e.g., which can result from the laser light), and can help achieve the smooth (e.g., flat-top) illumination profile. 
     The optical diffuser can increase etendue (or divergence) of the laser light. Accordingly, focusing the laser light using the focusing lens  2005  can advantageously help to maintain the etendue of the laser beam after the beam shaping element below a threshold etendue value. For example, the divergence of the laser beam after the dynamic diffuser  2007  can be between about 4 degrees and about 30 degrees, or any values or ranges therebetween, although other configurations are also possible. Without being bound by any theory, the smaller the spot size of the light focused by the focusing optical element  2005  onto the diffuser  2007 , the more the etendue of the light can be maintained. Focusing the light onto a relatively small spot size on the diffuser  2007  can produce light having lower etendue, as compared to focusing light onto a relatively large spot size on the diffuser  2007 . In various embodiments, the maximum spot size of the light focused by the focusing element  2005  at the diffuser can be determined based on the etendue of the optical element receiving the light from the diffuser  2007 . For example, as discussed below with reference to  FIG. 22 , for optical fiber based applications, the maximum spot size at the diffuser  2007  can depend on the core diameter and numerical aperture of the optical fiber into which the light output from the diffuser is coupled. As another example, for optical fiber based applications, the spot size at the diffuser  2007  can have a size that is sufficiently large to generate diffused light with RMS noise less than about 10% and that is small enough to be coupled into an optical fiber using compact coupling optical systems. 
     To minimize the etendue of the laser light after the dynamic diffuser  2007 , it is advantageous to adjust the distance between the focusing lens  2005  and the dynamic diffuser  2007  such that the laser light is focused onto the dynamic diffuser  2007  and the spot size of the laser light at the output of the dynamic diffuser  2007  is minimized. However, it was discovered that minimizing the etendue by minimizing the spot size of the laser light at the output of the dynamic diffuser  2007  can disadvantageously increase the intensity noise of the output light. This is illustrated in  FIG. 21  which shows the variation of the beam diameter in the horizontal direction (represented by curve  2105 ) and the vertical direction (represented by curve  2110 ) in the plane of the dynamic diffuser  2007  as a function of the distance between the focusing lens  2005  and the dynamic diffuser  2007 . The corresponding intensity noise as a function of the distance between the focusing lens  2005  and the dynamic diffuser  2007  is represented by curve  2115 . Without any loss of generality, the intensity noise is measured as the percentage variation in the root mean square (RMS) noise with respect to an average intensity. For example, RMS noise is obtained by calculating the ratio of the variation in time in the RMS value of the AC component of the electrical signal generated by the laser light in a photodiode to an average value of the DC component of the electrical signal generated by the laser light in the photodiode. As observed from  FIG. 21 , in this example, the smallest beam diameter in the horizontal direction (represented by curve  2105 ) is obtained when the distance between the focusing lens  2005  and the dynamic diffuser  2007  is about 5.75 mm and the smallest beam diameter in the vertical direction (represented by curve  2110 ) is obtained when the distance between the focusing lens  2005  and the dynamic diffuser  2007  is about 5.2 mm. The distance between the focusing lens  2005  and the dynamic diffuser  2007  that results in the smallest beam diameter in the horizontal/vertical direction can correspond to the focal distance of the focusing lens  2005 . The intensity noise has a maximum value when the distance between the focusing lens  2005  and the dynamic diffuser  2007  is about 5.2 mm. Accordingly, it can be concluded that when the distance between the focusing lens  2005  and the dynamic diffuser  2007  is equal to the focal distance of the focusing lens  2005  or is within ±10% of the focal distance, the spot size of the laser light at the output of the dynamic diffuser  2007  has the smallest beam diameter in the horizontal/vertical direction and an increased intensity noise. The increase in the intensity noise can be at least partially attributed to the variation in time in the transmissivity through the diffuser as the dynamic diffuser  2007  is moved/vibrated. As the dynamic diffuser  2007  is moved/vibrated the laser beam from the focusing lens  2005  is incident at different portions of the dynamic diffuser  2007  which can have different transmissivities. This can result in a variation in the intensity of light transmitted through the diffuser which manifests as intensity noise. From  FIG. 21  it is observed that as the dynamic diffuser  2007  is displaced toward or away from the focal plane of the focusing lens  2005  (e.g., by a