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.

Various embodiments may provide a method of illuminating a sample surface. The method may include arranging an illumination subsystem, the illumination subsystem including an optical source and at least one lens, having an optic axis at an incident angle greater than 0° and less than 90° to a normal of the sample surface such that a reference illumination distribution is directly generated on the sample surface based on optical light emitted by the illumination subsystem. The method may also include arranging an adjustment optical subsystem such that an adjusted illumination distribution which is more symmetrical compared to the reference illumination distribution is generated on the sample surface based on optical light emitted by the illumination subsystem.

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.

In-situ fluorimeters and methods and systems for collecting and analyzing sensor data to predict water source contamination are provided. In one embodiment, a method is provided that includes receiving sensor data regarding a water source. Changepoints may then be calculated within the sensor data and the sensor data may be split into intervals at the changepoints. A machine learning model may then be used to classify the intervals and a predicted contamination event for the water source may be identified based on the classified intervals. In another embodiment, an in-situ fluorimeter is provided. The in-situ fluorimeter comprises one or more UV LEDs centered around a pre-set excitation wavelength (e.g., a TLF excitation wavelength), a bandpass filter, a lens, a photodiode system, a machine learning platform; and an alarm triggered by contamination events, wherein the alarm is calibrated through the machine learning system.

A waveguiding structure (500) includes one or more fluid channels (518) intersected by a waveguide (514). An aperture layer (570) of the waveguide structure includes an array of apertures adjacent to the one or more fluid channels, such that the array of apertures may allow emission signals from analytes in the fluid channels to pass through the aperture layer for detection. The aperture layer may be etched using a first etching step, while an air-gap in a substrate of the waveguiding structure may be etched using a second etching step, wherein the first etching step has a higher level of precision than the second etching step. The array of apertures may comprise one or more one-dimensional signature patterns of apertures associated with specific fluid channels of the device, such that the signature patterns may be used to demultiplex signals and to correlate a signal with one of the plurality of channels.

A detection system suitable for detecting pathogens present in a sample is presented. The detection system includes: a microfluidic channel configured to receive a sample solution containing a target biochemical component and configured to support a flow of the sample solution; an imaging lens; an excitation light source configured to emit an excitation light into a focal volume of the imaging lens; and a detector. The microfluidic channel comprises an observation section where the flow is aligned with respect to a central axis of the imaging lens such that the focal volume is within the observation section and the target biochemical component moves through a focal plane of the imaging lens during a movement along the observation section. The detector is configured to detect a light signal emitted by the target biochemical component on excitation with the excitation light.

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.

In-situ fluorimeters and methods and systems for collecting and analyzing sensor data to predict water source contamination are provided. In one embodiment, a method is provided that includes receiving sensor data regarding a water source. Changepoints may then be calculated within the sensor data and the sensor data may be split into intervals at the changepoints. A machine learning model may then be used to classify the intervals and a predicted contamination event for the water source may be identified based on the classified intervals. In another embodiment, an in-situ fluorimeter is provided. The in-situ fluorimeter comprises one or more UV LEDs centered around a pre-set excitation wavelength (e.g., a TLF excitation wavelength), a bandpass filter, a lens, a photodiode system, a machine learning platform; and an alarm triggered by contamination events, wherein the alarm is calibrated through the machine learning system.

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.