A synthetic aperture optics (SAO) imaging method minimizes the number of selective excitation patterns used to illuminate the imaging target, based on the objects' physical characteristics corresponding to spatial frequency content from the illuminated target and/or one or more parameters of the optical imaging system used for SAO. With the minimized number of selective excitation patterns, the time required to perform SAO is reduced dramatically, thereby allowing SAO to be used with DNA sequencing applications that require massive parallelization for cost reduction and high throughput. In addition, an SAO apparatus optimized to perform the SAO method is provided. The SAO apparatus includes a plurality of interference pattern generation modules that can be arranged in a half-ring shape.

The present technology relates generally to devices, systems, and methods for detecting an analyte from a microfluidic assay. In some embodiments, a method for detecting the analyte includes binding an analyte and a plurality of quantum dots to a detection region of a porous membrane of a microfluidic device. The method further includes emitting ultraviolet (“UV”) light from a light source towards the microfluidic device and simultaneously capturing RGB image data of the microfluidic device with an image sensor of a portable computing device without an optical filter. The method further includes quantifying the amount of analyte present on the porous membrane based on the image data.

Provided herein are methods, systems, devices, and computer-readable storage media for measuring flatness (e.g., along a Z-axis) of a detection stage. In some aspects, measuring flatness of the detection stage includes obtaining two or more images representing different Z coordinates of a first XY coordinate on a substantially flat substrate positioned on the detection stage; determining a sharpest Z coordinate at the first XY coordinate based on sharpness of the two or more images; obtaining two or more images representing different Z coordinates of a second XY coordinate spaced apart from the first XY coordinate on the substantially flat substrate; determining a sharpest Z coordinate at the second XY coordinate based on sharpness of the two or more images; and calculating a difference between the sharpest Z coordinates at the first and the second XY coordinates to measure the flatness of the detection stage.

Methods, storage mediums, and systems for image data processing are provided. Embodiments for the methods, storage mediums, and systems include configurations to perform one or more of the following steps: background signal measurement, particle identification using classification dye emission and cluster rejection, inter-image alignment, inter-image particle correlation, fluorescence integration of reporter emission, and image plane normalization.

Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.

Method and system for compensating intensity biases in a plurality of digital images. Each digital image of the plurality of digital images contains a plurality of objects and each of the plurality of objects is configured to receive at least one molecule comprising genetic information, wherein the at least one molecule is configured to receive one of at least a first fluorescent compound and a second fluorescent compound. A first digital image of the plurality of digital images is taken by an optical imaging system during emission of electromagnetic radiation by the first fluorescent compound, and a second digital image of the plurality of digital images is taken by the optical imaging system during emission of electromagnetic radiation by the second fluorescent compound.

The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.

A system and method for collecting symptomatic data to screen for a targeted disease. Testing hardware incorporates a plurality of testing units with corresponding indicators that can be altered to indicate whether a symptom is present or not. The resulting data from the testing use can then be analyzed to determine the likelihood of presence of a disease.

A non-transitory computer-readable medium encoded with a computer-readable program, which when executed by a processor, will cause the processor to execute an image processing method, the image processing method including establishing a zero crossing region from a target image onto a screen, wherein the zero crossing region comprises a corresponding value. The method further includes receiving a variable input and an integration time input, wherein the variable input comprises a frequency number for an image accumulation procedure, and wherein the integration time comprises a time period for which an aperture for a sensor receives incoming signals. Additionally, the method includes performing the image accumulation procedure. Moreover, the method includes producing a final greyscale image by adding a plurality of sets of vertically shifted pixel values, wherein the frequency number for the image accumulation procedure ranges from 3 to 20.

Methods and systems for image analysis are provided, and in particular for identifying a set of base-calling locations in a flow cell for DNA sequencing. These include capturing flow cell images after each sequencing step performed on the flow cell, and identifying candidate cluster centers in at least one of the flow cell images. Intensities are determined for each candidate cluster center in a set of flow cell images. Purities are determined for each candidate cluster center based on the intensities. Each candidate cluster center with a purity greater than the purity of the surrounding candidate cluster centers within a distance threshold is added to a template set of base-calling locations.