distance that is greater than about 10% of the focal distance of the focusing lens  2005 ), then the intensity noise decreases. In other words, as the light output from the focusing lens  2005  is focused above or below the plane of the dynamic diffuser  2007  the intensity noise decreases. Without being bound by theory, it is believed that as the spot size of the light on the diffuser is increased and the light ‘samples’ a larger area of the diffuser, then the properties of the diffuser average across the illuminated area average out so that movement of the illuminated spot on the diffuser (e.g., by vibration of the diffuser) does not make a significant different in the averaged properties of the diffuser. In contrast, a very small spot size can experience more significant changes as it ‘samples’ different portions of the diffuser. Accordingly, it can be advantageous to increase the spot size of the light on the diffuser  2007 . However, a larger spot size on the diffuser can resulted in increased etendue or other undesired optical qualities. Accordingly, a balance can be performed between producing a sufficiently large spot size to have low noise, while also producing a sufficiently small spot size to have the desired optical qualities (e.g., low etendue). However, focusing the light output from the focusing lens  2005  above or below the plane of the dynamic diffuser  2007  can result in an increase in the beam diameter horizontal/vertical direction and/or an increase the spot size of the laser beam at the output of the dynamic diffuser  2007 . 
     Without being bound by any theory, the amount of intensity noise in the light at the output of the diffuser can depend on the size and distribution of the diffusing elements of the dynamic diffuser  2007 . For example, an implementation of a dynamic diffuser  2007  having regions with higher concentration of the diffusing elements interspersed with regions having lower concentration of the diffusing elements can have higher intensity noise as compared to an implementation of a dynamic diffuser  2007  in which the diffusing elements are uniformly dispersed. Accordingly, the spot size of the light focused on the implementation of the dynamic diffuser  2007  in which the diffusing elements are uniformly dispersed can be smaller (e.g., low etendue) than the spot size of the light focused on the implementation of the dynamic diffuser  2007  having regions with higher concentration of the diffusing elements interspersed with regions having lower concentration of the diffusing elements to achieve a similar amount of intensity noise. Thus, based on the physical and optical characteristics of the dynamic diffuser  2007 , the spot size of the light focused by the focusing element  2005  on the dynamic diffuser  2007  can be selected to achieve a desired intensity noise. 
     In some embodiments, the optical system can be configured so that the focusing optical element  2005  produces a spot of light on the diffuser  2007  that has a width (e.g., diameter) larger than about 20 microns, about 25 microns, about 30 microns, about 50 microns, about 75 microns, about 100 microns, about 150 microns, about 200 microns, about 250 microns, about 300 microns, or more (as shown in  FIG. 21 ), or any values therebetween, or any ranges bounded therebetween. In some embodiments, the optical system can be configured so that the focusing optical element  2005  produces a spot of light on the diffuser  2007  that has an area larger than about 200 square microns, about 300 square microns, about 500 square microns, about 750 square microns, about 1,000 square microns, about 1,250 square microns, about 1,500 square microns, about 1,750 square microns, about 2,000 square microns, about 2,500 square microns, about 3,000 square microns, about 4,000 square microns, about 5,000 square microns, about 7,500 square microns, about 10,000 square microns, about 15,000 square microns, about 20,000 square microns, about 25,000 square microns, about 50,000 square microns, about 75,000 square microns, about 100,000 square microns, about 150,000 square microns, or more, or any values therebetween, or any ranges bounded therein. In some embodiments, the diffuser  2007  can be spaced away from the focus or focal plane of the focusing optical element  2005  so that defocused light forms the spot of light on the diffuser. In some embodiments, the focusing optical element  2005  or other features of the optical system can be configured so that the spot of light produced at the focus or focal plane of the focusing optical element has a size that is sufficiently large to reduce light intensity noise, as discussed herein. Various embodiments described herein are configured such that the spot size of the light output from the focusing element  2005  at the diffuser  2007  has a spot size that is large enough to reduce intensity noise (e.g., spot size large enough such that the light at the output of the diffuser has a RMS noise less than 10%) and small enough to match the etendue of the optical element that receives the light output from the diffuser. For example, for some applications, the maximum spot size of the light at the diffuser can be 200 μm×200 μm. 
