Provided herein are systems, devices, and methods for improved optical waveguide transmission and alignment in an analytical system. Waveguides in optical analytical systems can exhibit variable and increasing back reflection of single-wavelength illumination over time, thus limiting their effectiveness and reliability. The systems are also subject to optical interference under conditions that have been used to overcome the back reflection. Novel systems and approaches using broadband illumination light with multiple longitudinal modes have been developed to improve optical transmission and analysis in these systems. Novel systems and approaches for the alignment of a target waveguide device and an optical source are also disclosed.

Described herein is a fluorescent nanocomposite. The fluorescent nanocomposite structure may include a plasmonic nanostructure comprising having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, at least one fluorescent agent having a maximum excitation wavelength (λEX), and at least one peptide-loaded major histocompatibility complex (MHC) molecule (pMHC). The fluorescent nanocomposite structure has a fluorescent intensity that is at least 500 times greater than a fluorescent intensity of the at least one fluorescent agent alone.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices include an integrated diffractive beam shaping element that provides for the spatial separation of light emitted from the optical reactions.

A structured substrate includes a substrate body having an active side. The substrate body includes reaction cavities that open along the active side and interstitial regions that separate the reaction cavities. The structured substrate includes an ensemble amplifier positioned within each of the reaction cavities. The ensemble amplifier includes a plurality of nanostructures configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity.

This disclosure pertains to a consumable product (microplate) suitable for use in assays utilizing single-molecule recognition through equilibrium Poisson sampling (SiMREPS) and in other assays employing total internal reflection fluorescence (TIRF) or HiLo microscopy. The disclosed microplate is also suitable for use in other high throughput assay systems, such as single-molecule FRET, ligand-receptor binding studies, membrane biology assays, cell-based TIRF and near-TIRF assays. The disclosure further pertains to the use of the microfluidic microplate for the detection of analytes, including nucleic acids, polypeptides, carbohydrates, lipids, post-translational modifications, amino acids, metabolites, and small molecules.

A microfluidic device comprises a microfluidic channel having at least an inlet for receiving a fluid plug or an outlet for removing a fluid plug and a pillar based flow distributor for reorienting the fluid plug in such a way that the long axis of the fluid plug essentially is oriented perpendicular to the walls of the microfluidic channel, as opposed to its original orientation, in which the longer axis is oriented in the longitudinal direction of the narrower inlet channel. The width W of the microfluidic channel is substantially larger than the width w of the inlet or outlet channel. The microfluidic device is adapted for detecting a physical or chemical property of the fluid, the microfluidic device being configured for detecting the property in a detection area positioned across the microfluidic channel in a width direction of the microfluidic channel.

The present invention relates to providing a detection device that has high robustness against a temperature change and a temporal change and that is capable of detecting a substance to be detected with high accuracy. The detection device of the present invention is a detection device that detects presence or an amount of a substance to be detected using an enhanced electric field based on surface plasmon resonance, the detection device having a light projecting unit for irradiating a metal film of a detection chip held by a chip holder with excitation light via a prism. The light projecting unit includes: a light source; a diaphragm for regulating an amount of light from the light source; and a conjugate optical system that optically conjugates an opening portion of the diaphragm and a region of the metal film irradiated with the excitation light.

A calibration standard for determining an intensity decay related to an evanescent field generated close to the interface between a sample to be tested and a substrate on which the sample is to be deposited, preparation and analysis methods and use thereof.

[Problem] To provide a target substance detection chip, a target substance detection device, and a target substance detection method, that can be manufactured easily in a small size at low costs with reduction of the number of parts involved in the detection chip constituted by an optical prism and a detection plate used for a SPR sensor and an optical waveguide mode sensor, that can detect a target substance quickly with high sensitivity, and in which an analyte liquid is easily delivered.

[Solution] A target substance detection chip of the present invention includes: a plate-like transparent base portion which allows light to pass therethrough; and a flow path which is formed in one surface of the transparent base portion as a groove and through which an analyte liquid verifying a presence of a target substance is delivered in a length direction of the groove, wherein the flow path is formed such that at least an electric field enhancement layer is disposed on an inner surface of a groove portion formed to at least partly have inclined surfaces appearing in cross section to be inclined at a gradient to the surface of the transparent base portion, and wherein a part or entirety of an uppermost surface of the groove which contacts the analyte liquid serves as a detection surface for the target 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.