Patent Publication Number: US-8987841-B2

Title: Backside stimulated sensor with background current manipulation

Description:
RELATED APPLICATIONS 
     This application is a continuation-in-part of U.S. patent application Ser. No. 13/950,116, filed Jul. 24, 2013, which is hereby incorporated by reference. U.S. patent application Ser. No. 13/950,116 is itself a continuation of U.S. patent application Ser. No. 12/853,160, filed on Aug. 9, 2010, now U.S. Pat. No. 8,519,490, also hereby incorporated by reference. 
    
    
     BACKGROUND 
     1. Technical Field 
     Embodiments of affinity based sensors are disclosed herein. In particular, but not exclusively, embodiments of backside stimulated CMOS (Complementary Metal Oxide Semiconductor) type sensors are disclosed herein. In embodiments, the sensors utilize their background current to measure affinity related stimuli to their backside surfaces. 
     2. Background Information 
     Affinity based detection is a fundamental method of identification and measurement. For example, affinity based detection may be used to identify and measure the abundance of biological and biochemical analytes. It is an important analytical method in many fields of endeavor including biotechnology. Affinity based biosensors utilize selective interaction and binding of a target analyte with immobilized capturing probes to specifically capture the target analyte onto a solid surface. Such specific capturing generates detectable signals based on the captured analytes. The generated signals correlate with the presence of target analytes, e.g., ions, toxins, polymers, hormones, DNA strands, protein, cells, etc., and hence are used to estimate the analytes&#39; abundance. 
     To create the target-specific signals, the target analytes in a sample first collide with a capturing layer that is equipped with probes, bind to the probes, and initiate a transduction process, i.e., a process that produces measurable signals, e.g., electrical, mechanical or optical signals, that are produced solely by the captured entities. The signals are then processed by various means, for example, semiconductor based signal processing techniques. 
     Various affinity based sensors are known in the arts. However, there is a general need in the art for new and useful affinity based sensors. 
    
    
     
       BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS 
       The invention may best be understood by referring to the following description and accompanying drawings that are used to illustrate embodiments of the invention. In the drawings: 
         FIG. 1  is a cross sectional view of a CMOS biosensor system showing bio-probes on the backside surface. 
         FIG. 2A  is a cross sectional view of a CMOS biosensor backside surface showing positive ions binding to the backside surface. 
         FIG. 2B  is a cross sectional view of a CMOS biosensor backside surface showing negative ions binding to the backside surface, 
         FIG. 2C  is a cross sectional view of a CMOS biosensor backside surface showing heparin molecules binding to protamine bio-receptors on the backside surface. 
         FIG. 2D  is a cross sectional view of a CMOS biosensor backside surface showing target DNA binding to probe DNA bio-probes on the backside surface. 
         FIG. 2E  is a cross sectional view of a CMOS biosensor backside surface showing target antigen binding to antigen bio-probes on the backside surface. 
         FIG. 2F  is a cross sectional view of a CMOS biosensor backside surface showing analyte binding to enzyme bio-probes on the backside surface. 
         FIG. 2G  is a cross sectional view of a CMOS biosensor backside surface showing analyte stimulating a cellular bio-probe on the backside surface. 
         FIG. 2H  is a cross sectional view of a CMOS biosensor backside surface showing analyte stimulating a tissue bio-probe on the backside surface. 
         FIG. 3A  is a perspective sectional view of a CMOS pixel that contains a diode and STI structure, without manipulation to the diode or the STI structure. 
         FIG. 3B  is a perspective sectional view of a CMOS pixel that contains a diode that has been manipulated to possess a different geometric shape from an unmanipulated diode. 
         FIG. 3C  is a cross sectional view of a CMOS pixel that contains an STI structure that has been manipulated to possess a surface that is rougher than that of an unmanipulated STI structure. 
         FIG. 3D  is a cross sectional view of a CMOS pixel that has been manipulated to contain dopant that affects the background current of the CMOS pixel. 
         FIG. 3E  is a cross sectional view of a CMOS pixel in the vicinity of an inductive element or member that alters the temperature of the CMOS pixel, thereby affecting the background current of the CMOS pixel. 
         FIG. 3F  is a cross sectional view of a CMOS pixel in the vicinity of a inductive element or member, a temperature sensor, and a reference pixel, forming a feedback mechanism that controls the temperature of the CMOS pixel, thereby affecting the background current of the CMOS pixel. 
         FIG. 4A  is a cross sectional view of a CMOS pixel array that detects the movement of charged entities at or near the backside surface. 
         FIG. 4B  is a cross sectional view of a modified backside surface of a CMOS pixel array where bump structures form channels that facilitates the detection of the movement of charged entities. 
         FIG. 5  is a cross sectional view of a CMOS biosensor system that contains a cantilever structure on its backside surface. 
         FIG. 6A  is a cross sectional view of the backside surface a CMOS biosensor pixel that includes a cantilever structure that couples to the backside surface through a block type structure. 
         FIG. 6B  is a cross sectional view of the backside surface a CMOS biosensor pixel that includes a cantilever structure that couples to the backside surface through a tip type structure. 
         FIG. 6C  is a cross sectional view of the backside surface a CMOS biosensor pixel that includes a cantilever structure that is substantially situated on the backside surface. 
         FIG. 7  is a block diagram illustrating a CMOS biosensor, in accordance with an embodiment. 
         FIG. 8  is a circuit diagram illustrating sample pixel circuitry of two CMOS biosensor pixels within a biosensor array, in accordance with an embodiment. 
         FIG. 9  is a cross sectional view of a CMOS ion sensor system with a reference electrode proximate to its backside surface, in accordance with an embodiment. 
         FIG. 10  is a cross sectional view of a CMOS ion sensor system having a reference electrode structure on its backside surface, in accordance with an embodiment. 
         FIG. 11  is a cross sectional view of a CMOS ion sensor system having a reference electrode structure opposite its backside surface, in accordance with an embodiment. 
     
    
    
     DETAILED DESCRIPTION 
     In the following description, numerous specific details are set forth. However, it is understood that embodiments of the invention may be practiced without these specific details. In other instances, well-known circuits, structures and techniques have not been shown in detail in order not to obscure the understanding of this description. 