     Without any loss of generality, the distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted to any distance greater than or less than the focal distance of the focusing lens  2005  that generates a laser spot having a size that matches or substantially matches (e.g., within ±10%, within ±5%, within ±2%, etc.) of the size of the region of the flow cell  2030  that is desired to be illuminated such that the RMS noise is less than or equal to about 10%. For example, the distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted to any distance greater than or less than the focal distance of the focusing lens  2005  that generates a laser spot having a size that matches or substantially matches (e.g., within ±10%, within ±5%, within ±2%, etc.) the size of the desired region of the flow cell  2030  such that the RMS noise is less than or equal to about 8%, less than or equal to about 5%, less than or equal to about 3%, less than or equal to about 2%, less than or equal to about 1.5%, less than or equal to about 1%, or less (as shown in  FIG. 21 ), or any value in a range defined by any of these values. The term “substantially” is s general term as used herein, and when used in conjunction with a number or a range forms a phrase that will be readily understood by a person of ordinary skill in the art. For example, is readily understood that such language will include a number or range were little difference is discernible or matters. For example, the term substantially can mean within 20% of the number or the range. In various implementations, the distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted to any distance greater than or less than the focal distance of the focusing lens  2005  that generates a laser spot having a size that is greater than or equal to about 10% of the size of the desired region of the flow cell  2030  such that the RMS noise is less than or equal to about 10%. For example, the distance between the focusing lens  2005  and the dynamic diffuser  2007  can be adjusted to any distance greater than or less than the focal distance of the focusing lens  2005  that generates a laser spot having a size that is greater than or equal to about 20% of the size of the desired region of the flow cell  2030 , greater than or equal to about 30% of the size of the desired region of the flow cell  2030 , greater than or equal to about 40% of the size of the desired region of the flow cell  2030 , greater than or equal to about 50% of the size of the desired region of the flow cell  2030 , greater than or equal to about 60% of the size of the desired region of the flow cell  2030 , greater than or equal to about 70% of the size of the desired region of the flow cell  2030 , greater than or equal to about 80% of the size of the desired region of the flow cell  2030 , greater than or equal to about 90% of the size of the desired region of the flow cell  2030 , and less than or equal to the size of the desired region of the flow cell  2030 . Although various embodiments are discussed in connection with the spot size relative to the size of the desired region of the flow cell, any suitable target can be used instead of a flow cell. For example, the embodiments discussed herein can be modified to have spot size relative to an optical fiber end or coupler, or any other suitable target. 
     In various implementations, the dynamic diffuser  2007  can be displaced toward or away from the focal plane of the focusing lens  2005  by a distance that is greater than about 12% of the focal distance of the focusing lens  2005 , a distance that is greater than about 15% of the focal distance of the focusing lens  2005 , a distance that is greater than about 20% of the focal distance of the focusing lens  2005 , a distance that is greater than about 25% of the focal distance of the focusing lens  2005 , a distance that is greater than about 30% of the focal distance of the focusing lens  2005 , a distance that is greater than about 35% of the focal distance of the focusing lens  2005 , a distance that is greater than about 40% of the focal distance of the focusing lens  2005 , a distance that is greater than about 45% of the focal distance of the focusing lens  2005 , and a distance that is less than about 50% of the focal distance of the focusing lens  2005 , or any values or ranges therebetween, such as to reduce the RMS noise percentage and/or to generate a laser or light spot having a size that is greater than or equal to about 10% of the size of the target (e.g., the desired region of the flow cell  2030 ) and less than or equal to the size of the target (e.g., the desired region of the flow cell  2030 ). It is noted that in the various implementations discussed above, the intensity across the target (e.g., the surface of the desired region of the flow cell  2030 ) is substantially uniform (e.g., within ±20% of an average light intensity) for a substantial portion thereof. 
