Disclosed herein is an apparatus comprising: a plurality of locations configured to have probes attached thereto, wherein interaction between the probes and an analyte generates a signal; an optical system comprising a plurality of collimators; a sensor comprising a plurality of pixels configured to detect the signal; wherein the collimators are configured to essentially prevent light from passing if a deviation of a propagation direction of the light from an optical axis of the collimators is greater than a threshold.

TECHNICAL FIELD

The disclosure herein relates to biosensors, particularly biosensors based on optical detection.

BACKGROUND

A biosensor is an analytical device for detection of an analyte involved in a biological process. For example, the analyte may be a DNA, a protein, a metabolite, or even a living organism (e.g., bacteria, virus).

A biosensor usually has a probe that interacts with the analyte. The probe may be designed to bind or recognize the analyte. Examples of the probe may include antibodies, aptamers, DNAs, RNAs, antigens, etc. Interaction between the probe and the analyte may lead to one or more detectable event. For example, the detectable event may be release of a chemical species or a particle, a chemical reaction, luminescence (e.g., chemiluminescence, bioluminescence, electrochemiluminescence, electroluminescence, photoluminescence, fluorescence, phosphorescence), change in a physical property (e.g., Raman scattering, color) or chemical property (e.g., reactivity, reaction rate).

A biosensor may have a detector that can detect the detectable event as a result of the interaction. The detector may transform the detectable event into another signal (e.g., image, electrical signal) that can be more easily measured and quantified. The detector may include circuitry that obtains data from the detectable event and processes the data.

One type of biosensor is microarray. A microarray can be a two-dimensional array on a solid substrate (e.g., a glass slide, a silicon wafer). The array may have different assays at different locations. The assays at different locations may be independent controlled or measured, thereby allowing multiplexed and parallel sensing of one or many analytes. A microarray may be useful in miniaturizing diagnosis assays. For example, a microarray may be used for detecting biological samples in the fields without sophisticated equipment, or be used by a patient who is not in a clinic or hospital to monitor his or her physiological symptoms.

SUMMARY

Disclosed herein is an apparatus comprising: a plurality of locations configured to have probes attached thereto, wherein interaction between the probes and an analyte generates a signal; an optical system comprising a plurality of collimators; a sensor comprising a plurality of pixels configured to detect the signal; wherein the collimators are configured to essentially prevent light from passing if a deviation of a propagation direction of the light from an optical axis of the collimators is greater than a threshold.

According to an embodiment, the sensor comprises a control circuit configured to control, acquire data from, or process data from the pixels.

According to an embodiment, the pixels are arranged such that each of the pixels is optically coupled to one or more of the locations.

According to an embodiment, the pixels are optically coupled to the locations by the collimators.

According to an embodiment, the signal is luminescence.

According to an embodiment, the signal is generated under excitation of an excitation radiation.

According to an embodiment, the optical system further comprises a filter, wherein the filter is configured to block at least a portion of the excitation radiation.

According to an embodiment, the filter is a dichroic filter.

According to an embodiment, the optical system further comprises or a transmissive layer.

According to an embodiment, the optical system further comprises a plurality of microlens.

According to an embodiment, the threshold is 10°.

According to an embodiment, the collimators comprises a meta-material or a photonic crystal

According to an embodiment, the collimators are configured to eliminate optical cross-talk between neighboring pixels among the plurality of pixels.

According to an embodiment, at least one of the collimators comprises a core and a sidewall surrounding the core.

According to an embodiment, the signal is generated under excitation of an excitation radiation; wherein the core is a material that essentially prevents the excitation radiation from passing through irrespective of propagation direction of the excitation radiation.

According to an embodiment, the signal is generated under excitation of an excitation radiation; wherein the core comprises a dichroic filter.

According to an embodiment, the core allows the signal to pass through essentially unabsorbed.

According to an embodiment, the core is a void space.

According to an embodiment, the sidewall attenuates a portion of the signal reaching the sidewall.

According to an embodiment, the sidewall is textured.

According to an embodiment, the apparatus further comprises a redistribution layer configured to route data from the pixels.

According to an embodiment, the filter comprises a meta-material or a photonic crystal.

DETAILED DESCRIPTION

FIG. 1Aschematically shows a system100including a microarray105. The system100may have an image sensor101, an optical system102, and/or an excitation source109. The image sensor101may be configured to measure an optical property (e.g., color, intensity) at different locations106of the microarray105. The locations106may have various probes107attached thereto. The probes107may interact with analyte and the interaction may generate signals108detectable by the image sensor101. The generation of the signals108may need excitation by the excitation source109(e.g., laser, UV light, etc.). The image sensor101and the optical system102of the system100tend to be bulky, fragile, or expensive and may not have high enough spatial resolution to distinguish one location from its neighboring locations.