     Throughout this specification, several terms of art are used. These terms are to take on their ordinary meaning in the art from which they come, unless specifically defined herein or the context of their use would clearly suggest otherwise. “Background Current” is defined herein as the current that flows in a sensor in the absence of an outside signal input such as incident light, and is produced by the inherent characteristics of the material property of the diode and also by stress in the sensor. “Affinity Based Binding” is defined herein as binding of analyte or analytes to probe or probes that are immobilized on a biosensor&#39;s detection surface, which produces signals, e.g., optical, magnetic, electrical, electrochemical, or electro-mechanical, that are detectable to the biosensor. “Backside” is defined herein as the side of the substrate that is opposite to the front side, where the metal stack architecture is situated. The terms “biosensor” and “bio-probes” are used to describe the sensor embodiments and the probe embodiments. However, the sensors and probes as described in this disclosure are not limited to bio-applications. The disclosed sensors and probes also pertain to other fields of application, including but not limiting to ionic, chemical, electrical, mechanical and magnetic applications. 
     In one or more example embodiments, a CMOS pixel, such as a backside stimulated biosensor pixel, for sensing at least one selected from a biological, chemical, ionic, electrical, mechanical and magnetic stimulus, may include a substrate including a backside. A source may be coupled with the substrate to generate a background current. In one aspect, the source to generate the background current may include a diode that is substantially disposed within the substrate. A detection element, such as a circuit, may be electrically coupled to measure the background current. In one or more embodiments, the detection element may be a circuit or other element (e.g., readout circuitry) suitable for reading a pixel of a pixel array. The backside surface of the CMOS pixel may include a layer of probes or bio-probes that affinitively binds to analyte. The affinity based binding increases or decreases electrical charge at or near the backside surface, thereby causing a change in the background current or a stimulus. The stimulus, which is to be provided to the backside, may affect a measurable change in the background current. While the term pixel is used herein, it is not required that the pixel be used for imaging or even that the pixel detect light or electrons corresponding to light. Rather, the pixel may have a photodiode or diode that is used as a source of background current but rather than the photodiode being used as a photodetector the photodiode may optionally be masked (e.g., with a light or electron blocking layer or material), covered, shielded or otherwise blocked from receiving light or corresponding electrons so that it need not actually detect light but may instead be used primarily as a source of background current. 
     A CMOS “backside” stimulated biosensor pixel is distinguished from a “frontside” stimulated biosensor pixel. A typical CMOS pixel includes a silicon substrate at the bottom, an active device such as a transistor positioned on the substrate, several metal and dielectric layers above the active device. Bio-probes could be positioned on the top surface. The interaction between analytes and bio-probes could produce signals that travel through the metal and dielectric layers to the active device. The signals could then be measured by the active device and supporting circuitry so as to quantify the affinity based effects or the amount of interaction between the analytes and the bio-probes. A significant drawback of a conventional CMOS pixel architecture is the multiple layers of metals and dielectrics that are stacked on top of the active device. These multiple interconnect layers are used to electrically access the transistors, to create a certain circuit topology, and to reduce undesired interaction between a fluidic sample to be analyzed and the semiconductor structures. However, these multiple layers also add to the stack height, would increase the bulk of the biosensor system, and lead to higher system complexity and cost. The thickness of the stack may also cause a reduction in detection sensitivity and accuracy. It is desirable to reduce or eliminate these layers while still allowing access to the transistors and protecting the semiconductor structures from interaction with the fluidic sample. 
     Instead of transmitting affinity based binding signals into the CMOS integrated circuit from the top of the chip through a top metal layer, the signals may be coupled into the CMOS pixel from the bottom and immediately through the substrate. Instead of being placed on a top metal layer, the bio-probes may be constructed at the backside of the CMOS pixel on the substrate&#39;s backside surface. A backside stimulation scheme has been successfully adopted for CMOS image sensor pixels, such as OmniVision™ Backside Illumination CMOS imager products. However, prevalent teaching in the CMOS biosensor art suggests that “electrical signals can only couple from the top and through the pads”, i.e., from the front side of the CMOS pixel where the metal/dielectric layers are formed (B. Jang and A. Hassibi, “Biosensor Systems in Standard CMOS Processes: Fact or Fiction?” Proc. of IEEE International Symposium on Industrial Electronics (ISIE), 2049, 2008). A backside stimulation scheme challenges this conventional wisdom. 
     In addition to backside stimulation, for certain biosensor embodiments, rather than using a conventional electrode to measure electrochemical signals, such as impedance, potential, current and I-V curves, at the analyte-electrode interface, embodiments utilize the CMOS pixel&#39;s background current as a measurement tool. 
     In electronic arts, background current is alternatively known as leakage current. It is primarily caused by electronic devices that are attached to capacitors, such as transistors or diodes, which conduct a small amount of current even when they are turned off. For a CMOS image sensor, background current is frequently referred to as dark current. It is the leakage current at the photodiode node, which discharges the pixel capacitance even though there is no light to stimulate the photodiode. Background current may be described as having at least two components, ideal background current and stress generated background current. 
     The ideal background current depends in part on the doping concentration, band gap, and the temperature of the photodiode. The ideal background current further includes two sub-components. The first is an injection-diffusion current due to the injection of thermal electrons and holes having a higher energy than the built-in potential energy of the p-n junction. The second is a generation-recombination current due to thermal electron-hole generation or recombination within the p-n junction. These two components depend on applied voltage and temperature. The ideal background current is a result of inherent characteristics of the material properties of the p-n junction. 
     The stress generated background current is determined by the characteristics of individual defects in the structure of the CMOS pixel. The properties of the material employed in the construction of the CMOS pixel and the supporting devices induce background current in the CMOS pixel through various mechanisms. These mechanisms may include the following. First, the background current may be produced by a junction leakage of the photodiode, as well as other leakages through structural defects or limitations of the photodiode and its surrounding structures. Second, the background current may be produced by a sub-threshold leakage of the transistors that are connected to the photodiode. Third, the background current may be produced by a drain-induced-barrier-lowering leakage, or by a gate-induced drain leakage current of the transistors that are connected to the photodiode. 
     Of particular significance is the leakage current associated with the depletion region of the photodiode edge and the shallow trench isolation (STI) structure due to the material properties at the interfaces. For example, point defects within the sidewalls of the silicon substrate that adjoin the STI structure may generate surface states that function as leakage paths for electrical charges. Further, dopant ions in general, and boron ions in particular, that are introduced into the STI structure during ion implantation steps, may affect the surface passivation of the silicon substrate that abuts the STI structure. These dopant ions may also generate interface charge states that function as leakage paths for electrical charges. 
