Patent Publication Number: US-2023136744-A1

Title: Particle manipulation system with cytometric capability and feedback loop and variable gain detector

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This nonprovisional U.S. Pat. Application claims priority to U.S. Provisional Application Serial No. 63275908 filed Nov. 4, 2021. This prior application is incorporated by reference in its entirety. 
    
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH 
     Not applicable. 
    
    
     STATEMENT REGARDING MICROFICHE APPENDIX 
     Not applicable. 
     BACKGROUND 
     This invention relates to a system and method for manipulating small particles in a microfabricated fluid channel. 
     Microelectromechanical systems (MEMS) are very small, often moveable structures made on a substrate using surface or bulk lithographic processing techniques, such as those used to manufacture semiconductor devices. MEMS devices may be moveable actuators, sensors, valves, pistons, or switches, for example, with characteristic dimensions of a few microns to hundreds of microns. A moveable MEMS switch, for example, may be used to connect one or more input terminals to one or more output terminals, all microfabricated on a substrate. The actuation means for the moveable switch may be thermal, piezoelectric, electrostatic, or magnetic, for example. MEMS devices may be fabricated on a semiconductor substrate which may manipulate particle passing by the MEMS device in a fluid stream. 
     MEMS devices can be used to count a population of target particles, such as particular types of biological cells, like stem cells or tumor cells. MEMS can also be used to separate such target cells from non-target material in a sample stream. Other particle manipulations can also be performed using MEMS device, as discussed further below. 
     For example, MEMS devices such as a movable valve, may be used as a sorting mechanism for sorting various particles from a fluid stream, such as cells from blood. The particles may be transported to the sorting device within the fluid stream enclosed in a microchannel, which flows under pressure. Upon reaching the MEMS sorting device, the sorting device directs the particles of interest such as a blood stem cell, to a separate receptacle, and directs the remainder of the fluid stream to a waste receptacle. 
     MEMS-based cell sorter systems may have substantial advantages over existing fluorescence-activated cell sorting systems (FACS) known as flow cytometers. Flow cytometers are generally large and expensive systems which sort and/or count cells based on a fluorescence signal from a tag affixed to the cell of interest. The cells are diluted and suspended in a sheath fluid, and then separated into individual droplets via rapid decompression through a nozzle. After ejection from a nozzle, the droplets are separated into different bins electrostatically, based on the fluorescence signal from the tag. Among the issues with these systems are cell damage or loss of functionality due to the decompression, difficult and costly sterilization procedures between sample, inability to sort sub-populations along different parameters, and substantial training necessary to own, operate and maintain these large, expensive pieces of equipment. For at least these reasons, use of flow cytometers has been restricted to large hospitals and laboratories and the technology has not been accessible to smaller entities. 
     A number of patents have been granted which are directed to such MEMS-based particle manipulation devices. For example, U.S. Pat. No. U.S. Pat. 6,838,056 is directed to a MEMS-based cell sorting device, U.S. Pat. No. 7,264,972 b1 is directed to a micromechanical actuator for a MEMS-based cell sorting device. U.S. Pat. No. 7,220,594 is directed to optical structures fabricated with a MEMS cell sorting apparatus, and U.S. Pat. No. 7,229,838 is directed to an actuation mechanism for operating a MEMS-based particle sorting system. Additionally, U.S. Pat. Application Nos. 13/374,899 and 13/374,898 provide further details of other MEMS designs. Each of these patents and patent application publications is hereby incorporated by reference, and each is assigned to Innovative Micro Technology and Owl biomedical, the assignee of the present invention. 
     SUMMARY 
     One feature of the MEMS-based particle sorting system is that the fluid may be confined to small, microfabricated channels formed in a semiconductor substrate throughout the sorting process. The MEMS device may be a valve which separates a target particle from other components of a sample stream. The MEMS device may redirect the particle flow from one channel into another channel, when a signal indicates that a target particle is present. This signal may be a photon from a fluorescent tag which is affixed to the target particle and excited by laser illumination in an interrogation region upstream of the MEMS device. Thus, the MEMS device may be a particle or cell sorter operating on a fluid sample. 
     More generally however, particles in the fluid stream may be manipulated rather than sorted, by some manipulation including heating, tagging, charging, altering or destroying a target particle flowing in a fluid stream. In this scenario, the target particle may be distinguished from the non-target particle by a fluorescence activated detection, such as that used in the above-described FACS flow cytometers. The identified cells may then be manipulated by the particle manipulation stage. This manipulation may be accomplished by a microfabricated device manufactured on a substrate which heats, tags, charges, alters or destroys the target particles. The fabrication substrate may also include microfabricated channels leading to and from the particle manipulation stage. 
     A system and method are described which makes use of this architecture which is particular to the particle manipulation systems such as those disclosed in the aforementioned patents. These techniques may form a particle manipulation system with cytometric capability, as described below. A microfabricated device may be used to manipulate the particles in the fluid stream enclosed in the microfabricated channel. In this system and method, a plurality of interrogation regions exist within the microfluidic pathways, with one laser interrogation region upstream of the MEMS device, and at least one additional laser interrogation region downstream of the MEMS device. The additional laser interrogation regions may be used to confirm the performance of the microfabricated manipulation device. 
     Accordingly, the particle manipulation system with cytometric capability may include an interrogation region that identifies the particles flowing in the sample stream. The identification methodology may include, but is not limited to, one or more laser interrogation regions that use laser excitation to induce identifying fluorescence from a fluorescent tags affixed to a target particle. This interrogation region may include laser light directed into a first laser interrogation region in first portion of a microchannel formed in a substrate, at least one particle manipulation stage formed in the substrate, and laser light directed into at least one additional laser interrogation region formed in a second portion of a microchannel formed in the substrate, wherein the first portion of the microchannel is disposed upstream of the particle manipulation stage, and the second portion of the microchannel is disposed downstream of the particle manipulation stage, and the particle manipulation stage comprises a movable structure microfabricated on the substrate which includes the microfluidic channels. Other types of identifying features may also be used to identify target particles, and this identification may be made upstream and/or downstream of the particle manipulation device, as described further below. 
     In one embodiment, the MEMS device is a flap-type cell sorter, which sorts a target cell (cancer cell, sperm cell, stem cell for example) from the other components of a fluid stream. The MEMS sorter may be a flap or diverter which is pulled down into the channel to redirect the flow in response to the detection of a target particle in the channel. This flap directs the flow into a sort channel rather than the waste channel. 
     In one embodiment, the additional interrogation region may be disposed in the sort channel, where the target particles are directed by the MEMS sorter. By counting the proportion of target particles to non-target particles, the effectiveness of the sorter can be ascertained, and properties or parameters can be adjusted as the sorting process is underway. 
     In other embodiments, the particle manipulation system may monitor a set of manipulation parameters which characterize or affect the performance of the particle manipulation system. These parameters can be updated to alter, improve, or optimize the functioning of the particle manipulation system. The operation of the particle manipulation system can be monitored of controlled remotely using internet services via wired or wireless connections. Data generated by the system can be stored digitally in a manner that allows the data to be shared or accessed by multiple users. 
     In another embodiment, a variable gain may be applied to the fluorescence detector that monitors the fluorescence signal, as described below. 
