Generation and use of a focus quality metric that is intensity independent is described. In one example, the focus quality metric is generated by acquiring an image, such as an image of a patterned surface of a flow cell, and processing all or part (e.g., a sub-region or sub-image) to generate a Fourier transform of the respective image data. By way of example, in one embodiment a discrete Fourier transform may be applied to a sub-region of an image of a patterned flow cell surface. A focus quality metric that is intensity independent may be derived from the Fourier transform of the image data.

Disclosed herein, inter alia, are devices, compositions, kits, and methods for interrogating biological samples.

An apparatus for characterizing luminescent entities by excitation comprising: • a substrate (6) being in contact with a solution comprising luminescent entities; • a source of electromagnetic radiation (4) providing at least a primary beam of radiation (8); an objective (5); a first optical element (1) capable of transforming the intensity profile of the primary beam (8) into an arbitrary secondary intensity profile (distribution) (9); a second optical element (2) capable of separating (discriminating) radiation by wavelength; and a detector (7), where the arbitrary secondary intensity profile has at least an off-center circular continuous intensity distribution (33) focused on the back focal plane (12) of the objective forming a collimated beam (10) capable of creating an evanescent field on the side of the substrate where the solution comprising luminescent entities are located, where the evanescent field excites the luminescent entities thereby creating emission radiation separated by the second optical element (2) and captioned by the detector (7). The invention also relates to an apparatus comprising two optical elements providing a final third intensity profile (distribution) which is the convolution of two mathematical transformations corresponding to each of optical element one and four, respectively.

A detection chip, a using method for the same, and a reaction system. The detection chip includes a first substrate, a micro-cavity defining layer, and a heating electrode. The micro-cavity defining layer is on the first substrate and defines a plurality of micro-reaction chambers. The heating electrode is on the first substrate and is closer to the first substrate than the micro-cavity defining layer, and is configured to heat a plurality of micro-reaction chambers. The orthographic projection of the plurality of micro-reaction chambers on the first substrate is within the orthographic projection of the heating electrode on the first substrate.

Valve assemblies and related systems are disclosed. An apparatus includes or comprises a system including or comprising an imaging system, a flow cell interface having a corresponding flow cell receptacle, a stage assembly, and a valve assembly including or comprising a valve and a valve drive assembly. The stage assembly moves the flow cell interface relative to the imaging system and the valve drive assembly is to drive the valve using shaped input signals to reduce vibration imposed on at least one of the stage assembly or another component of the apparatus based on movement of the valve.

The present invention relates to systems and methods for the arrangement of droplets in pre-determined locations. Many applications require the collection of time-resolved data. Examples include the screening of cells based on their growth characteristics or the observation of enzymatic reactions. The present invention provides a tool and related techniques which addresses this need, and which can be used in many other situations. The invention provides, in one aspect, a tool that allows for stable storage and indexing of individual droplets. The invention can interface not only with microfluidic/microscale equipment, but with macroscopic equipment to allow for the easy injection of liquids and extraction of sample droplets, etc.

Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.

The present invention relates to an apparatus for performing a nucleic acid amplification reaction and a fluorescence detection device for reaction analysis. The nucleic acid amplification apparatus of the present invention uses a plurality of blocks having different reaction temperatures by independent temperature control and the movement between the blocks is performed along sliding recesses formed in the blocks, enabling to greatly shorten the total amplification time (TAT). In the fluorescence detection device of the present invention, the positions of the light source and the photodetector are very unique for the reaction vessel in which an excitation light is provided and an emission light is generated.

A system and apparatus are provided for sensing a molecule in a sample for identifying the molecule in the sample. Also provided is a method of manufacturing an apparatus for sensing a molecule in a sample. The system and apparatus may contain a composition of a mixture of a buffer solution and a sample solution containing a sample. The apparatus contains a series of wells. The sample is deposited into the system and a molecule having an electric charge in the sample attaches to a layer in a well of the apparatus, allowing for a sensor connected to the apparatus to identify the molecule.

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.