     Although various embodiments are discussed in connection with directing light to a sample (e.g., a flow cell), various other targets for the light can be used, such as for fiber couplings. The beam shaping system described above can also be integrated with fiber-coupled illumination sources.  FIG. 22  illustrates an embodiment of a fiber coupled illuminator comprising two laser diodes  2201   a  and  2201   b  respectively coupled to a collimator  2203   a  and  2203   b . The light output from the two laser diodes  2201   a  and  2201   b  is combined with a beam combiner  2205  (e.g., a dichroic mirror) and focused by a focusing lens  2207 . A dynamic diffuser  2209  can be positioned away from the focal plane of the focusing lens  2207  such that the combined laser beam from the two laser diodes  2201   a  and  2201   b  is focused above or below the plane of the dynamic diffuser  2209 . Light output from the dynamic diffuser  2209  is coupled into a multimode fiber  2213 , such as using coupling lens system  2211 . In various implementations, the multimode fiber  2213  can comprise a square or a rectangle shaped core such that intensity profile of the light output from the multimode fiber has a smooth flat top as shown in  FIG. 19B . In various implementations, the multimode fiber can have a 300 micron core. In some implementations, a micro-lens array can be coupled at the output of the multimode fiber as discussed above with reference to  FIG. 20 . 
     As discussed above, the dynamic diffuser  2209  can be displaced toward or away from the focal plane of the focusing lens  2207  by a distance that is greater than about 10% of the focal distance of the focusing lens  2207 , a distance that is greater than about 12% of the focal distance of the focusing lens  2207 , a distance that is greater than about 15% of the focal distance of the focusing lens  2207 , a distance that is greater than about 20% of the focal distance of the focusing lens  2207 , a distance that is greater than about 25% of the focal distance of the focusing lens  2207 , a distance that is greater than about 30% of the focal distance of the focusing lens  2207 , a distance that is greater than about 35% of the focal distance of the focusing lens  2207 , a distance that is greater than about 40% of the focal distance of the focusing lens  2207 , a distance that is greater than about 45% of the focal distance of the focusing lens  2207 , and a distance that is less than about 50% of the focal distance of the focusing lens  2207 , or any values or ranges therebetween, such as generate a laser or light spot having a size that is greater than or equal to about 10% of the size of a region to be illuminated and less than or equal to the size of the region to be illuminated. The region to be illuminated can be a portion (e.g., a tile) of a flow cell or a portion of an optical fiber (e.g., single mode or multi-mode fiber), or coupling. The distance between the dynamic diffuser  2209  and the focusing lens  2207  can be selected such that the RMS noise percentage has a value less than about 10% (e.g., a value between about 1% or about 2% and about 10%). As discussed above, the intensity across a substantial portion of the region to be illuminated can be substantially uniform (e.g., within ±20% of an average light intensity). 
       FIGS. 23A-23E  show the variation in the spot size at the output of the dynamic diffuser  2209  as the distance between the focusing lens  2207  and the dynamic diffuser  2209  is increased from a value less than the focal distance to a value greater than the focal distance.  FIG. 23A  illustrates a laser spot having a size of about 360 μm×200 μm at the output of the dynamic diffuser  2209  when the dynamic diffuser  2209  is disposed several millimeters above the focal plane of the focusing lens  2207 .  FIG. 23B  illustrates a laser spot having a size of about 200 μm×170 μm at the output of the dynamic diffuser  2209  when the dynamic diffuser  2209  is moved closer toward the focal plane of the focusing lens  2207 .  FIG. 23C  illustrates a laser spot having a size of about 120 μm×140 μm at the output of the dynamic diffuser  2209  when the dynamic diffuser  2209  is moved further closer toward the focal plane of the focusing lens  2207 .  FIG. 23D  illustrates a laser spot having a size of about 2 μm×130 μm at the output of the dynamic diffuser  2209  when the dynamic diffuser  2209  is disposed at the focal plane of the focusing lens  2207 .  FIG. 23E  illustrates a laser spot having a size of about 120 μm×140 μm at the output of the dynamic diffuser  2209  when the dynamic diffuser  2209  is moved away from the focal plane of the focusing lens  2207  such that the focal plane of the focusing lens  2207  is above the plane of the dynamic diffuser  2209 . 
