Disclosed is an apparatus and method for fluorescence excitation and detection. The apparatus comprises one or more light sources for providing excitation light for fluorescence excitation at an observation spot along an optical axis for excitation, an optical collection element for collecting fluorescence light generated by the excitation light at two or more different observation spots into two or more different measurement channels with an optical axis for collecting non-parallel to the optical axis for excitation of each of the one or more light sources, and, for each of the two or more measurement channels and thereby for each of the two or more observation spots, a dedicated optical detector for detecting fluorescence from the fluorescence light collected by the optical collection element.

A method of performing antimicrobial susceptibility testing (AST) on a sample uses a reader device that mounts on a mobile phone having a camera. A microtiter plate containing wells preloaded with the bacteria-containing sample, growth medium, and drugs of differing concentrations is loaded into the reader device. The wells are illuminated using an array of illumination sources contained in the reader device. Images of the wells are acquired with the camera of the mobile phone. In one embodiment, the images are transmitted to a separate computing device for processing to classify each well as turbid or not turbid and generating MIC values and a susceptibility characterization for each drug in the panel based on the turbidity classification of the array of wells. The MIC values and the susceptibility characterizations for each drug are transmitted or returned to the mobile phone for display thereon.

An apparatus for performing nucleic acid amplification reactions includes a thermally-conductive receptacle holder with multiple receptacle wells. Each well has a through-hole extending from an inner surface of the well to an outer surface of the holder. A cover is rotatable between an open position and a closed position relative to the holder and is configured to exert a force onto any receptacles in the wells when the cover is in the closed position. The apparatus includes multiple optical fibers, and each of the optical fibers provides optical communication between one of the wells and an excitation signal source and/or an emission signal detector. A thermal element is positioned between a thermally-conductive support and the receptacle holder.

An apparatus for detecting an emission signal from each of a plurality of emission signal sources includes one or more excitation sources configured to generate an excitation light of an excitation wavelength and one or more associated emission detectors configured to detect light of an emission wavelength. A transmission fiber is associated with each of the emission signal sources. A carrier is configured to move the one or more excitation sources and the one or more emission detectors relative to the transmission fibers to sequentially place each emission detector and associated excitation source in an operative position with respect to each transmission fiber. Each transmission fiber transmits both the excitation light from the excitation source and the corresponding emission light to the associated emission detector.

Integrated target waveguide devices and optical analytical systems comprising such devices are provided. The target devices include an optical coupler that is optically coupled to an integrated waveguide and that is configured to receive optical input from an optical source through free space, particularly through a low numerical aperture interface. The devices and systems 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 provide for the efficient and reliable coupling of optical excitation energy from an optical source to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination. The devices and systems are well suited for miniaturization and high throughput.

An optofluidic diagnostic system and methods for rapid analyte detections. The system comprises an optofluidic sensor array, a test plate and an optical detection cartridge. The sensor array supports one or more distinct sensor units, each having a reactor section designed to temporarily enter a series of different kinds of wells in the test plate. One kind of well is a sample reservoir that holds reagent solution to be transferred into the reactor section. Another kind of well is a drainage chamber that removes reagent solution from the reactor section. A third kind of well is a colorant reservoir that holds a colorant reagent transferable into a reactor section. Finally, the sensor unit is transferred to the optical detection cartridge where it is placed into an isolation booth during the optical detection process so that its flat observation face is stationed in a viewing window opposite an optical detector lens.

The invention provides a multi-well plate reader for providing simultaneous transmission of stimulation light to, and detection of emission light from, individual wells of a multi-well plate at a plurality of distinct wavelengths.

An instrument for processing and/or measuring a biological process comprises a plurality of filter assemblies configured to be interchangeably located along at least one of the optical paths. The plurality of filter components includes a first filter assembly characterized by a first optical power and a first filter having a first filter function, the first filter function characterized by at least one of a first low-pass wavelength or a first high-pass wavelength. The second filter assembly is characterized by a second optical power and a second filter having a second filter function, the second filter function comprising at least one of a second low-pass wavelength that is different than the first low-pass wavelength or a second high-pass wavelength that is different than the first high-pass wavelength.

Registration of a patterned flow cell may utilize fiducials comprising sets or groupings of features (e.g., sites, sample wells, nanowells) having known locations and in which the placement of the features is not in accordance with a periodic pattern or is otherwise distinguishable from the periodic pattern of sites present in non-fiducial regions of the flow cell substrate. In certain embodiments the positioning of the sites that are part of the fiducial represent a break or discontinuity in the periodic pattern of sites that are otherwise present on the surface of a patterned flow cell.

A system for nucleic acid (NA) amplification includes a light source configured to emit a first excitation light based on a control signal, a reaction chamber configured to house a solution including a plurality of first nucleic acids (NAs), the plurality of first NAs being configured to amplify in response to the first excitation light, the solution being configured to emit a second light in response to heating by the first excitation light and to emit a third light in response to amplification of the plurality of first NAs, a detector configured to detect the second and third lights and to generate a temperature signal corresponding to the second light and a first fluorescence signal corresponding to the third light, and a lens module configured to focus the second and third lights onto the detector.