     Background current has been described in an empirical model as I=αA+, where I represents the background current, a represents the coefficient that determines the junction unity area contribution, A represents junction area, β represents the coefficient that determines the corner contribution, and n represents the number of corners in the design (Igor Shcherback, Alexander Belenky, and Orly Yadid-Pecht, “Empirical dark current modeling for complementary metal oxide semiconductor active pixel sensor.” Opt. Eng. 41(6) 1216-1219, June 2002). The αA term accounts for the ideal background current component, whereas the βn term accounts for the stress generated leakage current component. 
     Background current degrades image quality of a CMOS image sensor. Hence its reduction and elimination is an important goal of CMOS image sensor pixel design. Described herein are various embodiments that utilize the normally undesirable background current as a measurement tool for affinity binding of a biosensor. Rather than aiming to rid the CMOS pixel of the background current, embodiments described herein maintain an appropriate level of background current, and uses it to detect affinity based effects at the surface of a CMOS pixel, such as affinity based binding at a biosensor surface. 
     For a backside-stimulated CMOS pixel array surface, several sets of circumstances on the backside surface affect the CMOS pixel&#39;s background current. In one set of circumstances, the presence of electrical charge on the backside surface affects the background current. In another set of circumstances, mechanical stress on the backside surface affects the background current. 
     The following experimental results suggest that electrical charge present on the backside surface affects both the background current and the image quality of a CMOS image sensor. In a first experiment, the backside surface contained imperfections of an ionic nature. Accordingly, white spots were present at the sites of imperfection. These white spots had a higher background current value than the surrounding area. After a stripping process step, the surface charge imperfections were removed, thereby eliminating the white spots. Accordingly, the former white spots took on a background current value that was the same as the surrounding area. 
     In a second experiment, before application of a voltage to a CMOS image sensor array&#39;s backside surface, background current was observed for each pixel. Different pixels produced different, but still relatively similar background currents. After a positive voltage application, the surface acquired a positive electrical potential across the board. Accordingly, the background current in different pixels were increased to a point where the entire backside surface became a “white zone”. In short, by applying a uniform voltage bias to the backside of a CMOS image sensor, defect-free pixels may be made to look like defective, white spot like pixels, so long as a right voltage level is applied. Conversely, by applying a negative voltage bias, defective pixels may be made to look like defect-free pixels. 
     These experiments suggest that for a backside-stimulated CMOS pixel, surface charge affects background current behavior. Particularly, positive surface charges increase the background current, whereas negative surface charges decrease the background current. This principle may be used to design new types of CMOS sensors that utilize background current as an indicator to measure affinity based effects at the backside surface. Whereas conventional CMOS sensor systems, such as the biosensors disclosed in U.S. Patent Application Publications 2010/0122904, 2010/0052080, rely on the an active device, such as a diode, to measure input signals of affinity based effects, the background current-based sensor system disclosed in the present application cleverly utilizes the CMOS pixel&#39;s innate background current as the basis to measure input signals and affinity based effects. Here, the affinity based effects produce electrical charges at or near the backside surface. These electrical charges modulate the CMOS pixel&#39;s background current. 
     Apart from electrical charges at or near the backside surface, physical stress on the backside surface may also affect background current. As disclosed in U.S. Patent Application 2010/12708330, covering the surface with an extra light shielding layer introduces extra physical stress to the CMOS pixel that alters the background current. This surface stress affect on the CMOS pixel&#39;s background current may be employed to enable a CMOS biosensor similar to the one discussed immediately above. Here, instead of producing electrical charges at or near the surface, the affinity based effect produces additional surface stress that in turn affects the CMOS pixel&#39;s background current. 
     Several backside-stimulated CMOS biosensor systems are disclosed. Bio-probes are immobilized on the CMOS&#39;s substrate backside surface. The affinity based binding of target analyte and immobilized receptors produce signals that are detected by the CMOS pixel. The CMOS pixel utilizes its innate background current to measure the input signals. One class of embodiments relies on affinity based binding to produce electrical charges at or near the backside surface. An alternate class of embodiments relies on affinity based binding to produce physical stress on the backside surface. 
       FIG. 1  illustrates a backside stimulated CMOS biosensor pixel  100 , in accordance with an embodiment. CMOS biosensor pixel  100  includes metal stack  130 , interlayer dielectric  120  disposed over metal stack  130 , and substrate layer  110  disposed over interlayer dielectric  120 . The metal stack  130  may include one or more levels of interconnects disposed in one or more dielectric or insulating layers. Substrate layer  110  further includes STI structures  114 , diode  111 , transfer gate  113 , and floating diffusion structure  112 . The STI structures  114 , diode  111 , transfer gate  113 , and floating diffusion structure  112  are substantially disposed within the substrate  110 . On top of or coupled with backside surface  103  are at least one layer of at least one type of immobilized bio-probes  101 . During use, as analyte  102  binds to bio-probes  101 , the electrical charge characteristic at or near backside surface  103  changes. Such a change of surface characteristic affects the background current behavior of the CMOS biosensor pixel  100 . Accordingly, the affinity based binding affects the background current. The change in background current is detected and processed by the CMOS circuitry. It is to be appreciated that another embodiment may include an array of pixels similar to pixel  100 . 
       FIGS. 2A through 2H  illustrate several embodiments of affinity based binding at or near the backside surface portion of the CMOS biosensor pixel.  FIG. 2A  shows a positive ion affinity backside surface portion  210  that includes a substrate  211  and a negatively charged surface layer or negatively charged entity  212 . The negatively charged surface layer  212  may include SiO 2 , Si 3 N 4 , Al 2 O 3 , or Ta 2 O 5  in a proton-acceptor state. The proton-acceptor state of the negatively charged surface layer  212  allows it to bind to positive ion analyte  213  such as proton H+. 
       FIG. 2B  shows a negative ion affinity backside surface portion  220  that includes a substrate  221  and a positively charged surface layer or positively charged entity  222 . The positively charged surface layer  222  may include SiO 2 , Si 3 N 4 , Al 2 O 3 , or Ta 2 O 5  in a hydroxide-acceptor state. The hydroxide-acceptor state of the positively charged surface layer  222  allows it to bind to negative ion analyte  223 , such as hydroxide OH—. 