     These and other features and advantages are described in, or are apparent from, the following detailed description. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       Various exemplary details are described with reference to the following figures, wherein: 
         FIG.  1   a    is a simplified illustration of a microfabricated particle manipulation system; 
         FIG.  1   b    is a simplified illustration of a microfabricated particle manipulation system according to the present invention; 
         FIG.  2   a    is a simplified illustration of a microfabricated particle manipulation system having an intersection; 
         FIG.  2   b    is a simplified illustration of a microfabricated particle manipulation system having an intersection according to one embodiment of the present invention; 
         FIG.  2   c    is a simplified illustration of a microfabricated particle manipulation system having an intersection according to another embodiment of the present invention; 
         FIG.  3   a    is a simplified illustration of a microfabricated particle manipulation system according to one embodiment of the present invention, with the sort valve in the closed position; 
         FIG.  3   b    is a simplified illustration of a microfabricated particle manipulation system according to one embodiment of the present invention, with the sort valve in the open position; 
         FIG.  4   a    is a simplified illustration of a microfabricated particle manipulation system according to another embodiment of the present invention, with the sort valve in the closed position; 
         FIG.  4   b    is a simplified illustration of a microfabricated particle manipulation system according to another embodiment of the present invention, with the sort valve in the open position; 
         FIG.  5    is a simplified illustration of a microfabricated particle manipulation system according to an embodiment of the present invention, showing the field of view of the detector compared to the interrogation regions; 
         FIG.  6    is a simplified plan view of a microfabricated particle sorting system in the quiescent (no sort) position, showing the stationary magnetically permeable feature; 
         FIG.  7    is a plan view of the actuation mechanism for the microfabricated particle sorting system, showing the functioning of the external magnetic field in combination with the stationary magnetically permeable feature, in the actuated (sort) position; 
         FIG.  8    is a simplified schematic plan view of the microfabricated particle manipulation system with optical camera confirmation; 
         FIG.  9    is a simplified schematic plan view of the microfabricated particle manipulation system with camera confirmation, showing the path of a target particle within the system; 
         FIG.  10    is a simplified schematic plan view of the microfabricated particle manipulation system with camera confirmation showing the feedback loop between the camera and the controller to control the gate timing of the microfabricated particle manipulation system; 
         FIG.  11    is the simplified illustration of the feedback loop mechanism shown in  FIG.  10   ; 
         FIG.  12    is the simplified the illustration of an optimization routine involving trigger timing, and the camera confirmation; 
         FIG.  13    is a plan view of the microfabricated particle sorting system in combination with a hydrodynamic focusing manifold; 
         FIG.  14    is a simplified schematic diagram for triangularly shaped cavity; 
         FIG.  15    is a simplified schematic diagram of a fluid path containing a plurality of triangularly shaped cavities; 
         FIG.  16    is a simplified schematic illustration of the dean flow forces focusing particles in a specific area of the flow channel; (A), (B). (C), and (D) illustrate the flows within the channel or the locus of particles within the channel; 
         FIG.  17    is a simplified schematic illustration showing the dean flow forces forcing particles in a specific area of the flow channel, and the effect of the 90° out of plane turn.  FIG.  17 A  shows the cross section, and  FIG.  17 B  shows a plan view; 
         FIG.  18    is an exemplary embodiment of a sampling scheme that samples of the output of a variable gain detector, where in the detector is given a variable gain control.  FIG.  18 (A)  shows the signal and sampling scheme qualitatively;  FIG.  18 (B)  is a simplified schematic diagram of the digitization of the signals coming from the variable gain detector; 
         FIG.  19    is a simplified schematic illustration showing an embodiment for the variable gain detector; and 
         FIG.  20    is a schematic diagram of another embodiment of a particle manipulation system with multiple laser interrogation regions, having multiple laser sources. 
     
    
    
     DETAILED DESCRIPTION 
     The system described herein is a particle manipulation system which may make use of microchannel architecture of a MEMS particle manipulation system, such as those disclosed in the aforementioned patents. More generally, the systems and methods describe a particle manipulation system with multiple laser interrogation regions, which form a particle manipulation system with cytometric capability. A feedback loop may be implemented to monitor and/or control parameters that determine the performance of the particle manipulation system. Laser interrogation regions may provide information as to the effectiveness or accuracy of the particle manipulations, allowing the manipulations to be adjusted or controlled during the process in the aforementioned feedback loops. 
     In the figures discussed below, similar reference numbers are intended to refer to similar structures, and the structures are illustrated at various levels of detail to give a clear view of the important features of this novel device. 
       FIG.  1   a    is a schematic illustration of a MEMS-based particle manipulation system using lithographically formed microfluidic channels. One microfluidic channel  1  may be an input channel which directs a fluid flow. The fluid stream in microfluidic channel  1  flows through a first laser interrogation region  101 . In this region, light from one or more lasers is directed. The light may be focused to a spot and onto the particles flowing in the stream, wherein the laser interrogation region  101  is disposed upstream of a microfabricated manipulation stage  4 . If the particles have the appropriate fluorescent tag affixed thereto, the tag may be excited and emit a characteristic fluorescent photon. This photon may be detected by optical detectors and evaluated by appropriate logic circuits. The logic circuits may control the manipulation stage  4 , which may manipulate the tagged particles under the control of the logic circuits. 
     In one exemplary embodiment, the MEMS device may apply a charge to the target particle. In another exemplary embodiment discussed further below, the manipulation stage  4  may be an actuator, which diverts the target particle into a different flow path as the non-target particles. 
       FIG.  1   b    is a schematic illustration of a particle manipulation system with cytometric capability  10 , which uses lithographically formed microfluidic channels, according to the present invention. One microfluidic channel  1  may be an input channel which directs a fluid flow into a manipulation stage  4 . Microfabricated device  4  may alter the trajectory, morphology, shape, charge or other characteristic of the particle. Another microfluidic channel  2  directs the fluid flow away from the manipulation stage  4  and into an output channel. A second laser interrogation region  201  may be positioned in microfluidic channel  2 . Using laser interrogation region  201  to interrogate the passing particles, the effectiveness, accuracy and/or efficiency of MEMS manipulation stage  4  can be assessed. The simultaneous detection of fluorescence and the manipulated characteristic indicates accurate performance of the manipulation stage. 
     For example, manipulation stage  4  may apply a charge to a passing particle. Laser interrogation stage  2  may confirm the presence of both the charge and the fluorescent tag by measuring the voltage on a parallel plate capacitor (not shown) installed in the channel  2 . By so doing, the coincidence of both the fluorescence and the voltage signal is evidence that the charge is correctly place on tagged particles. In the case of a particle or cell sorter, the presence of the target sorted particle in the sort passage where the additional laser interrogation stage  201  is placed, may indicate correct and effective sorting. 
       FIG.  2   a    is a schematic illustration of another particle manipulation system with cytometric capability, using lithographically formed microfluidic channels. In  FIG.  2   a   , two or more channels are formed at the output of the manipulation stage  4 , forming an intersection point. One channel  2  may move in one path away from the manipulation stage  4 , whereas another channel  3  may move in another path away from manipulation stage  4 .  FIG.  2   b    depicts a particle manipulation system with cytometric capability. As shown in  FIG.  2   b   , channel  2  may be equipped with an additional laser interrogation stage  201 , which may identify the various particles according to their response to irradiation with laser light. If a particle emits a photon in response to irradiation, that is an indication that it is a tagged, target particle. If it does not, it is likely an untagged, non-target particle. 
     As shown in  FIG.  2   c   , both channels  2  and  3  may be equipped with an additional laser interrogation stage  201  and laser interrogation stage  301 , which may identify the various particles according to their response to irradiation with laser light. Indeed, any number of additional laser interrogation regions may be placed in any number of microfluidic channels, although large numbers of such regions may become difficult to separate, as described more fully below. As before, if a particle emits a photon in response to irradiation, that is an indication that it is a tagged, target particle. If it does not, it is likely an untagged, non-target particle. These two laser interrogation stages may measure the difference in density of target particles in one channel  2  relative to the other channel  3  or input channel  1 . 
       FIG.  3   a    is a schematic illustration of a particle manipulation system with cytometric capability  10  using multiple laser interrogation regions disposed in lithographically formed microfluidic channels. The manipulation stage  4  may be a MEMS flap-type actuator or sorter. The MEMS flap-type actuator is shown only schematically in  FIG.  5   , and may be a flap-type fluidic valve which separates a target particle from a remainder of the sample stream, based on a signal from the first laser interrogation region. The MEMS flap-like actuator may be a simple, hinge mounted movable member that may be drawn downward in response to a force acting on the movable member. The force may be, for example, electrostatic, magnetostatic or electromagnetic. The movable member may be formed lithographically on a silicon substrate, and methods for manufacturing such a device may be found in the above-incorporated patents and patent applications. 
     The MEMS actuator may divert the incoming fluid stream into one of the plurality of exit channels, for example into either channel  2  or channel  3 . For example, if a signal from laser interrogation region  101  indicates that a target particle is present, the logic circuit coupled to laser interrogation region  101  may send a signal to the MEMS actuator  4  to activate the flap. Drawing down the flap will divert the detected target particle into the sort channel  2  rather than allowing it to flow past into waste channel  3 . 
     As mentioned previously, waste channel  3  may also be equipped with an additional laser interrogation region  301 . This arrangement is shown in  FIGS.  4   a  and  4   b   , which are similar to  FIGS.  3   a  and  3   b   , except that two laser interrogation regions  201  and  301  are disposed in sort channel  2  and waste channel  3 , respectively. The two additional interrogation regions  201  and  301  may measure the increased density of target cells in sort channel  2  compared to waste channel  3 , and thus may provide evidence of the effectiveness and accuracy of the MEMS sorter  4  and laser interrogation region  101 . 
