Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits radiation; at least one element for directing the emission radiation in a particular direction; and a light path along which the emission radiation travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the integrated device. Each sensor may detect emission radiation from a sample in a respective sample well. The instrument includes an excitation light source for exciting the sample in each sample well.

The present invention relates to fluorescence microscopy and specifically to improvements of method for and a corresponding fluorescence microscopy system for allowing separate detection of a plurality of fluorochromes.

An instrument is provided that can monitor nucleic acid sequence amplification reactions, for example, PCR amplification of DNA and DNA fragments. The instrument includes a multi-notch filter disposed along one or both of an excitation beam path and an emission beam path. Methods are also provided for monitoring nucleic acid sequence amplifications using an instrument that includes a multi-notch filter disposed along a beam path.

Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include features and materials that are provided on or in the support of a patterned array and that return at least a portion of incident light by reflection. The fiducial markers may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the patterned array.

Systems and methods for detecting a target moiety are disclosed. A system includes a substrate holder including a porous matrix. The porous matrix includes a first detectable agent and a second detectable agent. The system includes a housing, optically coupled with the substrate holder, and shaped to optically couple with a radiation source and a radiation sensor and to optically isolate the radiation source and the radiation sensor. The system includes an excitation filter, disposed in or on the housing, configured to receive excitation electromagnetic radiation from the radiation source and to transmit a first portion of the excitation electromagnetic radiation to the porous matrix. The system also includes an emission filter, disposed in or on the housing, configured to receive emitted fluorescence electromagnetic radiation from the porous matrix and to transmit a second portion of the emitted fluorescence electromagnetic radiation, the second portion being different from the first portion.

An example system for inspecting a surface includes a laser, an optical system, a gated camera, and a control system. The laser is configured to emit pulses of light, with respective wavelengths of the pulses of light varying over time. The optical system includes at least one optical element, and is configured to direct light emitted by the laser to points along a scan line one point at a time. The gated camera is configured to record a fluorescent response of the surface from light having each wavelength of a plurality of wavelengths at each point along the scan line. The control system is configured to control the gated camera such that an aperture of the gated camera is open during fluorescence of the surface but closed during exposure of the surface to light emitted by the laser.

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.

A computer-implemented system and method for template-based imaging are disclosed. A first image of a first slide, a second image of a second slide, and a third image of a third slide are received, wherein the third image includes a representation of a sample disposed on the third slide. Values of pixels of a template image that are associated with a plurality of features common to the first and second slides and represented in the first and second images are set to a non-background value and values of pixels of the template image not associated with the plurality of features are set to a background value. An offset between the template image and the third image is developed and coordinates of pixels in the third image that are associated with the representation of the sample are determined in accordance with the offset.

A solution for illuminating plants is provided. An illustrative system can include: a set of visible light sources configured to emit visible radiation directed at the plant; a set of ultraviolet radiation sources configured to emit ultraviolet radiation directed at the plant; and a set of sensors, wherein at least one sensor is configured to detect a fluorescence emitted from the plant due to the ultraviolet radiation and a fluorescence emitted from the plant due to the visible radiation.

The present technology provides for a fluorescent detector that is configured to detect light emitted for a probe characteristic of a polynucleotide. The polynucleotide is undergoing amplification in a microfluidic channel with which the detector is in optical communication. The detector is configured to detect minute quantities of polynucleotide, such as would be contained in a microfluidic volume. The detector can also be multiplexed to permit multiple concurrent measurements on multiple polynucleotides concurrently.