There is provided a device (300;500;700) for collecting fluorescent light (322) emitted by particles (304) in a medium (302). The device (300;500;700) comprises a substrate (308) having a chamber (306) for holding the medium (302) including the particles (304) being capable of emitting fluorescent light (322). A first waveguide (310), which is arranged to receive and guide excitation light along a first direction (313), extends through the chamber (306). Fluorescent light (322) emitted by the particles (304) following an excitation is collected by the first waveguide (310). The device (300;500;700) further comprises a coupler (316;516) which includes a second waveguide (317) arranged to output collected fluorescent light (326) at one of its ends (318). The second waveguide (317) is arranged in relation to the first waveguide (310) such that collected fluorescent light (324) travelling in a direction opposite to the first direction (312) is coupled out from the first waveguide (310) directly into the second waveguide (317).

Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of luminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction. In some aspects, the disclosure provides compositions comprising luminescently labeled nucleotides.

Apparatus, sensor chips and techniques for optical sensing of substances by using optical sensors on sensor chips.

A biochip device includes a waveguide, chromophore elements, a diffusing structure, and a sloping surface. The chromophore elements are disposed on a portion of the waveguide and are configured to emit fluorescence in response to excitation by guided light waves transmitted by the waveguide. The diffusing structure is configured to generate guided light waves in the waveguide when illuminated. The sloping surface is sloped relative to a plane of the waveguide and is configured to direct excitation light into the waveguide, and the sloping surface and the waveguide are configured to deflect the excitation light to the diffusing structure to generate guided light waves within the waveguide. The sloping surface may be a face of a prism attached to or integrated with the waveguide, or the sloping surface may be a chamfer formed at an edge of the waveguide.

Systems and methods for multiplex detection through measurement of localized fluorescence ratios are disclosed herein. This can include creating a plurality of capture structures that each include a detection portion that can couple with a target analyte and a stem that can include a capture structure code uniquely identifying a type of the capture structure. The capture structures can be attached to a sample surface and mixed with a sample containing a plurality of target analytes. A location and the capture structure code of each of the capture structures can be determined. A location at which a target analyte is bound to one of the capture structures can be identified, and the target analyte can be determined based on the capture structure code of the capture structure at the location at which the target analyte is bound to one of the capture structures.

A device includes a nano-structure made of electrically conductive material. The nano-structure is covered by a barrier coating comprising Ti, Zr, Hf, Nb, Ta, Mo, Sc, Y, Ge, La, Ce, Pr, Nd, Sm, Eu, Gd, Dy, Ho, Er, Tm, Yb, Lu, Sr, Al, B, Ba, Bi, and/or Mg oxide in a thickness of at least about 1 nm. The barrier coating is deposited by atomic layer deposition (ALD). A method of detecting a target compound uses the device for surface specifically creating an evanescent field, measuring the dielectric properties of a medium, detecting the presence or the concentration of a target compound, determining the primary structure of a target compound, determining a deviation of the target compound from a control value, amplifying a target compound, or monitoring the amplification of a target compound.

Provided herein are systems, devices and methods for the rapid and accurate measurement of analytes by assay of binding events, by direct, digital measurement of individually resolved analyte/reporter binding events. The digital molecular assay systems, devices and methods disclosed herein are capable of particle-by-particle readout using optical reporter molecules that detect and report the binding of a single analyte molecule, and report each such binding in binary format. Such digital molecular assay systems, devices and methods are useful in a variety of applications, such as on mobile electronic devices for use in the field.

A waveguide sensor system is provided. The system includes a light source and a waveguide formed from a light transmitting material. Light from the light source enters the waveguide at an input area and travels within the waveguide by total internal reflection to an analyte area and light to be analyzed travels within the waveguide from the analyte area by total internal reflection to an output area. An optical sensor is coupled to the output area and is configured to interact with the light to be analyzed. The system includes a plurality of pores located along the outer surface within the analyte area and formed in the light transmitting material of the waveguide, and the pores are configured to enhance light interaction with the analyte within the analyte area. The pores and analyte area may be protected and/or enhanced with a hydrophobic layer overlaying the pores.

System and methods for identifying nucleotides based on data acquired from a sensor during sequencing of nucleic acids. The method may include obtaining characteristics of light detected from luminescent labels associated with the nucleotides during nucleotide incorporation events. The characteristics may include, for each nucleotide incorporation event, a temporal characteristic the light and an intensity characteristic of the light. The temporal characteristic representing a speed of decay of a probability of photon emission by a luminescent label after excitation. The method may further include grouping points representing the characteristics of the nucleotide incorporation events into groups of points. The individual points may represent at least the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event. The method may further include assigning the groups of points to individual nucleotides.

System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.