     Thus, as can be seen from the figures above, the additional laser interrogation regions  201  and  301  (or more) may act as a cytometer or as a quality control measure. The system  10  may give feedback as to the correct setting of any adjustable parameters in the sorting algorithm. Such parameters may include, for example, fluorescent pulse shape, width, magnitude or duration, laser intensity, optical alignment or focusing. These parameters may then be adjusted during the sort, rather than waiting for the entire sample to be processed before finding a problem in the sorting. The presence of additional laser interrogation regions  201  and/or  301  may provide cytometer capability to the sorter, in that it is able to count, enumerate, or quantify the density or purity of the sorted sample, while the sorting process is underway. This capability may allow the sort process to be adjusted in real time, that is, while it is underway. This may allow an optimization of sort parameters without performing multiple sorting operations on a sample, thus saving time and sample volume. 
     Also shown in  FIG.  5    is the field of view  200  of the detector monitoring laser interrogation region  101  as well as additional laser interrogation regions  201  and  301 . As indicated in  FIG.  5   , all laser interrogation regions may fall within the detector field of view, and thus may share at least a portion of the optical and electronic data detection channel. Accordingly, light collected from the at least one additional laser interrogation region is collected by an optical system which also collects light from the first laser interrogation region. Details as to how to exploit or implement this feature are set forth below with respect to the remaining figures. 
       FIGS.  6  and  7    illustrate one exemplary embodiment of a particle manipulation stage. In  FIGS.  6  and  7   , the manipulation may be a cell sorting stage  100 ,  100 ′ that separates at least one target particle flowing in a sample stream of target particles and non-target material. It should be understood that this embodiment is exemplary only, and that many other sorts of particle manipulations may be envisioned, including but not restricted to the particle manipulations described in detail below. 
       FIG.  6    is a plan view of an exemplary embodiment of device  100 . Device  100  may be a magnetically actuated cell sorter using a separate source of magnetic flux to move a small, magnetic MEMS structure  110 .  FIG.  6    shows the disposition of a stationary permeable feature  130  and further detail of the movable member  110 . In this embodiment, the movable member  110  may include the diverting surface  112 , the flexible hinge or spring  114 , and a separate area  116  circumscribed but inside the line corresponding to movable member  110 . This area  116  may be inlaid with a permeable magnetic material such as nickel-iron permalloy, and may function as described further below. 
     A magnetically permeable material should be understood to mean any material which is capable of supporting the formation of a magnetic field within itself. In other words, the permeability of a material is the degree of magnetization that the material obtains in response to an applied magnetic field. 
     The terms “permeable material” or “material with high magnetic permeability” as used herein should be understood to be a material with a permeability which is large compared to the permeability of air or vacuum. That is, a permeable material or material with high magnetic permeability is a material with a relative permeability (compared to air or vacuum) of at least about 100, that is, 100 times the permeability of air or vacuum which is about 1.26×10 -6  H·m -1 . There are many examples of permeable materials, including chromium (Cr), cobalt (Co), nickel (Ni) and iron (Fe) alloys. One popular permeable material is known as Permalloy, which has a composition of between about 60% and about 90% Ni and 40% and 10% iron. The most common composition is 80% Ni and 20% Fe, which has a relative permeability of about 8,000. 
     It is well known from magnetostatics that permeable materials are drawn into areas wherein the lines of magnetic flux are concentrated, in order to lower the reluctance of the path provided by the permeable material to the flux. Accordingly, a gradient in the magnetic field urges the motion of the movable member  110  because of the presence of inlaid permeable material  116 , towards areas having a high concentration of magnetic flux. That is, the movable member  110  with inlaid permeable material  116  will be drawn in the direction of positive gradient in magnetic flux. 
     An external source of magnetic field lines of flux may be provided outside the device  100 , as shown in  FIG.  7   . This source may be an electromagnet  500 . The electromagnet  500  may include a permeable core  512  around which a conductor  514  is wound. The wound conductor or coil  514  and core  512  generate a magnetic field which exits the pole of the magnet, diverges, and returns to the opposite pole, as is well known from electromagnetism. Accordingly, the movable member  110  is generally drawn toward the pole of the electromagnet  500  as shown in  FIG.  7   . 
     However, the performance of the device  100  can be improved by the use of a stationary permeable feature  130 . The term “stationary feature” should be understood to mean a feature which is affixed to the substrate and does not move relative to the substrate, unlike movable member or valve  110 . A stationary permeable feature  130  may be shaped to collect these diverging lines of flux and refocus them in an area directly adjacent to the movable member  110  with inlaid permeable material. The stationary permeable feature may have an expansive region  132  with a narrower throat  134 . The lines of flux are collected in the expansive region  132  and focused into and out of the narrow throat area  134 . Accordingly, the density of flux lines in the throat area  134  is substantially higher than it would be in the absence of the stationary permeable feature  130 . Thus, use of the stationary permeable feature  130  though optional, allows a higher force, faster actuation, and reduces the need for the electromagnet  500  to be in close proximity to the device  10 . From the narrow throat area  134 , the field lines exit the permeable material and return to the opposite magnetic pole of the external source  500 . But because of the high concentration of field lines in throat area  134 , the permeable material  116  inlaid into movable member  110  may be drawn toward the stationary permeable feature  130 , bringing the rest of movable member with it. 
     When the electromagnet is quiescent, and no current is being supplied to coil  514 , the restoring force of spring  114  causes the movable member  110  to be in the “closed” or “waste” position. In this position, the inlet stream passes unimpeded through the device  100  to the waste channel  140 . This position is shown in  FIG.  6   . When the electromagnet  500  is activated, and a current is applied through coil  514 , a magnetic field arises in the core  512  and exits the pole of the core  512 . These lines of flux are collected and focused by the stationary permeable feature  130  and focused in the region directly adjacent to the throat  134 . As mentioned previously, the permeable portion  116  of the movable member  110  is drawn toward the throat  134 , thus moving the movable member  110  and diverting surface  112  such that the inlet stream in inlet channel  120  is redirected to the output or sort channel  122 . This position is shown in  FIG.  7   . 
     Permalloy may be used to create the permeable features  116  and  130 , although it should be understood that other permeable materials may also be used. Permalloy is a well known material that lends itself to MEMS lithographic fabrication techniques. A method for making the permeable features  116  and  130  is described further below. 
     As mentioned previously, having the waste channel  140  and  142  directly beneath the movable member or valve  110  allows the movable permeable feature  116  to be disposed much closer to the stationary permeable feature  130 . If instead the waste channel were in the same plane, this gap would have to be at least large enough to accommodate the waste channel, along with associated tolerances. As a result, actuation forces are higher and valve opening and closing times are much shorter. This in turn corresponds to either faster sorting or better sorting accuracy, or both. 
     With the use of the electromagnetic actuation technique described above, actuation times on the order of 10 microseconds can be realized. Accordingly, the particle sorting device is capable of sorting particles at rates in excess of 50 kHz or higher, assuming 10 microseconds required to pull the actuator in, and 10 microseconds required to return it to the as-manufactured position. 
     A simplified plan view of the particle manipulation system with cytometric confirmation using an optical camera  160  is shown in  FIG.  8   . Shown in  FIG.  8    is the input channel  120 , the sort channel  122 , and the waste channel  140 . It should be understood that the waste channel  140  maybe in a different plane than the input channel  120  and sort channel  122 , as described above with respect to  FIG.  7   . However, for ease of the depiction, the waste channel  140  is shown as being in the same plane as the other two channels  120  and  122 . 
     Laser interrogation region  101  is shown in the input channel  120  upstream of the particle manipulation stage  100 . The output of a laser  102  may be directed into the laser interrogation region  101  in the input channel  120 . A particle manipulation stage  100  or  100 ′ may be disposed at the junction of the input channel  120  with the sort channel  122  and waste channel  140 . Particle manipulation stage  100  or  100 ′ may be any of the above described particle sorting mechanisms such as  100  shown in  FIGS.  6 , or  10   ′ shown in  FIGS.  7   a ,  7   b   . The optical camera  160  may be disposed in the sort channel  122  (or optionally in the waste channel) in proximity to the particle manipulation stage  100 . The optical camera  160  may have a field of view that includes at least a portion of the sort channel  122  and also may include a portion of the valve mechanism. The optical camera  160  may take an image of the particles in the stream passing through the sort channel  122  through the optically transmissive layer that covers the microfabricated channels  120  and  122  made in the substrate, as described above. The field of view of the camera  160  may include the sorting mechanism, which may be helpful for assessing its condition, as well as measuring the velocity pf the particle through the particle manipulation stage, for example. 