     In some embodiments, the CMOS ion sensors of  FIGS. 2A-2B  may be operable to sense and/or measure ions (e.g., ion concentrations) in a solution or electrolyte. In some embodiments, the CMOS sensors may be used to sense or measure hydronium ions (H 3 O + ), such as, for example, to measure the pH of a solution. The pH of a solution represents the negative logarithm of the hydronium ion (H 3 O + ) concentration of the solution. In other embodiments, the CMOS sensors may be used to measure other types of ions, such as, for example, sodium cations (Na + ), silver cations (Ag + ), lead cations (Pb +2 ), cadmium cations (Cd +2 ), chlorine anions (Cl − ), hydroxide anions (OH − ), and various other ions known in the arts. Measurement of these various different types of ions have various uses in industry, medicine, science, and otherwise. The CMOS sensors generally tend to offer an advantage of an ability to measure ion concentration in samples of very small volume. In addition, the arrays of pixels of the CMOS sensors may be used to measure distributions in ion concentrations over a two-dimensional area and/or the spatial distribution in ion concentrations in a very small sample. This may be used for various different purposes in industry, medicine, science, or otherwise. For example, this may be used to measure concentration gradients, measure diffusivity rates, etc. 
       FIG. 2C  shows a heparin affinity backside surface portion  230  that includes substrate  231  and protamine probes  232  that are attached to the substrate surface  234 . Protamine is a positively charged protein that affinitively binds to negatively charged heparin  233 , which is an anticoagulant, i.e., a blood thinner, that is widely used in medical procedures such as renal dialysis, open heart bypass surgery, and treatment of blood clots. Heparin level should be well controlled because heparin overdose leads to dangerous bleeding complications. Affinity based binding between protamine probes  232  and heparin  233  may change the electric charge characteristics at or near the heparin affinity backside surface portion  230 , which is part of the CMOS biosensor pixel  100  shown in  FIG. 1 . Such a change affects background current of the CMOS biosensor pixel  100 . In an alternative embodiment, heparin may be used as a bio-probe to detect protamine analyte. In such an embodiment, the CMOS biosensor system functions as a protamine sensor. Alternatively other positively and negatively charged proteins, or other complementary protein pairs entirely may be used. 
       FIG. 2D  shows a DNA affinity backside surface portion  240  that includes substrate  241  and DNA probes  242  that are attached to the substrate surface  246 . DNA probes  242  are single strand DNA molecules that complementarily bind to analyte, i.e., target DNA  243 . As target DNA  243  binds to DNA probes  242 , the electric charge characteristics of DNA affinity backside surface portion  240  changes. Such change affects the background current of the CMOS biosensor pixel  100  shown in  FIG. 1 . To increase detection sensitivity, target DNA may be modified to produce tagged target DNA  244  by attaching label  245  to the target DNA. Label  245  amplifies the effect of affinity based binding on the electrical characteristics of the CMOS biosensor pixel  100  shown in  FIG. 1 . For example, label  245  may be an electric charge that increases the presence of electric charge at or near the DNA affinity surface  240 . Label  245  may also be magnetic in nature, and affects surface characteristics through electromagnetic effects. Label  245  may also be a redox label such as ferrocene, that may either donate or accept electrons. 
       FIG. 2E  shows an antibody-antigen affinity backside surface portion  250  that includes substrate  251  and antibody probes  452  that are attached to the substrate surface  254 . As analyte antibody  253  affinitively binds to antibody probes  252 , the affinity based binding changes the electric charge characteristics of the antibody-antigen affinity surface  250 . In the present embodiment, antibodies are used as bio-probes and antigens are used as analyte. For example, the analyte may be an antigen toxin produced by an anthrax bacterium, and the bio-probe may be an antibody that specifically binds to the anthrax antigen. Alternatively, if analyte is an antibody, e.g., the HIV antibody in an HIV diagnostic test, then an HIV-specific antigen may be used as a bio-probe that is attached to the antibody-antigen affinity surface  250 . Similar to the DNA-related embodiment, the antigen and antibody in these antigen-antibody embodiments may be tagged with labels in order to increase detection sensitivity. 
       FIG. 2F  shows an enzyme affinity backside surface portion  260  that includes substrate  261  and enzyme probes  262  that are attached to the substrate surface  264 . By way of example, the enzyme probe may be a penicillinase that converts penicillin into penicilloic acid, a urease that converts urea into CO 2  and ammonium, or a glucose oxidase that converts glucose into gluconic acid. Examples of the analyte may be penicillin, urea, or glucose. As analyte  263  binds to enzyme probes  262 , the affinity based binding results in an enzymatic reaction that changes the electric charge characteristics of the enzyme affinity backside surface portion  260 . For example, the enzymatic reaction may produce a reaction product  265  that affects the surface characteristics of the enzyme affinity surface  260 . Examples of the reaction product may be penicilloic acid, CO 2  and ammonium, or gluconic acid. 
       FIG. 2G  shows a cell affinity backside surface portion  270  that includes substrate  271  and a cell probe  272  that is attached to the substrate surface  274 . The cell probe  272  may substantially cover the backside surface of a CMOS biosensor pixel  100  as shown in  FIG. 1 . As analyte stimulus  273  impacts the cell probe  272 , the resulting reaction changes the electric charge characteristics of the cell affinity backside surface portion  270 . For example, the reaction may produce a reaction product  275  that affects the surface characteristics of the enzyme affinity backside surface portion  270 . Alternatively, the cell probe  272  may be a cardiac cell, a muscular cell, or a neuronal cell that produces electrical impulses at or near the substrate surface  274 . 
       FIG. 2H  shows a tissue affinity backside surface portion  280  that includes substrate  281  and tissue probe  282  that are attached to the substrate surface  284 . The tissue probe  282  may substantially cover the backside surface of one or several CMOS biosensor pixels. As analyte stimulus  283  impacts tissue probe  282 , the resulting reaction changes the electric charge characteristics of the tissue affinity backside surface portion  280 . For example, the reaction may produce a reaction product  285  that affects surface characteristics of the tissue affinity backside surface portion  280 . Alternatively, the tissue probe  282  may be an insect antenna that senses analyte stimulus  283  in the environment. The sensing of analyte stimulus  283  produces electrical impulses at or near the substrate surface  284 . 
