This disclosure provides photonic integrated chip that has an optical waveguide located on a photonic circuit substrate that includes a photonic circuit that is optically coupled to the waveguide. A microfluidic channel is in a silicon substrate and is attached to the photonic circuit substrate. The microfluidic channel is positioned over the optical waveguide such that its side surfaces and an outermost surface extend into the microfluidic channel. The microfluidic channel extends along a length of the optical waveguide, and nanoparticles are located on or adjacent the optical waveguide located within the microfluidic channel.

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

Apparatuses and methods are described for the use of optically driven bubble, convective and displacing fluidic flow to provide motive force in microfluidic devices. Alternative motive modalities are useful to selectively dislodge and displace micro-objects, including biological cells, from a variety of locations within the enclosure of a microfluidic device.

Microdevices and methods provide for separating cells of a single type from a mixed biological sample containing multiple types of cells. A single microdevice may be configured to allow for separating out cells into multiple groupings, each grouping containing cells of only one cell type. Transfer of separated cells off the microdevice is performed by physical separation of part of the microdevice from a remainder of the microdevice. This step advantageously minimizes accidental cell losses in the transfer. Subsequent analysis may then be performed using non-microfluidic equipment and techniques.

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

Provided herein are devices, systems, and methods for analysis of objects, such as cells. The devices, systems, and methods organize a plurality of objects in a plurality of partitions by trapping an object in a trap and transferring the object to an adjacent partition. The devices, systems, and methods provide for parallel analysis of a plurality of objects.

A MEMS-based particle manipulation system which uses a particle manipulation stage and optical confirmation of the manipulation. The optical confirmation may be camera-based, and may be used to assess the effectiveness or accuracy of the particle manipulation stage. In one exemplary embodiment, the particle manipulation stage is a microfabricated, fluid valve, which sorts a target particle from non-target particles in a fluid stream. The optical confirmation stage is disposed in the microfabricated fluid channels at the input and output of the microfabricated sorting valve. Deep learning techniques are brought to bear on the camera output to increase speed, accuracy and reliability.

The present invention relates to a system for amplification of polynucleotides from a predefined number of single cells. The system comprise a device (or part) providing the predefined number of single cells, at a previously defined inlet site (or orifice) of a cartridge (microfluidic device), and the cartridge itself. The invention further relates to a method for amplification of polynucleotides from the one or more single cells using the system to provide an emulsion of aqueous droplets wherein the nucleic acid amplification occurs. Furthermore, the present invention relates to a kit comprising a plurality of microfluidic devices and a plurality of fluids configured for use with the system and the method.

Optically-actuated microfluidic devices permit the use of spatially-modulated light to manipulate micro-objects such as biological cells. Systems and methods are described for providing sequences of light patterns to move and direct a plurality of micro-objects within the environment of a microfluidic device. The sequenced light patterns provide improved efficiency in directing the transport of the plurality of micro-objects. Other embodiments are described.