       FIG.  9    is a schematic view of the particle manipulation system  400  with camera confirmation in operation. In operation, the particle manipulation system  400  with camera confirmation may have one or more target particles  150  flowing in the sample stream in the input channel  120  and through the laser interrogation region  101 . The laser will irradiate the target particle  150  which will then fluoresce as a result of the irradiation. The fluorescence will be detected by detector which is not shown in  FIG.  10   . The output of this detector may be delivered to a controller  1900  ( FIGS.  10 ,  18   ). This controller then may send out a sort trigger pulse which may cause the movable member  110  of the microfabricated particle manipulation stage  100  to move to the sort position as was shown in  FIG.  7   . 
     This sort trigger pulse may also arm optical camera  160 , and prepare it to capture an image of the sort channel  122 . Accordingly, the optical camera  160  and the particle manipulation stage  100  maybe controlled by the same signal, and based on the detected fluorescence. These control signals may be generated by a controller  1900 , which is shown in the system level view of  FIG.  14   . There may be a delay however, between the sort trigger delivered to the movable member  110  compared to the trigger for optical camera  160 . This delay may give the target particle  150  a chance to move into the sort channel  122 , and within the field of view of the optical camera  160 . 
     The optical camera  160  may be configured to generate repeated images of the same field view as triggered by the controller signal just described. These images may be overlaid to show the sequence and time evolution of the field of view of the optical camera  160 . Accordingly, as multiple target particles are sorted by particle manipulation stage  100 , this plurality of target particles will show appear in the field of view of the optical camera  160 . Thus, the output of the optical camera  160  may show multiple particles within the image, and the particles may be clustered in a particular location within the image. The location of this cluster of target particles may be an indication of the relative precision of the timing of the sort pulse relative to detection of fluorescence of the target particle  150  in the detection region  101 . The distribution of particles in the channel may be indicative of the variability of particle speed and location, within the flow, or variability in the fluid flow itself, for example. 
     The geometric center of the cluster is referred to herein as the “locus” of particles within the field of view. The locus may alternatively be understood as the center of the circle which includes most or all of the detected and sorted particles. If the locus appears in the downstream edge of the field of view of optical camera  160 , it may be an indication that the sort trigger is somewhat late. In other words, the position of the locus may be an indication that the timing between the detection of the particles by the laser interrogation region  101 , and the opening of the sort gate  110 , maybe slightly too early or slightly too late. Accordingly, by analyzing the locus of the target particles in the field of view of the optical him a  160 , the timing between the detection and sorting operations may be optimized. This may improve at least the purity and/or the yield of the particle manipulation system  100 . Accordingly, the particle manipulation system with optical confirmation may be capable of optimizing itself under computer control, that is the system maybe “self-aware”. With no other operator intervention, the system may be able to optimize its various parameters including sort gate timing, sort gate width, laser power and positioning, etc., based on the sequence of images captured by the optical camera and analyzed by the computer. 
     The particle manipulation system may use a camera to image the target particles and a controller to determine the locus of the particles within a field of view of the camera, and the controller may adjust sort gate timing thereby. 
     Accordingly, the particle manipulation system with camera confirmation  100  may be used in a feedback loop as illustrated in  FIG.  11   .  FIG.  11    shows the laser interrogation region  101  disposed in the input channel  120  which branches at the particle manipulation stage  100  into the waste channel  140  and sort channel  122 . As before, the plurality of target particles  150  may be flowing in the input channel  120  and may be diverted by the particle manipulation stage  100  when the fluorescent signal is detected. The target particle  150  then flows through the field of view of the optical camera  160  which takes an image of the passing target particle  150 . By overlaying the plurality of images taken by the optical camera, and analyzed by the controller  1900  ( FIGS.  10 ,  18   ), the system may find the locus of particles within the field of view. The controller  1900  may then make adjustments to the sort gate timing relative to the laser detection, in order to optimize either the purity, or the yield, of the sorted product. 
     This feedback loop is shown qualitatively and  FIG.  11    as the arrows connecting the optical camera  160  to the controller  1900 , and the controller  1900  to the movable member  110 . 
     Normal operation of the system  100  is depicted in  FIG.  12   . In  FIG.  12   , the controller regularly puts out a sort pulse in response to the detection of a target particle in the laser interrogation region  101 . These pulses are shown on the horizontal axis in  FIG.  12   . Coincidentally, the optical camera  160  collects overlaid images of the target particles passing through its field of view in the sort channel  122 . The data is collected and analyzed by the controller  1900 , and adjustments are made to the operating parameters. 
     The results of the closing of this feedback loop are illustrated in  FIG.  13   . When the controller, or human operator, analyzes the locus of particles appearing in the field of view of the optical camera  160 , a determination may be made that the locus is not placed accurately enough, or is shifted to an edge of the field of view, and that an improvement may be made. In this case, the controller, or an operator, may alter the timing between the laser detection and sort trigger. Before this adjustment is made, the controller may put out a sort trigger at a time T = T1, that is, at a time T1 after the identification of the target particle by the laser interrogation region  101 . The operation of the system in this mode will generate sorted population with a yield of some percent, and a purity of another percent. Upon a determination that this yield, or purity, may be improved, the controller  1900  may alter the pulse timing between the detection of the target particle, and the generation of the sort trigger pulse. The controller may determine that this delay should be increased from T = T1, to T = T1 + □T. This new value is then sent to the movable member  110  at a time T = T1 + □T. This may result in a relocation of locus of the target particles within the field of view, and improvement in either yield, or purity, or both. The situation is shown qualitatively in  FIG.  13   . 
     Because of the microfabricated nature of particle manipulation device  100 , it lends itself to techniques that can make use of such an enclosed, well defined architecture. One such technique is illustrated in  FIG.  13   , wherein the microfabricated particle manipulation device may be coupled to a microfabricated fluidic focusing element  300 . The focusing element  300  may include at least one additional sheath fluid inlet channel  320  that provides a sheath fluid to the sample stream and also a z-focusing curve  330  coupled to the sheath fluid inlet channel  320 . The sheath fluid may be used to adjust the concentration or positioning of the target particles within the sample inlet channel. The focusing element  300  may be configured to urge the target particles into a particular portion of the sample inlet channel  120 , such that the sorting process has fewer errors, as described further below. The focusing element  300  may be disposed in substantially the same plane as the movable member  110 , and may be formed in the same substrate surface as the movable member  110  and sample inlet channel  120 . The focusing element  300  may rely on inertial forces to focus the particles, as will be described further below. These forces may require relatively large flow rates to be effective. The microfabricated particle manipulation system with out-of-plane channel may be particularly suited to such an inertial focusing device, because of the narrow channels and high flow rates. 
       FIG.  13    depicts the microfabricated focusing element  300  which may be used to focus the particles in a certain area within the fluid stream. As the name suggests, the sheath fluid inlet channel  320  adds a sheath fluid to the sample stream, which is a buffering fluid which tends to dilute the flow of particles in the stream and locate them in a particular portion of the stream. The combined fluid then flows around a focusing element  300  coupled to the sample inlet channel  120 . The focusing element  300  may include here a z-focusing curve  330 , which tends to herd the particles into a particular plane within the flow. This plane is substantially in the plane of the paper of  FIG.  13   . The combined fluid in the focusing element  300  then passes another intersection point, a “y-intersection point”  350 , which introduces additional sheath fluid above and below the plane of particles. At the y-intersection point  350 , two flows may join the z-focus channel  330  from substantially antiparallel directions, and orthogonal to the z-focus channel  330 . This intersection may compress the plane of particles into a single point, substantially in the center of the stream. Accordingly, at the y-intersection point  350  the target particles may be compressed from a plane to a stream line near the center of the z-focus channel  330  and sample inlet channel  120 . Focusing the particles into a certain volume tends to decrease the uncertainly in their location, and thus the uncertainty in the timing of the opening and closing of the movable member or valve  110 . Such hydrodynamic focusing may therefore improve the speed and/or accuracy of the sorting operation. 
     In one exemplary embodiment of the microfabricated particle manipulation device  100  with hydrodynamic focusing illustrated in  FIG.  13   , the angular sweep of z-bend  330  is a curved arc of about 180 degrees. That is, the approximate angular sweep between the junction of the sheath fluid inlet channel  320  and the y-intersection point  350 , may be about 180 degrees. Generally, the radius of curvature of the z-bend  330  may be at least about 100 microns and less than about 500 microns, and the characteristic dimension, that is the width, of the channels is typically about 50 microns to provide the focusing effect. In one embodiment, the radius of curvature of the channel may be about 250 microns, and the channel widths, or characteristic dimensions, for the sample inlet channel  120  and z-bend channel  330  are on the order of about 50 microns. These characteristic dimensions may provide a curvature sufficient to focus the particles, such that they tend to be confined to the plane of the paper upon exit from the z-focus channel  330  at y-intersection point  350 . This plane is then compressed to a point in the channel at the y-intersection point  350 . Accordingly, the y-intersection  350  flows along with the z-focusing element  330  may urge the particles into a single stream line near the center of the microfabricated sample inlet channel  120 . 