       FIG. 24  is a flow diagram illustrating a process  2400  of illuminating a target. At block  2405  the process  2400  includes receiving light from one or more lasers at one or more beam combiners. Each of the one or more beam combiners is positioned and aligned to receive light from a corresponding one of the one or more lasers. In some embodiments, the one or more beam combiners can be dichroic beam combiners. At block  2410 , the process  2400  includes combining, by the one or more beam combiners, the received light and directing the received light along a common path. The beam combiners of an illumination system can be positioned in the system in various ways. For example,  FIG. 20  and the corresponding description illustrates an embodiment having beam combiners directing light from a plurality of lasers along a common path (or the light is at least substantially aligned along a common path). At block  2415 , the process  2400  receives the light propagating along the common path at a focusing optical element and focuses the light. For example, the focusing optical element focuses the light towards a focus point (or focal point). The focusing optical element can be, in some embodiments, focusing lens  2005  ( FIG. 20 ). At block  2420  of the process  2400 , the focused light is received at a diffuser. The diffuser can be positioned such that it is not at the focus point. That is, the diffuser is positioned at a location spaced apart from the focus point. In some embodiments, the diffuser is positioned between the focusing optical element and the focus point such that light propagating from the focusing optical element converging to the focus point is incident on the diffuser. In some embodiments, the diffuser is positioned such that the focus point is between the focusing optical element and the diffuser such that light propagating from the focusing optical element has propagated past the focus point and when the light is incident on the diffuser. For example, such that light propagating past the focus point is diverging when it is incident on the diffuser. At block  2425  of process  2400 , the light is diffused by the diffuser, and light propagating from the diffuser is diffused light. In various embodiments, the diffuser is moved, or vibrated diffusing the light, at least in part by vibrating the diffuser, and light from the diffuser is output as diffused light. In some embodiments, vibrating the diffuser comprises moving the diffuser in a two-dimensional motion. In some embodiments, the two-dimensional motion is substantially orthogonal to an optical axis of the focusing optical element. In some embodiments, vibrating the diffuser comprises moving the diffuser in a plane. In some embodiments, vibrating the diffuser comprises moving the diffuser in a circular motion. In some embodiments, vibrating the diffuser comprises moving the diffuser in a linear motion. At block  2530  of process  2400 , light from the diffuser is received by a collimating optical element, which outputs collimated light. Collimating lens  2009  in  FIG. 16  is one example of a device for performing this portion of the process. Light propagating from the diffuser enters the collimating lens  2009  and propagates through the collimating lens  2009 , and the light propagating from the collimating lens  2009  is more collimated than the light received by the collimating lens  2009 . At block  2435 , a microlens array receives light from the collimating optical element, and light propagating from the microlens array is provided towards a target to illuminate the target. In some embodiments, the target comprises a flow cell. The micro-lens array can modify the distribution of light, such as to increase uniformity. By way of example, various lenslets (e.g., each of a plurality of lenslets) of the micro-lens array  2011  ( FIG. 20 ) can sample (or receive) the incident illumination profile of light that is propagating from the diffuser. Each sample can be imaged onto the field of view (FOV) at the plane of a flow cell  2230  (e.g.,  FIG. 20 ; flow cell  1830   FIG. 18 ) with the focusing lens  2015 . The samples from the various lenslets (e.g., each lenslet) of the micro-lens array can add together to generate a flat-top profile in the plane of the flow cell. An example of such an intensity profile is illustrated in  FIG. 19B . 
     A wide variety of other variations are possible. Components can be added, removed, and/or rearranged. For example, in some embodiments, the optical system does not include a thermally conductive housing or a thermoelectric controller. In some embodiments, the optical fibers can be oriented to direct light to the flow cell without the use of lenses or other optical elements. Other variations are also possible. Similarly, in any method or process disclosed herein, steps or operations can be added, removed, and/or rearranged. 