       FIGS. 3A through 3E  illustrate several embodiments of manipulating a CMOS pixel&#39;s background current so that it may be utilized to measure the CMOS pixel&#39;s surface characteristics. By way of example, the background current may have a range of 10 to 100 electrons per second. In one embodiment, the background current may be approximately 50 electrons per second. An appropriate background current level allows a backside surface stimulus to produce a relatively high signal to noise ratio, which is desirable for detection sensitivity. 
     In one set of circumstances, the geometry of a diode in the CMOS pixel is manipulated or different than typical (e.g., not cubic) to generate a desirable level of background current. In another set of circumstances, the STI structure is manipulated or different than typical (e.g., rougher or different doping than adjacent areas) to generate a desirable level of background current. Yet in another set of circumstances, the background current is dynamically controlled. 
       FIG. 3A  is a perspective view that shows a CMOS pixel  310  that contains substrate  313 , a diode  311  and an STI structure  312  inside the CMOS pixel  310 . Neither the diode  311  nor the STI structure  312  has been manipulated. The geometry of the diode  311  is cuboid (e.g., cubic or rectangular solid). That is the planar cross section is rectangular or square. 
       FIG. 3B  is a perspective view that shows a CMOS pixel  320  that contains a manipulated diode  321 . By way of example, the manipulated diode has a cross sectional geometry that resembles a hexagon. The overall shape is hexagonal solid. This geometry is different from the unmanipulated cuboid diode  311  as shown in  FIG. 3A , whose cross sectional geometry resembles a rectangle or square. A hexagon shaped diode may produce a background current that is different from the background current produced by a cuboid diode. Several factors may cause the hexagon shaped diode to produce a different background current from the rectangular diode. An example of such factors may be that the hexagon shaped diode has more corners and/or angles. Other shapes besides hexagonal are possible, such as having cross sectional shapes with more than four sides. In one or more embodiments, a diode may have more vertical sides or more corners than a cubic or rectangular solid. In one or more embodiments, a diode  321  may have either more angles than a cuboid or less angles than a cuboid. 
     In one or more embodiments, the source to generate the background current may include a shallow trench isolation (STI) structure that is substantially disposed within the substrate. In one or more embodiments, the STI structure of the CMOS biosensor pixel is manipulated or different than typical (e.g., rougher than a typical STI structure or lighter doping profile around it) for the same purpose. 
       FIG. 3C  is a cross sectional view that shows a CMOS pixel  330  that contains a manipulated STI structure  332 . By way of example, the manipulated STI structure  332  contains one or more edges that are rougher than an unmanipulated STI structure. The relative roughness of the edges causes a different amount of stress from smooth edges, resulting in a different level of background current. 
       FIG. 3D  is a cross sectional view that shows a CMOS pixel  340  that contains dopant  345 . By way of example, dopant  345  may include boron ions. Dopant  345  may be around the STI structure  342 . Dopant  345  may have a higher concentration range, or a lower concentration range compared to regions farther away from the STI. An example of the dopant concentration range may be approximately 1014 to 1016 ions per cm3. Another example of the dopant concentration range may be approximately 1017 to 1020 ions per cm3. The presence of dopant  345  that is substantially within a predetermined concentration range affects the surface passivation of the part of substrate  343  that abut the STI structure  342 , and generates interface charge states that function as leakage paths for electrical charges, thereby affecting background current of the CMOS pixel  340 . 
       FIG. 3E  is a cross sectional view that shows a CMOS pixel  350  that contains substrate  353 , a diode  351  and an STI structure  352 . An inductive coil  354  or other heater or heating element such as a resistive heater is positioned in the vicinity of or proximate the CMOS pixel  350 , for example coupled with the substrate  353 . The inductive coil  354  may be manipulated in order to affect the temperature of the CMOS pixel  350 . As used herein the inductive coil is in the vicinity of or proximate the CMOS pixel if it is located sufficiently to affect the temperature of the CMOS pixel. By way of example, an electric current may be passed through the inductive coil  354  to heat it. The inductive coil  354  may serve as a temperature reference. The heating of the inductive coil  354  may affect the temperature of the CMOS pixel  350 . A change of temperature in the CMOS pixel  350  affects its background current. 
       FIG. 3F  is a cross sectional view that shows an inductive coil  364  that is positioned in the vicinity of a CMOS pixel  360 . A temperature sensor  366  is coupled to both a reference pixel  365  and the inductive coil  364  so that the inductive coil  364  controls the temperature of the CMOS pixel  360  relative to the reference pixel  365 . The reference pixel, the temperature sensor, and the inductive member may form a feedback mechanism to control a temperature of the CMOS pixel. 
       FIG. 4A  is a cross sectional view that shows a CMOS pixel array  400  that includes a multitude of CMOS pixels  402 ,  403  and  404 . The CMOS pixel array  400  includes a backside surface layer  401  that may sense the presence of electrical charges. Since each individual CMOS pixel can detect electrical charge or charges above it, the array of CMOS pixels may detect the movement of electrical charge or charges. Movement detection of charged entities may be used to measure the properties of these charged entities such as their mass, size, shape, or orientation. 
     In one or more embodiments, a biosensor system may include a backside of a substrate, an array of CMOS pixels underneath the backside of the substrate, and a multitude of bump structures coupled with the backside of the substrate. As used herein, a multitude includes at least 20, in some cases at least 50, in some cases at least 100, or more. The multitude of bump structures may be substantially separated by voids. 
       FIG. 4B  is a cross sectional view that shows a modified backside surface portion  410  of the CMOS pixel array  400  as disclosed in  FIG. 4A . The modified backside surface layer  410  includes a substrate  411 , and bump structures  412 ,  413  and  414  that are situated on surface  415 . The bump structures  412 ,  413  and  414  may form cavities  416  and  417  between them. The bump structures and the cavities may assist the measurement of the flow of particles, electrical charges and other entities on the surface  415 . By way of example, the bump structures and the cavities may be arranged to form channels that may direct the flow of particles, electrical charges and other entities. In another example, the cavities may be of different sizes, thereby allowing the separation and sorting of particles, electrical charges and other entities. 