       FIG.  13    shows another embodiment of a focusing element,  700 . In this embodiment, the focusing element  700  includes a plurality of segments having a variable lateral dimension or cross section. The variable cross section portion of the channel serves to urge or focus the particles into a particular portion of the stream flowing in the channel. The discussion now turns to the design and performance details of this variable cross section focusing channel as applied to the above described microfabricated particle sorter  100 . 
     The novel flow channel may possess portions of variable cross section, wherein the variable cross section arises from the shapes of the sidewalls of the flow channel. These variable portions may have one sidewall which is substantially straight with respect to the flow direction, and an adjacent side wall which is not straight, or at least not parallel to the substantially straight portion. In particular, this adjacent sidewall may be triangular or parabolic in shape, deviating away from the straight sidewall in an expanding region, to a point of maximum channel width, before coming back to the nominal distance between the sidewalls in a contracting region. The expanding portion, maximum point, and contracting portion may constitute what is hereafter referred to as a fluid “cavity”  620  in the microfabricated channel. Accordingly, the variable channel width segments may define expansion/contraction cavities  620 ,  620 ′ within the microfluidic channel, wherein the cavity is defined by the expanding portion followed by the contracting portion. 
     The cavity  720  should be understood to be in fluid communication with the microfabricated fluid channel, such as sample inlet channel  120 , such that fluid flows into and out of the cavity  620 . It should be understood that this cavity  620  may be a twodimensional widening of the channel in the expanding region, and narrowing of the channel in the contracting region. This shape of geometry is shown schematically in  FIG.  13   . 
     The variable cross section focusing channel  700  may be used instead of the curved focusing channel  300  shown in  FIG.  13   . That is, the variable crass section focusing channel  700  may be used in place of the z-focusing curve  330 , or in place of the entire focusing element  300 . The variable cross section focusing element  700  may be disposed upstream of the moveable member sorting device  110 . 
       FIGS.  14 - 17    depict another exemplary embodiment of the focusing structure which focuses the suspended particles into a portion, for example a particular quadrant, of the cross section of the fluid channel. 
       FIG.  14    is a simplified schematic diagram of a fluid path with a variable cross-section. In this embodiment, the shaped cavities  720  which are shown in  FIG.  14   , have a triangular shape  720  as shown in  FIG.  14   . Because of the asymmetry of this triangular shape, these cavities may cause a more effective focusing forces that concentrate particles within the flow. 
     In the embodiment shown in  FIG.  14   , the triangular cavity  720  may have a 60° angle with respect to the incoming streamline, and a 30° angle with respect to the outgoing streamline. These angles are as defined in  FIG.  14   , which shows that the first-encountered wall  725  may form an angle of about 60 degrees with respect to the parallel, horizontal wall of the flow channel. The second-encountered wall  727  may form an angle of about 30 degrees with respect to the parallel, horizontal wall of the flow channel. The third angle in the triangle is, of course, 90°. 
     The relatively wide entrance angle to the triangular region  720  may enforce pronounced Dean flow forces in this region, focusing particles as described above. The gentler 30 degree exit angle may urge the particles into their new stable positions. The series of triangular regions  720  may enforce this behavior again and again, until the stable positions shown in  FIG.  16 B  are reached. 
     The pitch between the triangular cavities may be about 2 mm. The height of each triangular cavity as defined in  FIG.  14   , maybe about 360 µm. The total length of the triangular cavity may be on the order of about 1000 µm, or 1 mm. It should be understood that these dimensions are exemplary only. 
     The incoming fluid channel may have a channel height of about 110 µm, as shown in the figure. The depth of this channel may be about 80 µm. This channel cross-section is maintained throughout the input to the triangle. Upon encountering the triangular cavity  760 , the 110 micron dimension expands dramatically, whereas the 80 micron depth is maintained, as further described below. 
     The 80 µm dimension may pertain to the depth of the channel, that is, the depth of the channel in the dimension into the paper. A perspective view of the flow channel also appears in  FIG.  14   . This 80 µm depth is maintained throughout the triangular cavity. In contrast, the 110 µm channel height varies from 110 µm at the entrance to a height of (360+110) µm at the apex of the triangular cavity  760 , before descending again to 110 µm at the output of the triangular cavity  760 . The curvature imparted to the streamlines by the existence of this cavity generates the Dean flow which provides the focusing force as described previously. It should be understood that all dimensions provided herein are exemplary only, and that other embodiments using different dimensions are included in the scope of the appended claims. 
       FIG.  15    is a simplified schematic illustration of the flow channel from a zoomed out perspective.  FIG.  15    shows a plurality of triangular cavities disposed in the fluid path. It should be understood, that this diagram is not to scale, and the details may be altered for ease of illustration. In particular whereas  FIG.  15    shows only about 18 triangles cavities, there may in fact be many more, for example 50 or even 75 triangular cavities in the flow path. 
     There may also be a transition region shown in  FIG.  14   , wherein the shape of the flow channel changes abruptly. In this transition region, the cross sectional shape of the flow channel may transition from shape “A” to shape “B”. The difference between the cross section A and cross section B is that the aspect ratio (AR = height divided by depth) changes from AR&gt;1 to AR&lt;1. In cross section A, the aspect ratio is 110/80 = 1.375, whereas in cross section B, the aspect ratio is 50/80 = 0.625. The effect of this transition is described below. 
     It should be understood that these dimensions and the ratios between them are exemplary only. More generally, the channel height may bt, for example, between 50 um and 500 um, and the channel width may be between about 30 um and about 120 um. Accordingly, the aspect ratio in the “tall” segment (AR&gt;1) may simply have an aspect ratio greater than 1 (for example, between 1+ and 50), and the aspect ratio in the “wide” segment may simply have an aspect ratio less than 1 (for example, between 0.4 and 1-). 
     Because the Dean flow forces take some time to urge the particles into the desired portion of the fluid channel, a substantial length of fluid path may be required to accomplish the focusing. In some embodiments, the total path length may be on the order of, for example, 8 cm or more. In view of this length, it may be advantageous to fold the fluid path in order to make the device more compact.  FIG.  15    shows six such turns, which gives a fluid path a serpentine shape. It should be understood that the path may be much longer with more turns. However, the features may not be drawn to scale because the details are impossible to render on the much larger scale of this 8 cm fluid path. Over this 8 cm distance, the particles in the fluid stream may be strongly focused into a single quadrant of the cross section. The location of the microfabricated fluid valve  100  is shown schematically in  FIG.  15   , but again, the details of the valve  100  are not rendered. 
     In some embodiments, a relatively large number of triangular cavities  760  is used, each having a shape general as depicted in  FIG.  14   . In one embodiment, 30-70 cavities are used, or more specifically on the order of 50 triangular cavities  760  may be used. With a pitch of 2 mm between the cavities  760 , it is apparent that the total channel length may be about 8-10 cm long. In view of these numbers, it should be appreciated that the features depicted in  FIG.  14    are not to scale. In fact, the triangular cavities  760  are smaller and more numerous than shown in  FIG.  14   , but for clarity of depiction and to keep the size of the drawing manageable, they are presented as shown in  FIG.  14   . 
     As mentioned earlier, another important detail in this design, is the change of aspect ratio of the cross-section of this fluidic path. As mentioned, at the input to the segment of the path containing the triangular cavities, the cross-section of the flow channel may be 110 µm × 80 µm = 1.375. The 110 µm dimension is variable because of the presence of these triangular cavities. However the 80 µm dimension is maintained throughout. As a result the aspect ratio of this portion of the flow channel, aspect ratio being defined as the height divided by the depth, maybe greater than one. In particular the aspect ratio of this flow channel may be 110/80 = 1.375 at the input, and increasing to almost 6 at the apex, before returning to 1.375 at the exit of the cavity. before encountering the transition region shown in  FIG.  14   . 
     After approximately 40-70 triangular cavities in the flow path, the flow may encounter the transition region shown in  FIG.  14   . As shown, this transition region may be located after the last triangular cavity  720  is encountered. In the embodiment shown in  FIG.  15   , this occurs at the fifth or the sixth turn in the fluid path, and after about 50 triangular cavities have focused the particles into either of two stationary positions exiting in the flow path, as described next. 
