Abstract: A closure for an apparatus comprises: a plurality of light sources; a lightguide to distribute light from the plurality of light sources, the lightguide having a first primary surface opposite a second primary surface, wherein the first primary surface has a first surface treatment, and wherein light emitted from the lightguide indicates a status of the apparatus; and a frame supporting the plurality of light sources and the lightguide for selective movement of the closure vertically or horizontally relative to the apparatus.

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

Abstract: The technology disclosed includes a system. The system includes a spatial convolutional neural network configured to process sequencing images of clusters, and produce spatially convolved features, a filtering logic configured to select, from the spatially convolved features, a subset of spatially convolved features that contain centers of the clusters, a compression logic configured to compress the subset of spatially convolved features into a set of compressed features, a contextualization logic configured to access state information for compressed features in the set of compressed features, a temporal convolutional neural network configured to process the set of stateful compressed features, and produce temporally convolved stateful features, and a base calling logic configured to generate base calls for the clusters based on the temporally convolved stateful features.

Abstract: Sequencing polynucleotides using nanopores is provided herein. A polynucleotide is disposed through a nanopore's aperture such that its 3? end is on the nanopore's first side and its 5? end is on the nanopore's second side. On the nanopore's first side, a duplex with the polynucleotide is formed that includes a 3? end. The duplex is extended on the first side of the nanopore by adding a nucleotide to the 3? end of the duplex. A first force is applied disposing the 3? end of the duplex within the aperture, and the nanopore inhibits translocation of the 3? end of the duplex to the second side of the nanopore. A value of an electrical property of the 3? end of the duplex and a single-stranded portion of the polynucleotide is measured. The nucleotide at the 3? end of the duplex is identified using the measured value.

Abstract: An example image sensor structure includes an image layer. The image layer includes an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with at least one light detector of the array of light detectors. A passivation stack is disposed over the device stack. The passivation stack includes a bottom surface in direct contact with a top surface of the light guides. An array of nanowells is disposed in a top layer of the passivation stack. Each nanowell is associated with a light guide of the array of light guides. A crosstalk blocking metal structure is disposed in the passivation stack. The crosstalk blocking metal structure reduces crosstalk within the passivation stack.

Abstract: Some examples herein provide methods for determining a sequence of a nucleic acid template hybridized to a complementary strand. A polymerase coupled to a magnetically-responsive sensor may capture the nucleic acid template hybridized to the complementary strand. The polymerase and the captured nucleic acid template hybridized to the complementary strand may be contacted with a first fluid comprising a nucleotide. The polymerase may incorporate the nucleotide into the complementary strand based on the sequence of the nucleic acid template. The polymerase and the captured nucleic acid template hybridized to the complementary strand, including the incorporated nucleotide, may be contacted with a second fluid comprising a magnetic particle. The incorporated nucleotide may capture the magnetic particle from the second fluid. The captured magnetic particle may cause a change in electrical resistance at the magnetically-responsive sensor.

Abstract: The technology disclosed relates to structured illumination microscopy (SIM). In particular, the technology disclosed relates to capturing and processing, in real time, numerous image tiles across a large image plane, dividing them into subtiles, efficiently processing the subtiles, and producing enhanced resolution images from the subtiles. The enhanced resolution images can be combined into enhanced images and can be used in subsequent analysis steps.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Abstract: The technology disclosed relates to detecting malfunction in a sequencer. In particular, the technology disclosed relates to receiving sensor data obtained from a sensor of the sequencer, applying a smoothing function to the sensor data to produce a smoothed time series, determining changes between smoothed successive datum in the smoothed time series that exceed a predetermined change, determining a degree of instability based upon the predetermined change, and generating an alert indicating that the sequencer is malfunctioning when the degree of instability exceeds a predetermined threshold.

Abstract: A system includes: a light source; first and second gratings; and at least one reflective component that in a first position forms a first light path originating at the light source and extending to the first grating and thereafter to a subsequent component in the system, and that in a second position forms a second light path originating at the light source and extending to the second grating and thereafter to the subsequent component.