     In another set of embodiments, a cantilever structure is constructed on top of the backside surface of a CMOS biosensor pixel. Bio-probes are attached to the cantilever structure. Affinity based binding between analyte and the bio-probes affect the stress condition of the CMOS pixel&#39;s backside surface, thereby causing a change in the background current. 
       FIG. 5  illustrates a backside stimulated CMOS biosensor pixel  500 , in accordance with an embodiment. Aside from differences specifically mentioned, the pixel  500  may be similar to and/or have features of the pixel  100  of  FIG. 1 . For brevity, these features will not be unnecessarily repeated. CMOS biosensor pixel  500  includes metal stack  530 , interlayer dielectric  520 , and substrate layer  510 . Substrate layer  510  further includes STI structures  514 , diode  511 , transfer gate  513 , and floating diffusion member  512 . On top of the CMOS backside surface  503  is a cantilever  504 . In one embodiment, the cantilever  504  is substantially situated on or coupled with the CMOS backside surface  503 . Cantilever  504  includes a detection surface  505 , onto which bio-probes  501  are immobilized or coupled. Analyte  502  may bind to bio-probes  501 , thereby adding mass to the cantilever  504 . Accordingly, the stress on the CMOS backside surface  503  changes. Such change of surface stress affects the background current behavior of the CMOS biosensor pixel  500 . The changes in the background current is detected and processed by the CMOS circuitry. 
     Cantilever  504  may have different modes of operation. By way of example, cantilever  504  may have a static mode of operation. In the static mode, affinity based binding of analyte  502  to bio-probes  501  causes a static bending of the cantilever  504 . The static bending changes the surface stress of the CMOS backside surface  503 , thereby causing a detectable change in the background current of the CMOS biosensor pixel  500 . 
     In another example, cantilever  504  may have a dynamic mode of operation. In the dynamic mode, cantilever  504  may be mechanically excited substantially at its resonant frequency. The mechanical excitation may be produced by various forces. By way of example, one mechanical excitation force may be a piezoelectric force. The mechanical excitation of cantilever  504  may cause dynamic stress cycles on the CMOS backside surface  503 . Affinity based binding of analyte  502  to bio-probes  501  may add additional mass to the cantilever  504 , causing a shift in the resonant frequency. The shift of resonant frequency may cause a corresponding frequency shift of dynamic stress cycles on the CMOS backside surface  503 , which is detectable by monitoring the background current of the CMOS biosensor pixel  500 . An alternate embodiment may include an array of cantilevers with each cantilever corresponding to a pixel in a corresponding array of pixels. 
       FIGS. 6A through 6C  illustrate several embodiments of coupling between the cantilever and the CMOS backside surface in additional to  FIG. 5 .  FIG. 6A  shows a cantilever  610  having a cantilever arm  611 . Bio-probes  612  are attached to a cantilever arm surface  614 . The cantilever arm  611  is substantially coupled to a CMOS backside surface  616  through an intermediate member  615 . By way of example, as analyte  633  may bind to bio-probes  612 , the cantilever arm  611  bends. The resulting stress may be transferred to the CMOS backside surface  616  through the intermediate member  615 . The intermediate member  615  may be various convenient materials. In another example, the cantilever arm  611  may be mechanically excited, resulting in cyclic motion of the cantilever arm  611 . The resulting stress cycles may be transferred to the CMOS backside surface  616  through the intermediate member  615 . 
       FIG. 6B  shows a cantilever  620  having a cantilever arm  612 . Bio-probes  622  are attached to a cantilever arm surface  624 . The bio-probes  622  may be affinitively bound to analyte  623 . The cantilever arm  621  may be coupled to a CMOS backside surface  626  through a tip member  625 . The tip member  625  may transfer stress and motion of the cantilever arm  621  to the CMOS backside surface  626 . Similar to the embodiment disclosed in the previous paragraph, the present embodiment may have several modes of operation, including a static mode and a dynamic mode. 
       FIG. 6C  shows a cantilever  630  having a cantilever arm  632 . The cantilever  630  includes a base portion  637 . The cantilever  630  may be substantially situated on a CMOS backside surface  636 , with the base portion  637  substantially situated onto a notch-like structure  638  that is within the CMOS backside surface  636 . The interaction between the base portion  637  and the notch-like structure  638  may facilitate the transfer of stress between the cantilever  630  and the CMOS backside surface  636 . Bio-probes  632  may be attached to a cantilever arm surface  634 . The bio-probes  632  may be affinitively bound to analyte  633 . The affinity based binding adds to the mass of the cantilever  630 . In a static mode of operation, the added mass affects the stress on the CMOS backside surface  636 . In a dynamic mode of operation, the added mass affects the frequency of cyclic stress of the CMOS backside surface  636 . 
       FIG. 7  is a block diagram illustrating a CMOS biosensor  700 , in accordance with an embodiment. The illustrated embodiment of the CMOS biosensor  700  includes pixel array  702 . The pixel array  702  or the individual CMOS pixels  701  making up the pixel array  702  may have some or all of the above described characteristics. The CMOS biosensor  700  also includes at least a readout circuitry  710 , a function logic  715 , and a control circuitry  720 . The readout circuitry  710  represents an example embodiment of a detection element to measure the background current. Pixel array  702  may be a two-dimensional array of individual CMOS pixels  701  (e.g., pixels P1, P2 . . . , Pn). As illustrated, each individual pixel  701  is arranged into a row (e.g., rows R1 to Ry) and a column (e.g., column C1 to Cx) to acquire data of an affinity based binding between an analyte and a bio-probe. These data can then be used to render a two-dimensional data set of analyte information. For example, each individual pixel may be used to detect a particular DNA sequence. An array of different pixels may allow a simultaneous detection of various DNA sequences that make up an entire genome, which is an ensemble of these various DNA sequences. In short, the CMOS biosensor  700  permits the determination of DNA sequence information of an entire genome in one measurement. 
     After each pixel  701  has acquired its data, the data is readout by the readout circuitry  710  and transferred to the function logic  715 . By way of example, the readout circuitry  710  may include at least an amplification circuitry, an analog-to-digital conversion circuitry, or otherwise. The function logic  715  may simply store the data or even manipulate the data by applying post measurement effects. In one embodiment, readout circuitry  710  may readout a row of data at a time along readout column lines (illustrated) or may readout the data using a variety of other techniques (not illustrated), such as a column/row readout, a serial readout, or a full parallel readout of all pixels simultaneously. Control circuitry  720  is connected with the pixel array  702  to control operational characteristic of some or all of the pixels  701  that make up the pixel array  702 . For example, control circuitry  720  may generate a signal or signals to alter the background current in some or all of the pixels  701  so as to improve the detection sensitivity of a particular affinity based binding bio-assay. 