     This length of fluid path, with aspect ratio 1.375, will result in a focusing of the particles in a particular portion of the fluid channel. In particular, the particles may be arranged in two points along the depth dimension. That is, across the 80 µm depths of this flow channel there may exist to concentrated areas where the target particles are urged. This behavior is driven by the Dean flow forces existing in the curved channel with the aspect ratio being greater than one. If this aspect ratio is suddenly changed to a value less than one, the effect will be to urge the target particles into two new, and different paths plus spots with respect to the short dimension of the aspect ratio short dimension of the channel. 
     This behavior is illustrated by  FIG.  16   . In  FIG.  16   , the cross-sectional shape A corresponds to the aspect ratio of 110/80 = 1.375, that is, and aspect ratio greater than one. As illustrated in the figure, the result of this fluid channel shape is to concentrate the particles in two stable locations in the right hand side of the long dimension, or in other words, two positions occur along the short (depth) dimension of the flow channel. 
     Also illustrated in  FIG.  16    is the effect of a sudden change in the aspect ratio, in particular an aspect ratio less than one, such that the channel is deeper than it is tall. In this case, what was the long dimension becomes the short dimension, and the stable locations within the flow channel cross section shift. In  FIG.  16    The cross-section B, what was the long dimension  110  is altered to become the short dimension 50 µm. Using the same definition for aspect ratio, the aspect ratio of this cross-sectional channel B is now less than one. As a result, the particles are urged again into a two spots along the short dimension of the flow channel, which is now the height dimension, 50 microns. Or in other words, the particles tend to be focused in two spots along the long dimension, which is now the depth dimension 80 microns. 
     The effect of this change is therefore to suppress the second stable position that was formed in the AR&gt;1 channel. That is, the AR&gt;1 channel tends to focus particles on the right hand side of the channel, but the transition to cross section B suppresses the second stable position and encourage all the particle to flow in a single location of the right hand side of the channel. This effect is illustrated in  FIGS.  16 A-D  where one of the two stable positions is effectively eliminated. Accordingly, the two stable previously focused regions shown in  FIG.  16    may be collapsed into one focal region located within a portion of the cross section of the particle focusing channel. 
     To further clarify, because the target particles were urged into two spaces with aspect ratio greater than one, but two different spaces with aspect ratio less than one, the effect is to undermine or suppress one of the stable positions of the particles as illustrated in  FIG.  16 B ,  FIG.  16 C  and  FIG.  16 D . In these illuatrations, the lone of the two loci of particles is effectively suppressed, leading only one locus in the flow channel, that being on the right side of the short dimension of the channel as illustrated in  FIG.  16 D .  FIG.  16 C  and  FIG.  16 D  show the flows and the remaining focal spot within the cross section. 
     Another way to shift the locations of the stable position within the flow channel, is to impose a 90° turn in the fluid path. This may provide an effect similar to the change in aspect ratio from AR&gt;1 to AR&lt;1, but in the orthogonal dimension. As such, the effect is difficult to render in a 2-dimensional drawing. Nonetheless, the novel flow path is depicted in  FIG.  17   . It should be understood that the dashed portions of the flow pass shown in  FIG.  17    may lie under, over, or adjacent to their projection of the solid lines shown in  FIG.  17   . 
     One of the limiting issues in the particle manipulation system described above, is the dynamic range of the detector. The detector may be, for example, a photomultiplier tube (PMT) which creates a cascade of charges when a photon strikes the detector surface. Weak signals, for example a single photon, may be detected by these sensitive devices. However, for stronger fluorescent signals, the cascade may saturate, limiting the dynamic range and thus reducing the quality of the information collected by the detector. 
     A single photodetector has a limited dynamic range at a given gain setting. If light levels need to be measured that are outside of this range, the gain must be manually adjusted in order to put the light levels within the limited dynamic range of the detector. The invention applies to flow cytometry and to automatically adjust the detector gain during the measurement of each particle. Downstream processing will combine the signal from the detector with the gain setting that was used for each instant of time to generate a high dynamic range output signal. This technique eliminates the manual gain adjustment and effectively increases the dynamic range of the sensor so that a larger range of light levels can be measured. 
     The system and circuit described below may provide a high resolution, wide dynamic range optical detector when using a high sample rate Analog to Digital Converter (ADC). 
     The detection platform does not require special front-end optics or multiple optical detectors in order to achieve a high dynamic range. The resulting dynamic range will be higher than the optical detector can deliver when using a fixed gain. 
     This platform generates a high speed gain modulation signal which is synchronized to the clock used for the ADC. The gain modulation signal is 50% of the frequency of the ADC clock, and is phase-locked to the ADC clock. The phase between these signals is adjusted such that every other sample from the ADC will be measuring the response of the detector when it is using the high gain setting, and every other sample will be measuring the response of the detector when it is using the low gain setting. 
     The signal processing system separates the high gain and low gain digital sample streams and performs digital signal processing (DSP) on these streams. The conditioned streams are then scaled and recombined into a single, high resolution, wide dynamic range stream. 
     The optical detector and amplification electronics are able to respond properly to the high frequency gain control signal. The signal processing can be tuned to the detector and amplifier electronics in order to generate an accurate output stream. 
     In one embodiment, the gain may be switched between two discrete gain levels, called a lower level and a higher level. Obviously, the higher gain level is higher than the lower gain level. The downstream processing may be synchronized to the timing of the lower and higher gain levels to generate the high dynamic range output signal. 
     In one embodiment, the gain may be switched between more than two discrete gain levels.] 
     In another embodiment, the gain is adjusted continuously between two gain levels using a predetermined sequence or pattern. A simple example would be a sine wave at a fixed frequency. Because the pattern of the gain control signal is known, the downstream electronics can use timing to determine the precise gain setting that was used for each instant of time. 
     In another embodiment, the gain is adjusted continuously to keep the output signal within the range of the measurable levels of the downstream electronics. Commonly called automatic gain control. The downstream processing may combine the precise gain setting with the output signal of the detector for each instant of time. 
     Accordingly,  FIGS.  18  and  19    describe such a system, wherein the gain on the detector is changed dynamically by a circuit including, in some embodiments, a gain changer or gain modulator, an ADC and a signal processing circuit that demultiplexes and then applies a suitable gain to the higher and the lower sample streams, independently. The sampler streams may then be recombined. 
       FIG.  18    a is a simplified schematic illustration of a manner for implementing a gain change function on the florescence detector, here a photomultiplier tube (PMT). The gain on the detector may be modulated, toggled, or varied between a higher value and a lower value by a gain controller  1610 . This will result in a signal which varies or is modulated between a higher value  1601  and a lower value  1602 . 
     In  FIG.  18 (A) , portions of the plot labeled with reference number  1601  correspond to the signal amplitude when the gain is at the first higher value, i.e. a higher gain is applied to the signal. The modulation may be characterized by an amplitude and a frequency f. Reference number  1602  indicates the portions of the signal curve where the gain is set to the lower value, i.e. less gain is applied to the signal. The amplitude of the signal thus cycles back and forth between two levels, a higher level  1601  and a lower level  1602 . 
     This variable signal can then be sampled using a clock phase-locked to the gain changing frequency. As mentioned previously, the frequency of the sampling clock may be 2f, whereas the modulation frequency is f. The sample stream from the sampling circuit may then consist of a sequence of values at the higher level  1601 , interleaved with a sequence of values at the lower level  1602 . The phase locked sample stream may then be sent to an ADC  1605 , as shown in  FIG.  18 (B) . As mentioned, the sampling clock and ADC  1605  may be synchronized with the gain controller  1610  of detector, such that the analog to digital converter samples first a high value,  1601 , followed be a lower value  1602 . As a result, the data coming from the ADC  1605  may consist of a sequence of interleaved higher and lower digitized numbers. 
     The output of the analog to digital converter may then be provided to a splitter,  1620  or demultiplexer, as shown in  FIG.  19   . The purpose of the splitter divides the higher gain elements, and the lower gain elements, into two different data streams. The upper path in  FIG.  19    corresponds to the higher amplitude samples  1601  and the lower path corresponds to the lower amplitude samples  1602 . These two pulse trains may be applied to digital signal processors  1630  and  1630 ′ respectively. The DSP may provide whetever additional signal conditioning may be desired. 
     A scaling circuit  1640 ,  1640 ′ may then provide a final opportunity to adjust the magnitude or amplitude of the data, or other attributes. The signals may then be recombined by a combiner or multiplexer  1650 . 
     It should be understood that the embodiment shown and  FIGS.  18  and  19    are exemplary only, and many other circuits may be envisioned to accommodate the particle manipulation system with cytometric capability and feedback loop and variable gain detector. 
