Disclosed herein is an apparatus comprising: a probe carrier, an optical system and a sensor; wherein the probe carrier comprises a substrate, a first layer and a second layer; wherein the substrate comprises a first surface, a second surface, one or more locations on the first surface configured to be deposit sites for one or more probes; wherein the second surface is at an opposite side of the substrate from the first surface; wherein the first layer is on the first surface of the substrate or is embedded in the substrate under the first surface; wherein the second layer is on the second surface of the substrate or is embedded in the substrate under the second surface; the first and second layers are configured to reduce crosstalk between probes at different locations.

This invention provides substrates for use in various applications, including single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates and dielectric omnidirectional reflectors are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.

Apparatus and methods for improving optical signal collection in an integrated device are described. A microdisk can be formed in an integrated device and increase collection and/or concentration of radiation incident on the microdisk and re-radiated by the microdisk. An example integrated device that can include a microdisk may be used for analyte detection and/or analysis. Such an integrated device may include a plurality of pixels, each having a reaction chamber for receiving a sample to be analyzed, an optical microdisk, and an optical sensor configured to detect optical emission from the reaction chamber. The microdisk can comprise a dielectric material having a first index of refraction that is embedded in one or more surrounding materials having one or more different refractive index values.

An integrated device and related instruments and systems for analyzing samples in parallel are described. The integrated device may include sample wells arranged on a surface of where individual sample wells are configured to receive a sample labeled with at least one fluorescent marker configured to emit emission light in response to excitation light. The integrated device may further include photodetectors positioned in a layer of the integrated device, where one or more photodetectors are positioned to receive a photon of emission light emitted from a sample well. The integrated device further includes one or more photonic structures positioned between the sample wells and the photodetectors, where the one or more photonic structures are configured to attenuate the excitation light relative to the emission light such that a signal generated by the one or more photodetectors indicates detection of photons of emission light.

According to one embodiment, a specimen detection device includes a light source, a filter, a sensor, and a controller. The light source executes a first operation and a second operation. The first operation causes a first light of a first peak wavelength to be incident on a specimen. The second operation causes a second light of a second peak wavelength to be incident on the specimen. The filter attenuates the first and second lights and transmits at least a portion of a third light and at least a portion of a fourth light. The third light is emitted from the specimen. The fourth light is emitted from the specimen. The sensor outputs a first signal and a second signal. The first signal corresponds to the third. The second signal corresponds to the fourth light. The controller calculates a result value by processing the first and second signals.

Some embodiments of the present disclosure provide an optical sensor. The optical sensor includes a semiconductive substrate. A light sensing region is on the semiconductive substrate. A waveguide region is configured to guide light from a wave insert portion through a waveguide portion and to a sample holding portion. The waveguide portion includes a first dielectric layer including a first refractive index. A second dielectric layer includes a second refractive index. The second refractive index is smaller than the first refractive index. A first interconnect portion is positioned in the waveguide portion, configured to transmit electrical signal from the light sensing region to an external circuit. The sample holding portion is over the light sensing region.

A biosensor is provided. The biosensor includes a substrate, a plurality of photodiodes, a polarizing element and a plurality of reaction sites. The plurality of photodiodes are embedded in the substrate. The polarizing element is disposed on the substrate. The plurality of reaction sites are disposed on the polarizing element.

A photodiode (112,200,400,500) includes a semiconductor substrate (210) having a first surface (211) and a second surface (212,412,512), and a light sensing junction (220) located adjacent to the first surface (211). The second surface (212,412, 512) is located opposite the first surface (211), and the second surface (212,412,512) includes a concave surface covering a recessed region (415,515) in the semiconductor substrate (210).

The present disclosure describes a throughput-scalable sensing system. The system includes a plurality of semiconductor dies sharing a common semiconductor substrate and a plurality of transmembrane pore based sensors configured to detect a change of current flow as a result of analyzing biological or chemical samples. Two immediately neighboring transmembrane pore based sensors are arranged on respective two semiconductor dies separated by a dicing street. Each transmembrane pore based sensor is arranged on a separate semiconductor die of the plurality of semiconductor dies. At least one transmembrane pore based sensor includes one or more detection electrodes disposed above the common semiconductor substrate and a lipid bilayer disposed above the one or more detection electrodes.

Memory efficient methods determine corrected color values from image data acquired by a nucleic acid sequencer during a base calling cycle. Such methods may: (a) obtain an image of a substrate (e.g., a portion of a flow cell) including a plurality of sites where nucleic acid bases are read; (b) measure color values of the plurality of sites from the image of the substrate; (c) store the color values in a processor buffer of the sequencer's one or more processors; (d) retrieve partially phase-corrected color values of the plurality of sites, where the partially phase-corrected color values were stored in the sequencer's memory during an immediately preceding base calling cycle; (e) determine a prephasing correction; and (f) determine the corrected color values. In various implementations, these operations are all performed during a single base calling cycle. In certain embodiments, the methods additionally include using the corrected color values to make base calls for the plurality of sites. Sequencers may be designed or configured to implement such methods.