FIG. 1Bschematically shows a system150where detector capability is integrated into a microarray155. The microarray155may have multiple locations156with various probes157attached thereto. The probes157may interact with various analytes and the interaction may generate signals158detectable by a sensor151integrated to the microarray155. For example, the analytes are fluorophore-labeled nucleic acid or protein fragments; the probes are oligonucleotides or antibodies. Locations with fluorophore-labeled analytes captured by the probes can be identified by detecting fluorescence from the fluorophores on the captured analytes. The sensor151may have multiple pixels170configured to detect the signals158(e.g., color, intensity). The pixels170may have a control circuit171configured to control, acquire data from, and/or process data from the pixels170. The pixels170may be arranged such that each pixel170is optically coupled to one of the locations156. However, the signals158generated at one location156may not entirely reach the pixel170optically coupled to that location156. A portion172of the signals158may reach the pixel170optically coupled to that location156but another portion173may be scattered into neighboring pixels (“optical cross-talk”) and/or away from all pixels170. Generating the signals158may need an excitation radiation161(e.g., laser, UV light, etc.). A portion162of the excitation radiation161may pass through the locations156unscattered. A portion163of the excitation radiation161may be scattered into some of the pixels170or away from all pixels170. The portion162may be blocked by a filter190from reaching the pixels170. The filter190may be position below or above a transmissive layer191. However, the filter190may be sensitive to incident directions and may not block the portion163, despite portions162and163have the same wavelength. If the portion163reaches the pixels170, it can overshadow signals158.

FIG. 2Aschematically shows a system200, according to an embodiment. The system200includes a micro array255including an integrated sensor251and an optical system285. The microarray255may have multiple locations256with various probes257attached thereto. The probes257may interact with various analytes and the interaction may generate signals258detectable by the sensor251. The sensor251may have multiple pixels270configured to detect the signals258(e.g., color, intensity). The pixels270may have a control circuit271configured to control, acquire data from, and/or process data from the pixels270. The pixels270may be arranged such that each pixel270is optically coupled to one or more of the locations256. The optical system285may include a filter290positioned below or above a transmissive layer291(FIG. 2Bshows an example where the filter290is below the transmissive layer291). The optical system285may include a plurality of collimators295configured to optically couple the pixels270to the locations256. The filter290and the transmissive layer291may not have to be fabricated on the same substrate as the collimators295. Instead, the filter290and the transmissive layer291may be fabricated and bonded to the collimators295.

In an embodiment, the transmissive layer291may include oxide or nitride. For example, the transmissive layer291may include glass.

In an embodiment, the filter290may be a dichroic filter (also known as interference filter). The filter290may be a low-pass (passing frequency below a threshold) or band-pass filter. The filter290may include a meta-material or a photonic crystal. A meta-material has component materials arranged in repeating patterns, often at microscopic or smaller scales that are smaller than the wavelengths of the light the meta-material is designed to influence. The structure of the repeated patterns and the properties of the component materials may be selected to tailor the properties of the meta-material. For example, the meta-material may provide optical transparency at all frequencies except at the selected frequency or frequencies which it is configured to block (for example particular laser frequencies that could cause harm to a user). A photonic crystal is a periodic dielectric structure that has a band gap that forbids propagation of a certain frequency range of light. The filter290may have multiple thin layers of materials with different refractive indices and may be made by alternately depositing thin layers of these materials. The filter290may be an absorptive filter but it would have sufficient thickness to be effective.

In an embodiment, the transmissive layer291may be an insulating material such as silicon oxide or silicon nitride. In an embodiment, the transmissive layer291may even be omitted. In an embodiment, the optical system285may have a plurality of microlens292positioned at the locations256, as shown inFIG. 2C. The microlens292may be fabricated directly on an exposed surface of the locations256and the probes257may be attached to the microlens292. Alternatively, the microlens292may be fabricated in the passivation layer291as shown inFIG. 2D. Further alternatively, the microlens292may be fabricated in the collimators295as shown inFIG. 2E. The microlens292may be configured to focus light generated at the locations256into the collimators295. The microlens292may be configured to direct a greater portion of luminescence from locations256into the pixels coupled thereto. For example, a microlens292may capture the portion273that otherwise would not reach the pixel coupled to the location256where the portion273is from.

In an embodiment, the filter290, the transmissive layer291if present, the microlens292if present and the collimator295may be integrated on the same substrate.