     Configurations other than those described herein are possible. The structures, devices, systems, and methods may include additional components, features, and steps and any of these components, features, and steps may be excluded and may or may not be replaced with others. The arrangements may be different. Reference throughout this specification to “some embodiments,” “certain embodiments,” or “an embodiment” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least some embodiments. Thus, appearances of the phrases “in some embodiments” or “in an embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment and may refer to one or more of the same or different embodiments. Furthermore, the particular features, structures or characteristics may be combined in any suitable manner, as would be apparent to one of ordinary skill in the art from this disclosure, in one or more embodiments. 
     As used in this application, the terms “comprising,” “including,” “having,” and the like are synonymous and are used inclusively, in an open-ended fashion, and do not exclude additional elements, features, acts, operations, and so forth. Also, the term “or” is used in its inclusive sense (and not in its exclusive sense) so that when used, for example, to connect a list of elements, the term “or” means one, some, or all of the elements in the list. 
     Similarly, it should be appreciated that in the above description of embodiments, various features are sometimes grouped together in a single embodiment, figure, or description thereof for the purpose of streamlining the disclosure and aiding in the understanding of one or more of the various inventive aspects. This method of disclosure, however, is not to be interpreted as reflecting an intention that any claim require more features than are expressly recited in that claim. Rather, inventive aspects lie in a combination of fewer than all features of any single foregoing disclosed embodiment. 
     Some examples of some of certain embodiments disclosed and/or described herein are listed below. These examples of various embodiments are not meant to be limiting, but rather illustrate some of the embodiments of systems and methods that that are disclosed by this description and accompanying figures. Such embodiments can include: 
     Embodiment 1. An illumination system comprising:
         at least one laser configured to output light having at least one wavelength;   a focusing optical element configured to receive the light combined by the one or more beam combiners, wherein the focusing optical element is configured to focus light towards a focus;   a diffuser spaced away from the focus so that the diffuser is configured to diffuse defocused light from the focusing optical element;   an actuator configured to vibrate the diffuser; and   a collimating optical element configured to receive light output by the diffuser, wherein the collimating optical element is configured to substantially collimate the light; and   a microlens array configured to receive light output by the diffuser, wherein the microlens array is configured to alter the distribution of light.       

     Embodiment 2. The illumination system of Embodiment 1, further comprising a plurality of lasers and one or more beam combiners configured to combine light output by the plurality of lasers. 
     Embodiment 3. The illumination system of Embodiment 2, wherein the one or more beam combiners comprise one or more dichroic mirrors. 
     Embodiment 4. The illumination system of any of Embodiments 1-3, further comprising at least one filter configured to filter a portion of the output light. 
     Embodiment 5. The illumination system of any of Embodiments 1-4, wherein the focusing optical element comprises a lens. 
     Embodiment 6. The illumination system of any of Embodiments 1-5, wherein the diffuser is positioned to diffuse the light as the light is converging towards the focus. 
     Embodiment 7. The illumination system of any of Embodiments 1-6, wherein the diffuser is positioned to diffuse the light as the light is diverging away from the focus. 
     Embodiment 8. The illumination system of any of Embodiments 1-7, wherein the light forms a spot on the diffuser that has first width along a first direction and a second width along a second direction that is orthogonal to the first direction, wherein the first width is larger than the second width, and wherein the actuator is configured to vibrate the diffuser in substantially the first direction. 
     Embodiment 9. The illumination system of any of Embodiments 1-8, wherein the actuator is configured to vibrate the diffuser in one-dimensional motion. 
     Embodiment 10. The illumination system of any of Embodiments 1-9, wherein the actuator is configured to vibrate the diffuser in a two-dimensional motion in a plane that is substantially orthogonal to the optical axis of the focusing optical element. 
     Embodiment 11. The illumination system of any of Embodiments 1-10, wherein the actuator is configured to vibrate the diffuser in a circular motion. 
     Embodiment 12. The illumination system of any of Embodiments 1-11, wherein the microlens array is configured to output a substantially flat-top distribution of light. 
     Embodiment 13. The illumination system of any of Embodiments 1-12, wherein the diffuser is positioned at least about 0.2 mm from the focus. 
     Embodiment 14. The illumination system of any of Embodiments 1-13, wherein the diffuser is positioned at least about 0.5 mm from the focus. 