Abstract: A biosensor is provided including a detection device and a flow cell mounted to the detection device. The detection device has a detector surface with a plurality of reaction sites. The detection device also includes a filter layer that is configured to at least one of (a) filter unwanted excitation light signals; (b) direct emission signals from a designated reaction site toward one or more associated light detectors that are configured to detect the emission signals from the designated reaction site; or (c) block or prevent detection of crosstalk emission signals from adjacent reaction sites.

Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.

Abstract: Disclosed herein is a novel method of producing monodisperse aqueous droplets, as well as a novel microfluidic droplet generator. In some examples, the method comprises flowing an aqueous solution through a microchannel and into a sample reservoir of the microfluidic droplet generator, wherein monodisperse droplets of the aqueous solution form by step-emulsification at a step change in height at an intersection of a reservoir end of the microchannel and a sidewall of the sample reservoir. In some examples, the aqueous solution is a hydrogel precursor solution and monodisperse droplets of the hydrogel precursor solution form by step-emulsification at the step change in height at the intersection of the reservoir end of the microchannel and the sidewall of the sample reservoir. In some examples, the monodisperse droplets of the hydrogel precursor solution are incubated under conditions suitable for gelation to form hydrogel beads.

Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.

Abstract: There is set forth herein a device comprising: a detector surface for supporting biological or chemical samples; an array of doped areas formed in a semiconductor formation, wherein the semiconductor formation receives excitation light and emission light from the detector surface, and wherein doped areas of the array of doped areas define photodiodes; a doped region formed in the semiconductor formation in a receive light path of the excitation light and emission light intermediate the detector surface and a doped area of the array of doped areas; and wherein the doped region is configured to impact a travel direction of electrons generated in the doped region as a result of photon absorption.

Abstract: Coordinated application processing. A method identifies processing engines available for coordinated application processing, distributes to the processing engines an application configured for execution to perform image processing, and distributes images to the processing engines.

Abstract: We propose a neural network-based base caller that detects and accounts for stationary, kinetic, and mechanistic properties of the sequencing process, mapping what is observed at each sequence cycle in the assay data to the underlying sequence of nucleotides. The neural network-based base caller combines the tasks of feature engineering, dimension reduction, discretization, and kinetic modelling into a single end-to-end learning framework. In particular, the neural network-based base caller uses a combination of 3D convolutions, 1D convolutions, and pointwise convolutions to detect and account for assay biases such as phasing and prephasing effect, spatial crosstalk, emission overlap, and fading.

Abstract: Systems and methods for conducting designated reactions utilizing a base instrument and a removable cartridge. The removable cartridge includes a fluidic network that receives and fluidically directs a biological sample to conduct the designated reactions. The removable cartridge also includes a flow-control valve that is operably coupled to the fluidic network and is movable relative to the fluidic network to control flow of the biological sample therethrough. The removable cartridge is configured to separably engage a base instrument. The base instrument includes a valve actuator that engages the flow-control valve of the removable cartridge. A detection assembly held by at least one of the removable cartridge or the base instrument may be used to detect the designated reactions.

Abstract: Devices, systems, and methods for non-volatile storage include a well activation device operable to modify one or more wells from a plurality of wells of a flow cell to provide a set of readable wells. Readable wells are configured to allow exposure of a well to substances from nucleotide sequencing fluids, and prevent exposure to other substances and fluids, such as nucleotide synthesizing fluids. The well activation device may also modify wells to provide a set of writeable wells. This set of wells is configured to allow exposure to the nucleotide synthesizing fluids and substances; and prevent exposure to the nucleotide sequencing fluids and substances. There may also be provisions made for risk mitigation for data errors such as generating commands to write specified data to a nucleotide sequence associated with a particular location in a storage device, reading the nucleotide sequence and performing a comparison.