In an embodiment, the collimator295may be configured to essentially prevent (e.g., prevent more than 90%, 99%, or 99.9% of) light from passing if the deviation of the propagation direction of the light from an optical axis of the collimator295is greater than a threshold (e.g., 10°, 5°, or 1°). A portion272of the signals258may propagate towards the pixel270optically coupled to that location156but another portion273may be scattered towards neighboring pixels (“optical cross-talk”) and/or away from all pixels270. The collimator295may be configured to essentially eliminate optical cross-talk by essentially preventing the portion273from passing through the collimator295. Generating the signals258may need an excitation radiation261(e.g., laser, UV light, etc.). A portion262of the excitation radiation261may pass through the locations256unscattered. A portion263of the excitation radiation261may be scattered into other directions towards some of the pixels270or away from all pixels270. The portion262may be blocked by the filter290from reaching the pixels270. The filter290may be sensitive to incident directions and may not block the portion263, despite portions262and263have the same wavelength. The collimators295may be configured to essentially prevent the excitation radiation from passing through irrespective of the propagation direction, or to essentially prevent the portion263scattered away from the propagation direction of the portion261from passing through.

In an embodiment, each of the collimators295extends from one of the locations256to the pixel270optically coupled to that one location.

In an embodiment, the collimator295may have a core296surrounded by a sidewall297.

In an embodiment schematically shown inFIG. 3A, the core296may be a material that essentially prevents (e.g., prevents more than 90%, 99%, or 99.9% of) the excitation radiation261from passing through irrespective of the propagation direction of the excitation radiation261. For example, the core296may be a material that attenuates (absorbs) the excitation radiation261. The core296may allow the signals258to pass through essentially unabsorbed. In this embodiment, the filter290may be omitted.

In an embodiment schematically shown inFIG. 3B, the core296may have a structure299that essentially prevents (e.g., prevents more than 90%, 99%, or 99.9% of) a portion of the excitation radiation261from passing through if the deviation of the propagation direction of the portion (e.g., portion272) from the optical axis of the collimator295is smaller than a threshold (e.g., 10°, 5°, or 1°). For example, the structure299may have a dichroic filter, a meta-material or a photonic crystal. The core296may allow the signals258to pass through essentially unabsorbed (i.e., less than 10% absorbed). In this embodiment, the filter290may be omitted.

In an embodiment, schematically shown inFIG. 3C, the sidewall297of the collimator295may attenuate (absorb) the excitation radiation. The portion263of the excitation radiation261may pass through the filter290and enter the collimator295but is likely to reach the sidewall297before it can reach the pixels270. The sidewall297that can attenuate (absorb) the excitation radiation will essentially prevent stray excitation radiation from reaching the pixels270. In an embodiment, the core296may be a void space. Namely, the sidewall297surrounds a void space.

In an embodiment, the sidewall297may attenuate (absorb) any portion of the signal258reaching the sidewall, which will essentially prevent optical cross-talk.

In an embodiment, schematically shown inFIG. 3D, the sidewall297is textured. For example, the interface298between the sidewall297and the core296(which can be a void space) may be textured. Textured sidewall297can help further attenuate light incident thereon.

In an embodiment, schematically shown inFIG. 3E, the filter290and the transmissive layer291may be both omitted. The collimator295may have a top surface294exposed. The top surface294may be of a different material from its neighboring surface, thereby facilitating functionalization of the top surface294. The probes257may be selectively attached directly to the top surface294.

In an embodiment, schematically shown inFIG. 3FandFIG. 3G, the optical system285may have a plurality of collimators295arranged in an array. For example, the optical system285may have a dedicated collimator295for each pixel270. For example, the optical system285may have a collimator295shared by a group of pixels270. The collimator295may have any suitable cross-sectional shape, such as circular, rectangular, and polygonal.

In an embodiment, the collimators295may be made by etching (by e.g., deep reactive ion etching (deep RIE), laser drilling) holes into a substrate. The sidewall297may be made by depositing a material on the sidewall of the holes. The core296may be made by filling the holes. Planarization may also be used in the fabrication of the collimators295.

In an embodiment, the filter290may be omitted or its function may be integrated into the collimators295.

In an embodiment, schematically inFIG. 4, the optical system285may have a microfluidic system to deliver reactants such as the analyte and reaction product to and from the locations256. The microfluidic system may have wells, reservoirs, channels, valves or other components. The microfluidic system may also have heaters, coolers (e.g., Peltier devices), or temperature sensors. The heaters, coolers or temperature sensors may be located in the optical system285, above or in the collimators295. The heaters, coolers or temperature sensors may be located above or in the sensor251. The system200may be used for a variety of assays. For example, the system200can be used to conduct real-time polymerase chain reaction (e.g., quantitative real-time PCR (qPCR)). Real-time polymerase chain reaction (real-time PCR) detects amplified DNA as the reaction progresses. This is in contrast to traditional PCR where the product of the reaction is detected at the end. One real-time PCR technique uses sequence-specific probes labelled with a fluorophore which fluoresces only after hybridization of the probe with its complementary sequence, which can be used to quantify messenger RNA (mRNA) and non-coding RNA in cells or tissues.