     Embodiment 15. The illumination system of any of Embodiments 1-14, wherein the diffuser is positioned at least about 0.8 mm from the focus. 
     Embodiment 16. The illumination system of any of Embodiments 1-15, wherein the diffuser is positioned less than or equal to about 2 mm from the focus. 
     Embodiment 17. The illumination system of any of Embodiments 1-16, wherein the focusing optical element is configured to focus the light to a spot having a first area at the focus, and wherein the diffuser is positioned so that the light forms a spot on the diffuser that has a second area larger than the first area. 
     Embodiment 18. The illumination system of any of Embodiments 1-17, wherein the second area is at least about 50% larger than the first area. 
     Embodiment 19. The illumination system of any of Embodiments 1-18, wherein the second area is at least about 100% larger than the first area. 
     Embodiment 20. The illumination system of any of Embodiments 1-19, wherein the second area is at least about 200% larger than the first area. 
     Embodiment 21. The illumination system of any of Embodiments 1-20, wherein the second area is at least about 300% larger than the first area. 
     Embodiment 22. The illumination system of any of Embodiments 1-21, wherein the second area is less than or equal to about 25 times the first area. 
     Embodiment 23. The illumination system of any of Embodiments 1-22, further comprising one or more additional optical elements configured to focus light output by the micro-lens array onto a target. 
     Embodiment 24. The illumination system of any of Embodiments 1-23, wherein the target comprises a flow cell. 
     Embodiment 25. An illumination system comprising:
         one or more light sources;   a focusing optical element configured to receive light emitted by the one or more light sources, wherein the focusing optical element is configured to focus the light towards a focus; and   a dynamic diffuser positioned to diffuse the light being focused by the focusing optical element at a location other than the focus.       

     Embodiment 26. The illumination system of Embodiment 25, wherein the one or more light sources comprise one or more lasers. 
     Embodiment 27. The illumination system of any of Embodiments 25-26, wherein the one or more light sources comprises a plurality of lasers, the system further comprising one or more beam combiners configured to combine light emitted by the plurality of lasers. 
     Embodiment 28. The illumination system of any of Embodiments 25-27, wherein the focusing optical element comprises an aspherical lens. 
     Embodiment 29. The illumination system of any of Embodiments 25-28, wherein the dynamic diffuser is between the focusing optical element and the focus so that the light being focused by the focusing optical element impinges on the dynamic diffuser before reaching the focus. 
     Embodiment 30. The illumination system of any of Embodiments 25-29, wherein the focus is between the focusing optical element and the dynamic diffuser so that the light being focused by the focusing optical element impinges on the dynamic diffuser after being focused at the focus. 
     Embodiment 31. The illumination system of any of Embodiments 25-30, wherein the dynamic diffuser is configured to vibrate. 
     Embodiment 32. The illumination system of any of Embodiments 25-31, wherein the dynamic diffuser comprises a vibrating actuator. 
     Embodiment 33. The illumination system of any of Embodiments 25-32, wherein light being focused by the focusing optical element forms a spot of light on the dynamic diffuser that is generally elliptical in shape, having a major axis and a minor axis, and wherein the dynamic diffuser is configured to move in one dimension in substantially the same direction as the major axis. 
     Embodiment 34. The illumination system of any of Embodiments 25-33, wherein the dynamic diffuser is configured to move in two dimensions. 
     Embodiment 35. The illumination system of any of Embodiments 25-34, wherein the dynamic diffuser is a two-dimensional circular moving diffuser. 
     Embodiment 36. The illumination system of any of Embodiments 25-35, wherein the focusing optical element is configured to focus the light to a spot having a first width at the focus, wherein the dynamic diffuser is positioned so that the light forms a spot having a second width on the diffuser, and wherein the second width is larger than the first width. 
     Embodiment 37. The illumination system of any of Embodiments 22-36, wherein the second width is at least about 25% larger than the first width. 
     Embodiment 38. The illumination system of any of Embodiments 25-37, wherein the second width is at least about 50% larger than the first width. 
     Embodiment 39. The illumination system of any of Embodiments 25-38, wherein the second width is at least about 75% larger than the first width. 