     In some embodiments, for example when CMOS biosensor  700  is used as an ion sensor, a reference electrode  703  may optional be included. During use, the reference electrode  703  may be inserted into a sample (e.g., an electrolyte or solution under test). In some embodiments, the reference electrode may represent an electrode with a relatively stable and relatively well-known electrode potential. The reference electrode may help to stabilize the potential of the electrolyte and/or keep the potential of the electrolyte substantially constant. By substantially constant it is meant more constant than would be expected without the reference electrode but allowing for the possibility of generally small fluctuations that tend to occur despite attempts to maintain constant levels using the reference electrode. As shown, in some embodiments, the reference electrode  703  may include a voltage reference VREF. Alternatively, a current reference may optionally be used instead. In some cases, the reference electrode  703  may be relatively simple, for example, a plate electrode, a parallel plate, adjacent plates, etc. A more sophisticated electrode assembly may optionally be used, if desired. In various embodiments, any of the reference electrodes shown and described in any of  FIGS. 9 ,  10 , and  11  may optionally be used. 
       FIG. 8  is a circuit diagram illustrating a pixel circuitry  800  of two four-transistor pixels within a pixel array, in accordance with an embodiment of the disclosure. Pixel circuitry  800  is one possible pixel circuitry architecture for implementing each pixel within pixel array  702  of  FIG. 7 . However, it should be appreciated that embodiments are not limited to four-transistor pixel architectures; rather, one of ordinary skill in the art having the benefit of the instant disclosure will understand that the present teachings are also applicable to three-transistor designs, five-transistor designs, and various other pixel architectures. 
     In  FIG. 8 , pixels Pa and Pb are arranged in two rows and one column. The illustrated embodiment of each pixel circuitry  800  includes a diode DD, a transfer transistor T 1 , a reset transistor T 2 , a source-follower (“SF”) transistor T 3 , and a select transistor T 4 . During operation, affinity based binding between analytes and bio-probes may modulate the level of a background current in pixels Pa and Pb. Further, diode DD may have an interface with its surrounding substrate, wherein the interface may be a primary source of the background current. Transfer transistor T 1  receives a transfer signal TX, which transfers the background current from the vicinity region of diode DD to a floating diffusion node FD. In one embodiment, floating diffusion node FD may be coupled to a storage capacitor for temporarily storing charges from the background current. 
     Reset transistor T 2  is coupled between a power rail VDD and the floating diffusion node FD to reset the pixel (e.g., discharge or charge the FD and the DD to a preset voltage) under control of a reset signal RST. The floating diffusion node FD is coupled to control the gate of SF transistor T 3 . SF transistor T 3  is coupled between the power rail VDD and select transistor T 4 . SF transistor T 3  operates as a source-follower providing a high impedance connection to the floating diffusion FD. Finally, select transistor T 4  selectively couples the output of pixel circuitry  800  to the readout column line under control of a select signal SEL. 
     In some embodiments, for example when the pixel circuitry  800  is used as an ion sensor, each of the pixels may optional include a reference electrode  803 . During use, each reference electrode may participate electrically with its corresponding pixel via an electrical connection through an electrolyte or solution when the pixels are employed as part of an ion sensor system. The reference electrodes may participate in the ion sensing action when pixels are employed as ion sensor pixels. As shown, in some embodiments, each reference electrode  803  may include a voltage reference VREF. Alternatively, current reference electrodes or other electrical reference element may optionally be used instead. 
       FIG. 9  is a cross sectional view of a CMOS ion sensor system with a reference electrode  540  proximate to its backside surface, in accordance with an embodiment. Certain features shown in  FIG. 9  are similar to those shown in  FIG. 5  (except for the cantilever  504  and immobilized bio-probes  501 ). However, in  FIG. 9 , a surface at the backside is exposed to an electrolyte, solution, or other sample  570 , with the reference electrode  540  inserted into the sample. The reference electrode  540  is inserted in the electrolyte to help keep the potential of electrolyte substantially constant. In some embodiments, the reference electrode  540  may be biased at a voltage. In various embodiments, the reference electrode  540  may represent a pin, probe, plate, member, or other structure.  FIG. 9  also shows optional dielectric layer  550  formed on the surface at the backside of substrate  510 . Depending on whether reference electrode  540  is a voltage reference electrode or a current reference electrode, and depending on the physical location of reference electrode  540 , the incorporation of dielectric layer  550  may be desirable, but is not required. Dielectric layer  550  may be optically opaque or transparent, and may consist of either a single layer or multiple layers. 
       FIG. 10  is a cross sectional view of a CMOS ion sensor system having a reference electrode  560  on its backside surface, in accordance with an embodiment.  FIG. 10  shows reference electrode  560  formed on at least a portion of a surface at the backside of the substrate. In this case, the reference electrode  560  is formed over (in this case directly on) dielectric layer  550 . In the illustration, the dielectric layer  550  is disposed or sandwiched between the reference electrode  560  and the substrate  510 , although one or more other layers may optionally be disposed therebetween as well. The dielectric layer  550  may be able to insulate the metallic or otherwise conductive reference electrode from sensor substrate  510 . In the illustrated embodiment, the dielectric layer  550  is formed substantially over the entire backside surface, including under the reference electrode  560  and at an intended location where a sample  570  is to be contacted, although this is not required. In other embodiments, the dielectric layer  550  may be formed only under reference electrodes  560  but not over part of the substrate  510  where the sample  570  is to be contacted. This may allow the sample  570  to contact the backside surface of substrate  510  directly, which in some cases may help to improve ion detection. A method of an embodiment may include patterning (e.g., lithographically patterning) the reference electrode  560  and optionally the dielectric layer  550 . 