The optical system285and the sensor251may be fabricated in separate substrates and bonded together using a suitable technique, such as, flip-chip bonding, wafer-to-wafer direct bonding, or gluing.

In an embodiment, schematically shown inFIG. 5A, the sensor251has a signal transfer layer252. The signal transfer layer252may have a plurality of vias510. The signal transfer layer252may have electrically insulation materials (e.g., silicon oxide) around the vias510. The optical system285may have a redistribution layer289with transmission lines520and vias530. The transmission lines520connect the vias530to bonding pads540. When the sensor251and the optical system285are bonded, the vias510and the vias530are electrically connected. This configuration shown inFIG. 5Aallows the bonding pads540to be positioned away from the probes257.

FIG. 5Bshows a top view of the sensor251inFIG. 5Ato illustrate the positions of the vias510relative to the pixels270and the control circuit271. The pixels270and the control circuit271are shown in dotted lines because they are not directly visible in this view.FIG. 5Cshows a bottom view of the optical system285inFIG. 5Ato illustrate the positions of the vias530relative to the transmission lines520(shown as dotted lines because they are not directly visible in this view).

In an embodiment, schematically shown inFIG. 6A, the sensor251has a redistribution layer629. The redistribution layer629may have a plurality of vias610and a plurality of transmission lines620. The redistribution layer629may have electrically insulation materials (e.g., silicon oxide) around the vias610and the transmission lines620. The vias610electrically connect the control circuit271to the transmission lines620. The optical system285may have a layer619with bonding pads640. The redistribution layer629may also have vias630electrically connecting the transmission lines620to the bonding pads640, when the sensor251and the optical system285are bonded. The bonding pads640may have two parts connected by a wire buried in the layer619. This configuration shown inFIG. 6Aallows the bonding pads640to be positioned away from the probes257.

FIG. 6Bshows a top view of the sensor251inFIG. 6Ato illustrate the positions of the vias610, the vias630and the transmission lines620, relative to the pixels270and the control circuit271, according to an embodiment. The pixels270, the control circuit271and the transmission lines620are shown in dotted lines because they are not directly visible in this view.FIG. 6Cshows a bottom view of the optical system285inFIG. 6Ato illustrate the positions of the bonding pads640, which are positioned to connect to the vias630shown inFIG. 6B. The bonding pads640may have two parts connected by a wire buried in the layer619.

FIG. 6Dshows a top view of the sensor251inFIG. 6Ato illustrate the positions of the vias610, the vias630and the transmission lines620, relative to the pixels270and the control circuit271, according to an embodiment. The pixels270, the control circuit271and the transmission lines620are shown in dotted lines because they are not directly visible in this view. The pixels270may be read out column by column. For example, signal from one270may be stored in register in the control circuit271associated with that pixel270; the signal may be successively shifted from one column to the next, and eventually to other processing circuitry through vias630.FIG. 6Eshows a bottom view of the optical system285inFIG. 6Ato illustrate the positions of the bonding pads640, which are positioned to connect to the vias630shown inFIG. 6D. The bonding pads640may have two parts connected by a wire buried in the layer619.

FIG. 6Fshows a top view of the sensor251inFIG. 6Ato illustrate the positions of the vias610, the via630and the transmission lines620, relative to the pixels270and the control circuit271, according to an embodiment. The pixels270, the control circuit271and the transmission lines620are shown in dotted lines because they are not directly visible in this view. The pixels270may be read out pixel by pixel. For example, signal from one270may be stored in register in the control circuit271associated with that pixel270; the signal may be successively shifted from one pixel to the next, and eventually to other processing circuitry through via630.FIG. 6Gshows a bottom view of the optical system285inFIG. 6Ato illustrate the positions of the bonding pad640, which are positioned to connect to the via630shown inFIG. 6F. The bonding pads640may have two parts connected by a wire buried in the layer619.

In an embodiment, schematically shown inFIG. 7, the sensor251has a redistribution layer729. The redistribution layer729may have a plurality of vias710and a plurality of transmission lines720. The redistribution layer729may have electrically insulation materials (e.g., silicon oxide) around the vias710and the transmission lines720. The vias710electrically connect the control circuit271to the transmission lines720. The redistribution layer729may also have vias730(e.g., through-silicon vias (TSV)) electrically connecting the transmission lines720to bonding pads740on the side opposite from the redistribution layer729. This configuration shown inFIG. 7allows the bonding pads740to be positioned away from the probes257.