     In another embodiment, the excitation laser described previously can be modulated instead of the gain of the detector. This accomplishes the same thing. There may be at least two ways. In one embodiment, a single laser may be modulated between a higher and lower power setting. In another embodiment, two lasers may be used, one at higher power that is turned on/off at high speed, and one lower power laser that is continuously on. This low power laser can be very inexpensive. Another alternative is to provide an external variable optical attenuator (VOA) on the output of the laser. 
     Machine learning and artificial intelligence techniques as described above may also be applied to the variable gain controller  1610  and the sampling clock  1615 , to fine tune their performance with respect to the control variables and performance metrics. 
       FIG.  20    is a system-level view showing, among other things, an exemplary layout and connections between the various components of a particle manipulation system  1000  using camera/classifier confirmation. The microfabricated particle manipulation device  100  or  100 ′ with camera/classifier confirmation  400  may be used in a particle manipulation system  1000  and enclosed in a housing containing the components shown in  FIG.  20   . The MEMS particle manipulation devices  100  or  100 ′ may be enclosed in a plastic, disposable cartridge which may be inserted into the system  1000 . The insertion area may be a movable stage with mechanisms available for fine positioning of the particle manipulation device  100  or  100 ′ and associated microfluidic channels against one or more data, which orient and position the detection region and particle manipulation device  100  or  100 ′ with respect to a set of collection optics  1100 . If finer positioning is required, the inlet stage may also be a translation stage, which adjusts the positioning based on observation of the location of the movable member  110  relative to a datum. 
     A camera/classifier confirmation system  1600  may also be included in the particle manipulation system  1000  as show schematically in  FIG.  20   . It should be understood that although  FIG.  20    shows a particle sorting system  1000  which uses a single laser source  1400 , multiple light sources, multiple detection optics and multiple channels may also be used. As mentioned previously, other interrogation means may be used instead of or in addition to lasers. The camera system  1600  may be analogous or equivalent to the camera system  160  shown in the previous figures. 
     Another module,  1680 , may perform the gain modulation, ADC, and DSP functions described above with respect to  FIGS.  18  and  19   . 
     The embodiment shown in  FIG.  20    may be based on a FACS-type detection mechanism, wherein one or more lasers  1400  impinges on the sample inlet channel  120  as described above. The relative amount of light may be monitored by a computer  1900 . The computer  1900  may then generate a control signal that controls the force-generating means or electromagnet  500 . Upon receipt of a fluorescence signal from a target particle, the controller  1900  may output a sort trigger that causes the electromagnet  500  to be energized, thus moving the movable member  110  into the sort position shown in  FIG.  7   . The movable member thus diverts the target particle from the input channel  120  into the sort channel  122  rather than the waste channel  140 . This is normal operation of the microfabrication particle sorting system  1000 . The controller  1900  may generate a camera trigger (as well as a sort trigger) based on the detection of this fluorescence signal. 
     The other optical components in particle manipulation system  1000  may include a beamsplitter  1500  and multiple color detectors  1300 . The beam splitter  1500  may reflect the incoming light from laser  1400  onto the MEMS manipulation device  100 . 
     The output of detectors  1300  may be analyzed by the controller  1900  and compared to a threshold in normal operation. The controller  1900  may be understood to be operating in conjunction with the deep learning module  1950  described above, where in the deep learning module may include an annotated image library  1960  and a classifier  1970  and an analyzer  1980 . 
     Accordingly, the particle manipulation system may include a particle manipulation stage and a sample stream in a microfluidic inlet channel, an optical interrogation device upstream of the particle manipulation stage which identifies target particles, and an optical confirmation device downstream of the particle manipulation stage, wherein the optical confirmation device uses a camera to determine the presence or absence of a target particle. 
     In one embodiment, the MEMS particle manipulation system  1000  may be used in conjunction with one or more additional downstream cameras  160 , wherein the additional cameras are used to confirm the effectiveness or accuracy of a manipulation stage in manipulating a stream of particles. The downstream evaluation by camera, as described above, may occur beyond the sorting stage  100  or  100 ′ and may allow the operator to measure one event number (e.g. the captured event rate post-sort) divided by another event number (e.g. the initial event rate pre-sort) for individual particle types, and to feedback to adjust initial interrogation parameters (e.g. such as x, y, z position and also “open window” length in time) based on this ratio. This method may thus be used to optimize the yield or accuracy of the system  1000 . 
     Alternatively, the operator could measure the event rate post-sort of target cells, divided by total event rate post-sort feedback to adjust initial laser interrogation parameters such as x, y, z position and also “open window” length in time, in order to optimize the purity of the sorting system  1000 . These sorting parameters may be adjusted by changing control signal  2000  which is sent by computer  1900  to electromagnet  500 , or by changing the optical detection parameters or by changing the laser control signals, as shown in  FIG.  20   . In any case, the camera system  1600  may be used in conjunction with controller  1900  to improve or optimize the performance of the system with respect to at least one measured parameter. 
     Accordingly, the particle manipulation system may image the target particles with the camera, determine the locus of the particles within a field of view of the camera with a controller, and adjust a sorting parameter. The system may optionally be used with machine learning or artificial intelligence techniques to choose superior sorting parameters. One such sorting parameter is the timing of the sort gate, but other parameters may include at least one of laser fluorescent pulse shape, width, magnitude or duration, laser intensity, optical alignment or focusing, gate duration, and so forth. These parameters may be optimized with respect to purity, yield, or some other measured output of the system  1000 . 
     The particle manipulation system described above may make use of any of a number of particle manipulations. These manipulations may include moving the particles using a pressure pulse, so as to guide them in a particular direction. Other manipulations may include washing, mechanical interference such as pushing or squeezing, application of heat, cooling, application of fields such as magnetic or electric fields. This field-based manipulation may result in electroporesis, transfection, or electrophoresis which may alter the trajectory of the particles. More broadly, the particle manipulation system may be combined with transfection of wide-ranging sorts and methodologies. 
     As discussed further below, the system  1000  may include internet capability, remote operation and remote data storage. The required connections to the internet, cloud, or data repository  5000  may be hardwired or wireless, and may allow non-local operation by a remote operator  4000 . 
     Many sorts of particle manipulations are envisioned using this system. The manipulations may include, for example, mechanical probing, squeezing, slicing, rupturing. Other embodiments may use heating, tagging, sorting, imaging, counting. The particle may be focused into a particular streamline, which may improve performance of the system. 
     In some embodiments, the particle manipulation system may be coupled to a fluidic focusing structure as described above, which tends to concentrate the particles in a particular portion of the microfabricated channel. The fluidic focusing system may include the three-dimensional focusing channel described above, which may focus the ensemble of particle into stream lines near the center of the channel. 
     In some embodiments, the particle manipulation system may be coupled to a droplet generator which generates droplets containing one or more known, identified particles. These droplets may optionally be dispensed into an immiscible fluid, such as water droplets into a hydrophobic fat or an oil. These particles may be brought into the droplet or sequence of droplets in a particular desired order, under computer control, by proper manipulation of the system. The target particles may also be coupled to a bar coded bead which identifies uniquely the bead/particle combination, and thus identifies uniquely the bound particle. 
     In some embodiments, the particle manipulation system may be coupled to a genetic sequencer, that may sequence the DNA or RNA of the particles enclosed in the droplet. 
     In some embodiments, the particle manipulation system may be combined with a device that can activate a particular bioactive compound, for example a protein. The protein may be activated optically (photoactivation) or chemically, for example. The activated compound may then interact with the manipulated particle. 
     In other embodiments, the particle manipulation system may be combined with a selective lysis system. In this case, the manipulated particles may be lysed on demand, and only particular cells subjected to the lysing. The lysant may be photoactivated. 
     Similarly, the particle manipulation system may be combined with a selective optical activation system, for example a selectable UV light source. The UV light may photoactivate a bleaching/quenching system, wherein the UV light is applied to a fluorophore to quench the fluorescence. This system may use the above described hardware and software system to apply the photoactivation to only a subset of targeted particles. 
     In many of these embodiments, a measurement (of a control variable) is made using a sensor, and this measurement may form the basis of a feedback system wherein a manipulation parameter is adjusted based on the value of the measurement (of the control variable), and the measurement is taken again after the adjustment. Thus the “manipulation parameters” may be those variables used by the control loop to alter the performance of the manipulation system in some way. Accordingly, the feedback loop may be used to drive the measurement of this control variable to a predefined level, using the manipulation parameters. 
     Examples of control variables may include Hall effect detection, fluorescence intensity, scatter, side scatter, locus of particle detected, statistics as to the relative location of particles in the channel. Additionally, capacitive measurements may be used to detect the passage of the target particle within the channel. Other indicators may include the deflection of an mechanical device, sensor or actuator. Accordingly, the control variable may be, for example, fluorescence, capacitance, mechanical or spectroscopic data, the number of live or dead cells passing through the device, or their ratio. The feedback loop may be operable to improve or maximize an aspect of the manipulated population, such as their purity or yield, ratio of live to dead. 
