A method comprises: directing, using an objective and a first reflective surface, first autofocus light toward a sensor, the first autofocus light reflected from a first surface of a substrate; preventing second autofocus light from reaching the sensor, the second autofocus light reflected from a second surface of the substrate; and directing, using the objective and a second reflective surface, emission light toward the sensor, the emission light originating from a sample at the substrate.

An integrated semiconductor device for manipulating and processing bio-entity samples and methods are described. The device includes a lower substrate, at least one optical signal conduit disposed on the lower substrate, at least one cap bonding pad disposed on the lower substrate, a cap configured to form a capped area, and disposed on the at least one cap bonding pad, a fluidic channel, wherein a first side of the fluidic channel is formed on the lower substrate and a second side of the fluidic channel is formed on the cap, a photosensor array coupled to sensor control circuitry, and logic circuitry coupled to the fluidic control circuitry, and the sensor control circuitry.

The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.

The invention provides a device and a process for analysing the effect of a concentration of a gas on a sample, especially measurement of the gas concentration within a sample, and/or measurement of the effect of the absorption and/or desorption of a gas by the sample, using spectrophotometric detection of a gas-sensitive and optically detectable analyte of the sample while measuring the concentration of the gas in a gas composition that is continuously delivered to each sample well in order to contact the samples with a gas having a predetermined and/or measured concentration, respectively a pre-determined and/or measured partial pressure.

The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.

A measurement apparatus according to the present disclosure is a measurement apparatus capable of measuring particles in a fluid and comprises: a flow path device including a first flow path with translucency through which a first fluid including the particles passes and a second flow path with translucency through which a second fluid which does not include the particles passes; an optical sensor facing the flow path device, irradiating each of the first flow path and the second flow path with light, and receiving light passing through each of the first flow path and the second flow path; and a controller measuring the particles by comparing an intensity of light passing through the first flow path and an intensity of light passing through the second flow path, each of which is obtained by the optical sensor.

The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.

Disclosed are methods, systems, and apparatuses for the free solution measurement of molecular interactions by backscattering interferometry. In one aspect, the invention relates to method and systems for detecting molecular interaction between analytes in free-solution wherein the analytes are label-free and detection is performed by back-scattering interferometry. Also disclosed are label-free, free-solution, and/or real-time measurements of characteristic properties and/or chemical events using the disclosed techniques. The disclosed methods can have very low detection limits and/or very low sample volume requirements. Also disclosed are various biosensor applications of the disclosed techniques. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present invention.

A new liquid flow cell assembly for light scattering measurements is disclosed which utilized a floating manifold system. The assembly operates with minimal stacked tolerances by aligning the cell to the windows within a manifold and independently aligning the cell to the read head directly. This configuration enables the ability to replace the flow cell or the flow cell/manifold assembly within a light scattering instrument without the need to realign the flow through elements with the light scattering illumination source while still maintaining reproducible, quality data. Some embodiments employ wide bore cells which enable the measurement of process analytic technology (PAT) including online monitoring of reactions.

A method for forming sequencing flow cells can include providing a semiconductor wafer covered with a dielectric layer, and forming a patterned layer on the dielectric layer. The patterned layer has a differential surface that includes alternating first surface regions and second surface regions. The method can also include attaching a cover wafer to the semiconductor wafer to form a composite wafer structure including a plurality of flow cells. The composite wafer structure can then be singulated to form a plurality of dies. Each die forms a sequencing flow cell. The sequencing flow cell can include a flow channel between a portion of the patterned layer and a portion of the cover wafer, an inlet, and an outlet. Further, the method can include functionalizing the sequencing flow cell to create differential surfaces.