       FIG. 11  is a cross sectional view of a CMOS ion sensor system having a reference electrode  580  opposite its backside surface, in accordance with an embodiment. Reference electrode  580  is positioned proximate to substrate  510  with electrolyte  570  disposed there between. In some embodiments, reference electrode  580  may be a single electrode plate extending over substantially all the pixels in the array of pixels. For example, the reference electrode  580  may occupy a plane substantially parallel to the surface at the backside and may be displaced from the surface at the backside to allow introduction of the electrolyte into a space between the surface at the backside and the reference electrode. Alternatively, reference electrode  580  may include an array of electrode plates with positioned above corresponding pixels or sets of pixels. For example, there may be a first reference electrode portion over one pixel and a second reference electrode portion over another pixel. Reference electrode  580  may be biased with a voltage, or comprise a current source, or other electrical reference useful to the operation of ion sensor pixel  500 . In the illustrated embodiment, optional dielectric layer  550  is shown to be formed only partially covering the backside surface of substrate  510  (e.g., outside of and peripherally surrounding a contact region for sample  570 ). In another embodiment, dielectric layer  550  may optionally be formed over the entire backside surface of substrate  510 . In still other embodiments, the dielectric layer  550  may optionally be omitted entirely from the backside surface of substrate  510 . 
     The CMOS ion sensors of  FIGS. 9-11  may be able to sense or measure ions in samples. In some embodiments, the ions in the samples may affect a measurable effect on a background current which is measurable by the CMOS ion sensors. In some embodiments, the measurable effect may be related to a concentration or amount of the ions in the samples. The CMOS ion sensors may be used to measure concentrations or amounts of the ions in the samples. In some embodiments, the CMOS ion sensors may represent CMOS hydronium ion sensors that are operable to sense or measure hydronium ions, or concentrations of hydronium ions, in the samples. In some embodiments, the effect on the background current of the hydronium ions may be used to measure a pH of the samples. Other embodiments are not limited to hydronium ions but rather may be used to sense or measure various other ions known in the arts. 
     The CMOS ion sensors in  FIGS. 9-11  may also included various other aspects disclosed elsewhere herein. In some embodiments, the CMOS ion sensors may incorporate the features or characteristics of the ion sensors of  FIGS. 2A-2B . The various detection systems and circuits disclosed herein for detecting the changes in the background current, or others that will be apparent to those skilled in the art, are generally suitable. For example, transistors and circuitry as described for  FIG. 8  may be leveraged. The various sources of background current mentioned elsewhere herein, or others that will be apparent to those skilled in the art, are generally suitable for these ion sensors. For example, the sources of  FIGS. 3B ,  3 C,  3 D,  3 E, and  3 F may optionally be used. Also, the features of  FIGS. 4A-4B  may optionally be used for the ion sensors, if desired. In some embodiments, at least one of a blocking layer and a blocking material may be included to block light from pixels. 
     An example CMOS pixel to sense at least one stimulus selected from a biological, chemical, ionic, electrical, mechanical and magnetic stimulus includes (1) a substrate, (2) a source, (3) a first diode and a detection system, (4) at least one charge sensitive layer, and (5) a reference electrode. The substrate includes a backside. The source is coupled with the substrate to generate background current. The first diode and detection system are electrically coupled with the substrate to measure an effect on the background current. The at least one charge sensitive layer has electrical charge and is coupled with the backside. In one embodiment, the charge sensitive layer is the insulating layer (e.g. dielectric layer  550 ). In one embodiment, the charge sensitive layer is within the substrate and is of a same material as the substrate and is adjacent to the backside of the substrate. The at least one charge sensitive layer is to interact with an analyte that is to be exposed to the at least one charge sensitive layer. Interaction of the at least one charge sensitive layer with the analyte is to provide a non-light emitting stimulus that is to alter the electrical charge of the at least one charge sensitive layer and is to affect the measureable effect on the background current which is measureable by the detection system. The reference electrode is proximate to the backside of the substrate. 
     An example ion sensor includes (1) a substrate, (2) at least one of a diode and a structure, (3) a circuit, (4) an electrical charge located at the backside of the substrate, and (5) a reference electrode proximate to the backside. The substrate includes a frontside and a backside opposite the frontside. The frontside has a metal stack over CMOS circuitry. The at least one of a diode and a structure is disposed within the substrate and is operable to generate a background current. The circuit is electrically coupled with the substrate and operable to measure the background current. The electrical charge has a magnitude and is to be coupled with an ionic charge magnitude of an electrolyte that is to be disposed on a surface at the backside of the substrate, wherein the coupling of the electrical charge with electrolyte, without need for light emission, is to cause a change in the background current that is to be measured by the circuit. 
     The above description of illustrated embodiments of the invention, including what is described in the Abstract, is not intended to be exhaustive or to limit the invention to the precise forms disclosed. While specific embodiments of, and examples for, the invention are described herein for illustrative purposes, various modifications are possible within the scope of the invention, as those skilled in the relevant art will recognize. 
     These modifications can be made to the invention in light of the above detailed description. The terms used in the following claims should not be construed to limit the invention to the specific embodiments disclosed in the specification. Rather, the scope of the invention is to be determined entirely by the following claims, which are to be construed in accordance with established doctrines of claim interpretation. 
     In the above description and in the claims, the term “coupled” may mean that two or more elements are in direct physical or electrical contact. However, “coupled” may instead mean that two or more elements are not in direct contact with each other, but yet still co-operate or interact with each other, such as, for example, through one or more intervening components or structures. 
     In the description above, for the purposes of explanation, numerous specific details have been set forth in order to provide a thorough understanding of the embodiments of the invention. It will be apparent however, to one skilled in the art, that other embodiments may be practiced without some of these specific details. The particular embodiments described are not provided to limit the invention but to illustrate it. The scope of the invention is not to be determined by the specific examples provided above but only by the claims below. In other instances, well-known circuits, structures, devices, and operations have been shown in block diagram form or without detail in order to avoid obscuring the understanding of the description. 
     Reference throughout this specification to “one embodiment”, “an embodiment”, or “one or more embodiments”, for example, means that a particular feature may be included in the practice of the invention. Similarly, in the description 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 various inventive aspects. This method of disclosure, however, is not to be interpreted as reflecting an intention that the invention requires more features than are expressly recited in each claim. Rather, as the following claims reflect, inventive aspects may lie in less than all features of a single disclosed embodiment. Thus, the claims following the Detailed Description are hereby expressly incorporated into this Detailed Description, with each claim standing on its own as a separate embodiment of the invention.