     Embodiment 40. The illumination system of any of Embodiments 25-39, wherein the second width is at least about 100% larger than the first width. 
     Embodiment 41. The illumination system of any of Embodiments 25-40, wherein the second width is at least about 150% larger than the first width. 
     Embodiment 42. The illumination system of any of Embodiments 25-41, wherein the second width is at least about 200% larger than the first width. 
     Embodiment 43. The illumination system of any of Embodiments 25-42, wherein the second width is at least about 250% larger than the first width. 
     Embodiment 44. The illumination system of any of Embodiments 25-43, wherein the second width is less than or equal to about 10 times the first width. 
     Embodiment 45. The illumination system of any of Embodiments 25-44, wherein the dynamic diffuser is positioned to diffuse the light at a location that is at least about 0.2 mm from the focus. 
     Embodiment 46. The illumination system of any of Embodiments 25-45, wherein the dynamic diffuser is positioned to diffuse the light at a location that is at least about 0.5 mm from the focus. 
     Embodiment 47. The illumination system of any of Embodiments 25-46, wherein the dynamic diffuser is positioned to diffuse the light at a location that is at least about 0.8 mm from the focus. 
     Embodiment 48. The illumination system of any of Embodiments 25-47, wherein the dynamic diffuser is positioned to diffuse the light at a location that is less than or equal to about 2 mm from the focus. 
     Embodiment 49. The illumination system of any of Embodiments 25-48, wherein the dynamic diffuser is positioned to diffuse the light at a location that is less than or equal to about 1 mm from the focus. 
     Embodiment 50. The illumination system of any of Embodiments 25-49, where the divergence of light emitted from the dynamic diffuser is between about 4 degree and about 30 degrees. 
     Embodiment 51. The illumination system of any of Embodiments 25-50, wherein a value of root mean square (RMS) noise of the light at the output of the dynamic diffuser is between about 2% and about 10%. 
     Embodiment 52. The illumination system of any of Embodiments 25-51, further comprising a micro-lens array configured to receive light output by the diffuser. 
     Embodiment 53. The illumination system of Embodiment 52, wherein the micro-lens array is configured to output light having a substantially flat-top distribution. 
     Embodiment 54. The illumination system of any of Embodiments 52-53, further comprising a collimating optical element configured to substantially collimate the light diffused by the dynamic diffuser, and wherein the micro-lens array is configured to receive the collimated light. 
     Embodiment 55. The illumination system of any of Embodiments 25-54, further comprising one or more additional optical elements configured to focus light output by the dynamic diffuser onto a target. 
     Embodiment 56. The illumination system of Embodiment 55, wherein the target comprises a flow cell. 
     Embodiment 57. The illumination system of any of Embodiments 55-56, wherein the target comprises an optical fiber. 
     Embodiment 58. An illumination system comprising:
         one or more light sources;   a focusing optical element configured to receive light emitted by the one or more light sources, wherein the focusing optical element is configured to focus the light towards a focus; and   a dynamic diffuser positioned to diffuse the light output by the focusing optical element, wherein a spot size of the light output from the focusing optical element at the dynamic diffuser is configured such that RMS intensity noise of the light output from the diffuser is less than a threshold.       

     Embodiment 59. The illumination system of Embodiment 58, wherein the diffuser is positioned at the focus of the focusing optical element. 
     Embodiment 60. The illumination system of Embodiment 58, wherein the diffuser is positioned above or below the focus of the focusing optical element. 
     Embodiment 61. The illumination system of any of Embodiments 58-60, wherein a maximum value of the spot size of the light output from the wherein a spot size of the light output from the focusing optical element at the dynamic diffuser is less than or equal to etendue of an optical element receiving light output from the dynamic diffuser. 
     Although the inventions presented herein have been disclosed in the context of certain preferred embodiments and examples, it will be understood by those skilled in the art that the inventions extend beyond the specifically disclosed embodiments to other alternative embodiments and/or uses of the inventions and obvious modifications and equivalents thereof. Thus, it is intended that the scope of the inventions herein disclosed should not be limited by the particular embodiments described above.