Disclosed herein are systems, methods, and techniques for optical detection of analytes (e.g., biomarkers or other objects) using a liquid-core waveguide in which the analytes are suspended in a high-index liquid inside a liquid channel of the waveguide. The term high-index may indicate a refractive core index of the carrier liquid that is higher than or equal to that of one or more surrounding cladding layer(s) (e.g., ethylene glycol liquid inside a glass channel). In some embodiments, a method includes illuminating, by a light-source, one or more particles in a liquid-core waveguide, wherein the liquid-core waveguide comprises a first cladding layer having a first index of a refraction, and a hollow core comprising a liquid inside the hollow core, wherein the liquid has a second index of refraction higher than the first index of refraction; and detecting, by a detector, light emitted from the one or more particles.

A flow cell for use with a spectrometer is described. The flow cell includes a waveguide having a hollow core. An inlet is fluidly coupled at a first end of the hollow core, and an outlet is fluidly coupled at a second end of the hollow core. A window at the inlet is optically coupled to the waveguide at the second end, and a mirror at the outlet is optically coupled to the waveguide at the second end. The flow cell also includes a first conduit configured to couple a fluid to the inlet, and a second conduit configured to couple the fluid to the outlet. Methods and systems using the flow cell are described. For example, methods and systems for monitoring a bioreactor.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

Improved flow cells, as well as systems and methods for using the improved flow cells, are provided.

An apparatus for volumetric imaging is provided. The apparatus comprises an illumination assembly arranged to direct light to illuminate a plurality of planes in a sample region sequentially at an illumination rate, each plane extending over a plurality of depths in the sample region; an image sensor comprising a plurality of sections of pixels and arranged to sense each section of pixels sequentially at a sensing rate; and a light-receiving assembly arranged to receive light from the sample region and to direct light received from each of said planes in the sample region to a different respective section of said sections of pixels. The light-receiving assembly comprises a multi-plane optical assembly arranged to receive light from the plurality of depths in the sample region and, for each section of said sections of pixels, to direct light simultaneously from each of the plurality of depths in the respective plane to a different respective subsection of said section. The illumination rate is equal to the sensing rate, such that each section of pixels is arranged to sense light from the plurality of depths in the respective plane as the plane is illuminated by the illumination assembly.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.