     Fourier-transform infrared (FTIR) spectroscopy may also be used to measure a fluorescence spectrum of a particle. FTIR is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An FTIR spectrometer simultaneously collects high-resolution spectral data over a wide spectral range. 
     Examples of the manipulation parameters may include timing of a gate for a sorter, duration of the gate signal, waveform of the valve timing signal. Other manipulation parameters may include fluid velocity, fluid pressure, particle concentration. The feedback loop may attempt to improve or maximize the tightness of distribution of the particles in the channel, and the location of their locus. Alternatively, sort efficiency, yield, timing information, velocity, fluid flow rate, disturbances in the flow arising for example from the opening or closing of a valve. As mentioned previously, the parameters that may be adjusted based on the measurements may be valve timing, sort gate, flow rate, viscosity, laser algorithms, and adjusting the timing of the leading and/or trailing edges of the valve gate signal. 
     In some embodiments, the particle manipulation system may be coupled with a cell counter/analyzer or cytometer, such as the MACS Quant, developed and manufactured by Miltenyi Biotec B.V. &amp; Co. KG. The cytometer may provide valuable analytical information such as particle size and distribution, wherein this information is then shared with the particle manipulation system to further optimize the manipulation in terms of target particle and cell populations. 
     The cytometer may alternatively by disposed downstream of the particle manipulation system, in order to gather information or statistics as to the performance of the particle manipulation system. The cytometer may assess the sort purity or yield, for example. 
     In other embodiments, the particle manipulation system may be coupled to a particle sorting system. The particle sorting system can be configured to perform a pre-sort or debulking, to remove a large number of non-target species, before routing the sorted stream to the particle manipulation system. A magnetic bead cell separation, for example using Miltenyi Biotec B.V. &amp; Co. KG MACSiMag, may do a pre-sort/debulking to reduce the concentration of cells in a sample. A cell handling system such as the Miltenyi Biotec B.V. &amp; Co. KG CliniMACS Prodigy may be used to increase automation and reduce handling of the fluids and samples, for example. 
     In other embodiments, the particle manipulation system may be operated in conjunction with a cloud computing system, wherein operational software is downloaded from the cloud, and the results of the procedure may be uploaded. After downloading an algorithm with control parameters and target quantities for the feedback loop, the results of the particle manipulation may then be uploaded to the cloud for remote evaluation. The cloud may serve as a repository of data for manipulations occurring in different geographic locations, such that results may be quickly and easily compared. 
     In other embodiments, the particle manipulation system may be coupled to a robotically controlled automation system. The system may perform the manipulations of fluids such as buffers, reagents and lysants, to name just a few. When combined with a plurality of fluid receptacle such as multiwell titer plates,, large scale parallel operations can be performed, greatly improving throughout and efficiency. Very few human operators would be needed to oversee the operations, and the oversight could b done remotely, increasing the overall safety of the system. As before, remote operation could be easily combined with robotic control over the system, cloud-housed software and global data repositories. 
     The particle manipulation system can be implemented on manufacturing lines, such as cell manufacturing lines, and can thus serve as quality control devices, to maintain the integrity of the manufacturing process. Any deviation from expected values, for example, purity, yield and viability, could prompt the interruption of the manufacturing process for failure analysis to take place. Again, this can all be done remotely. 
     The particle manipulation system may be combined with PCR testing to amply the effluent or to confirm the identity of the pathogen. 
     In other embodiments, the particle manipulation system may be coupled with other cell manufacturing or research tools, such as incubators and centrifuges. In other embodiments, the system may be coupled to at least one of a mixer, a stirrer, a well plate, an optical analyzer, and an imaging system. 
     The coupling may be done through direct fluidic plumbing, or alternatively by robotic transfer such as pipetting, or, of course, under human control. 
     As mentioned, the data may be uploaded to an internet-enabled data repository  5000 , and a remote operator  4000  may be notified that the algorithm has run to completion, and that results are available. The operator can be notified by SMS texting, a cell phone message or an email, for example. The communications may be effected over Bluetooth, WiFi or cellular service to an operators phone, computer or other mobile device. 
     The algorithm could be self-correcting, that is, under feedback control, for a largely completely automated process. Combined with robotically controlled tasks such as the movement of fluids, the entire process may be possible with little or no human intervention. 
     Alternatively, the system can adaptively respond to events occurring, such as an unexpected change in pressure or flow, indicating that a clog is forming in a channel. 
     The algorithm may make use of a preconfigured setup, designed around the particular application. For example, if it is desired to sort a particular sort of cell such as a tumor, stem or immune cell, a pre-determined package of parameters may be downloaded from the cloud and installed on the particular particle manipulation system. Upon successfully running that algorithm, the operator may be informed wirelessly of the outcome, and that the data has been posted to the cloud or to some other data storage device. The data storage device may be made accessible to other researchers, clinicians or operators, in order to compare the data and outcomes. The parameters may include compensation parameters related to size, fluorescence or some other attribute of the particle. 
     Accordingly, disclosed here is a variable gain detector, using a circuit that varies the gain applied to a detector between at least two values, a higher value and a lower value, based on an intensity of an incoming signal. The detector may further comprise a sampling circuit that samples the higher value and the lower value, and digitizes these samples.- The detector may further comprise a demultiplexer that separates the digitized higher value and digitized lower value. The detector may further comprise at least two signal conditioning circuits that separately condition the digitized higher value and the digitized lower value. The detector may further comprise at least two signal conditioning circuits apply a first gain to the digitized higher value and a second gain to the digitized lower value. A variable gain detector, comprising: a circuit that varies the gain applied to a detector dynamically between at least two values, a higher value and a lower value, based on an intensity of an incoming signal. 
     The variable gain detector may further comprisea sampling circuit that samples the higher value and the lower value, and digitizes these samples. The detector may further comprise a demultiplexer that separates the digitized higher value and digitized lower value. Within the variable gain detector, the circuit may include a gain modulator, an ADC and a signal processing circuit that demultiplexes and then applies a suitable gain to the higher and the lower sample streams, independently. 
     The variable gain detector may further compriseat least two signal conditioning circuits that separately condition the digitized higher value and the digitized lower value. the at least two signal conditioning circuits apply a first gain to the digitized higher value and a second gain to the digitized lower value. 
     The variable gain detector may further comprise a splitter that divides the higher gain elements, and the lower gain elements, into two different data stream, an upper path and a lower path. 
     The upper path may correspond to the higher amplitude samples and the lower path may correspond to the lower amplitude samples 
     The two different data streams are applied to two different digital signal processors. 
     A system for manipulating particles is also disclosed. The system may include a microfabricated cell sorting system, which distinguishes target cells from non-target material, wherein the target cells are distinguished by a laser-induced fluorescent signal, and wherein this laser-induced fluorescent signal is detected by the variable gain. 
     The system for manipulating particles of claim  7 , wherein the cell sorting system includes a microfabricated valve that separates the target particle from non-target material. 
     The system for manipulating particles of claim  8 , wherein the valve moves in a plane parallel to a fabrication plane, and uses electromagnetic actuation. 
     Also disclosed here is a method for operating a variable gain detector. The method may include providing a circuit having variable gain, and applying dynamically a higher value and a lower value, based on an intensity of an incoming signal.The method may further include providing a sampling circuit that samples the higher value and the lower value, and digitizes these samples into higher digitized values and lower digitized values. 
     The method may further include providing a demultiplexer that separates the digitized higher digitized values and the lower digitized lower values into two different data streams. 
     The method may further include providing a gain modulator, an ADC and a signal processing circuit that demultiplexes and then applies a suitable gain to the higher and the lower sample streams, independently. The method may further include providing at least two conditioning circuits, wherein the two conditioning circuits condition the higher digitized values and the lower digitized values separately. 
     Within the method, the at least two signal conditioning circuits may apply a first gain to the higher digitized values and a second gain to the lower digitized values. 
     The method may further comprise providing a splitter that divides the higher digitized values, and the lower digitized values, into two different data streams, an upper path and a lower path. Within the method, the upper path may correspond to the higher amplitude samples and the lower path may correspond to the lower amplitude samples. 
     While various details have been described in conjunction with the exemplary implementations outlined above, various alternatives, modifications, variations, improvements, and/or substantial equivalents, whether known or that are or may be presently unforeseen, may become apparent upon reviewing the foregoing disclosure. Accordingly, the exemplary implementations set forth above, are intended to be illustrative, not limiting.