An apparatus (1) for detecting the presence and/or the quantity of a target component in a biological fluid in an integrated assay cartridge (52) of predetermined configuration, the assay cartridge comprising a capture component (22) at a predetermined location in the assay cartridge, the apparatus comprising: a detector (12)for detecting the amount of light scattered, transmitted or emitted by the sample to provide an indication of the presence and/or the quantity of the target component within the sample; three location positions (30), the three positions defining a location along the optical path of the detector on which to locate the cartridge of a predetermined size; wherein location positions are configured such that the capture component of the assay cartridge is located, in use, at the focal plane of the detector. Measures to ensure quality control may also be provided.

This invention provides devices for use in various analytical applications including single-molecule analytical reactions. Methods for detecting analytes optically by propagating optical energy by waveguides within a substrate are provided. Analytical devices are provided which have both shallow and deep waveguides in which illumination light is transported through the deep waveguides and coupled into the shallow waveguides. The shallow waveguides provide evanescent field illumination to analytes, such as single-molecule analytes, within nanometer scale wells. Integrated devices including integrated detectors such as CMOS detectors are included.

The present invention provides for metallic structures comprising a sulfhydryl or amino-terminated hydrophilic coating to provide a layer of hydrophilic character on the surface of the metallic structures thereby allowing the use of low volumes of aqueous solvents of fluorophores that have the ability to “spread out” across the surfaces of the metallic structures and to provide for a more uniform surface coating of fluorophores attached to or near the metallic structures.

A method for sample analysis that employs a signal-amplifying nanosensor is provided. An implementation of the present method may include a) obtaining a sample, b) applying the sample to a signal-amplifying nanosensor containing a capture agent that binds to an analyte of interest, under conditions suitable for binding of the analyte in a sample to the capture agent, c) washing the signal-amplifying nanosensor, and d) reading the signal-amplifying nanosensor, thereby obtaining a measurement of the amount of the analyte in the sample. In some embodiments, the analyte may be a biomarker, an environmental marker, or a foodstuff marker. Also provided herein are kits that find use in performing the present method.

A biosensor is provided. The biosensor includes a plurality of sensor units. Each of the sensor units includes one or more photodiodes, a first aperture feature disposed above the photodiodes, an interlayer disposed on the first aperture feature, a second aperture feature disposed on the interlayer, and a waveguide disposed above the second aperture feature. The second aperture feature includes an upper grating element and the first aperture feature includes one or more lower grating elements, and a grating period of the upper grating element is less than or equal to a grating period of the one or more lower grating elements. A difference of the absolute values between a first polarizing angle of the upper and lower grating elements in one of the sensor units and a second polarizing angle of the upper and lower grating elements in adjacent one of the sensor units is 90°.

Integrated target waveguide devices and optical analytical systems comprising such devices are provided. The target devices include an optical coupler that is optically coupled to an integrated waveguide and that is configured to receive optical input from an optical source through free space, particularly through a low numerical aperture interface. The devices and systems are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices provide for the efficient and reliable coupling of optical excitation energy from an optical source to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination. The devices and systems are well suited for miniaturization and high throughput.

Apparatus and methods relating to photonic bandgap optical nanostructures are described. Such optical nanostructures may exhibit prohibited photonic bandgaps or allowed photonic bands, and may be used to reject (e.g., block or attenuate) radiation at a first wavelength while allowing transmission of radiation at a second wavelength. Examples of photonic bandgap optical nanostructures includes periodic and quasi-periodic structures, with periodicity or quasi-periodicity in one, two, or three dimensions and structural variations in at least two dimensions. Such photonic bandgap optical nanostructures may be formed in integrated devices that include photodiodes and CMOS circuitry arranged to analyze radiation received by the photodiodes.

The present disclosure provides a sensor substrate capable of detecting a trace amount of an analyte. This sensor substrate according to the present disclosure is a sensor substrate comprising a metal microstructure that generates surface plasmon when irradiated with excitation light. The metal microstructure is composed of a plurality of protrusions disposed in a planar shape. The plurality of the protrusions are disposed in such a manner that imaginary lines V each passing through a center between adjacent protrusions draw a honeycomb shape in a plan view. Each of the plurality of the protrusions has a substantially hexagonal shape in the plan view. A depth in a thickness direction of the sensor substrate of a gap present between the adjacent protrusions is larger than a radius of an imaginary circle inscribed in a hexagon forming the honeycomb shape.

Provided are a metal-based particle assembly including a plurality of metal-based particles arranged apart from each other, wherein the plurality of metal-based particles are each arranged so that an average distance between metal-based particles adjacent to each other is 1 nm or more and 1000 nm or less, and a standard deviation of the average distance is 25 nm or less; a layered body including the metal-based particle assembly; and a sensing apparatus including the layered body, a capturing layer that is arranged on the metal-based particle assembly and has a capturing substance for capturing an analyte, the analyte being labeled with a luminescent substance, a light-transmitting member, a light source that emits excitation light for exciting the luminescent substance, and a detector that detects emission from the luminescent substance.

A method includes obtaining, from one or more sequencing devices, raw data detected from luminescent labels associated with nucleotides during nucleotide incorporation events; and processing the raw data to perform a comparison of base calls produced by a learning enabled, automatic base calling module of the one or more sequencing devices with actual values associated with the raw data, wherein the base calls identify one or more individual nucleotides from the raw data. Based on the comparison, an update to the learning enabled, automatic base calling module is created using at least some of the obtained raw data, and the update is made available to the one or more sequencing devices.