A fluorescence detection system, including apparatus and methods, suitable for qPCR and other fluorescence-based analyses. The system may comprise various components, including a stage, an illumination module, a detection module, and an optical relay structure. The stage may be configured to support a sample holder. The illumination module may include one or more discrete light sources configured to produce excitation light. The detection module may be configured to detect fluorescence emission light produced, in response to the excitation light, by a fluorescent sample positioned in the sample holder. The optical relay structure may include a beamsplitter assembly configured to direct the excitation light from the illumination module along an illumination path to the sample holder and to direct the fluorescence emission light from the sample holder along a response path to the imaging module. The system may enhance the quality of excitation light hitting samples in the sample holder.

Disclosed are liquid and solid assay compositions and portable sample reader devices for use in a sample-to-answer diagnostic system for the detection of one or more analytes, preferably the detection of circulating histones in whole blood. Further provided are methods of making and using the assay compositions and portable sample reader, including the collection of a raw sample, testing the sample using the assay compositions, and analyzing the sample via the portable sample reader. More particularly, assay compositions comprising a sacrificial partition, target molecule, detectable label, and sacrificial partition are used in combination with a sample reader comprising an optical system and a housing unit as part of a sample-to-answer diagnostic system for quantifying circulating histones in whole blood as a mechanism of predicting the risk of multiple organ failure.

A fluorescence observation apparatus according to an embodiment of the present technology includes a stage, an excitation section, and a spectroscopic imaging section. The stage is capable of supporting a fluorescently stained pathological specimen. The excitation section irradiates the pathological specimen on the stage with a plurality of line illuminations of different wavelengths, the plurality of line illuminations being a plurality of line illuminations situated on different axes and parallel to a certain-axis direction. The spectroscopic imaging section includes at least one imaging device capable of separately receiving pieces of fluorescence respectively excited with the plurality of line illuminations.

Provided are processes, methods, kits, devices and software for testing and detecting proteins such as antigens, cytokines or antibodies, particles or cells in specimens of or samples from human or animals; and in alternative embodiments the protein are induced by or derived from viruses, bacteria, an immune system, a cancer cell or any cell which can cause a disease, infection or condition such as a COVID-19 infection. Provided are portable imaging systems comprising flat static surfaces or slides, wherein the flat static surfaces or slides can be fabricated as printed microarrays, or biochips that can support protein or bioparticle precipitates. Provided are portable imaging systems comprising imaging systems with light sheet illumination to image two dimensional (2D) planes in liquids to detect proteins, bioparticles, cells, and organisms. Portable imaging systems provided herein can be used for point-of-care diagnosis, immunity analysis, epidemiological surveillance, and therapeutics and vaccine development.

A system for and method of producing a virtually stained histological tissue sample is provided that includes: a) acquiring a plurality of autofluorescence (AF) images of an unstained tissue sample, each AF image of the plurality of images produced by interrogating the tissue sample at an AF excitation wavelength configured to produce AF emissions at an AF emission wavelength, wherein the AF excitation wavelength and the AF emission wavelength used to produce each AF image of the plurality of AF images is different from the AF excitation wavelength and the AF emission wavelength used to produce the other AF images of the plurality of AF images; b) virtually staining the tissue sample using the plurality of AF images using artificial intelligence to represent a coloration of at least one histological stain; and c) producing a virtually stained histological tissue sample from the virtual staining.

A system for analysis of a sample at a substrate comprises: a light source to generate first light; and a spatial light modulator to form second light from the first light, wherein the substrate includes at least one sensor to detect an emission emitted based on the second light, wherein at the substrate the second light forms a shape selected based on the at least one sensor, wherein the second light illuminates an area of the substrate corresponding to the shape.

A structured substrate includes a substrate body having an active side. The substrate body includes reaction cavities that open along the active side and interstitial regions that separate the reaction cavities. The structured substrate includes an ensemble amplifier positioned within each of the reaction cavities. The ensemble amplifier includes a plurality of nanostructures configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity.

A fluorescent in-situ hybridization imaging and analysis system includes a flow cell to contain a sample to be exposed to fluorescent probes in a reagent, a fluorescence microscope to obtain sequentially collect a plurality of images of the sample at a plurality of different combinations of imaging parameters, and a data processing system. The data processing system includes an online pre-processing system configured to sequentially receive the images from the fluorescence microscope as the images are collected and perform on-the-fly image pre-processing to remove experimental artifacts of the image and to provide RNA image spot sharpening, and an offline processing system configured to, after the plurality of images are collected, perform registration of images having a same field of view and to decode intensity values in the plurality of images to identify expressed genes.

A particle analysis system comprising: a light detector that acquires light generated by irradiating a particle with excitation light; and an information processing unit that outputs a spectral plot including spectrum information of an autofluorescence population specified in a two-dimensional plot of measurement data each of which corresponds to the acquired light and spectrum information of the measurement data and that records the spectrum information of the autofluorescence population as an autofluorescence reference spectrum in a fluorescence separation process.

Techniques are described for reducing the number of angles needed in structured illumination imaging of biological samples through the use of patterned flowcells, where nanowells of the patterned flowcells are arranged in, e.g., a square array, or an asymmetrical array. Accordingly, the number of images needed to resolve details of the biological samples is reduced. Techniques are also described for combining structured illumination imaging with line scanning using the patterned flowcells.