Abstract: 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.

Abstract: In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, for in situ spatial profiling of biological materials such as DNA, RNA and protein in cells, tissues, and organisms for investigating biology and for conducting biomarker/drug discovery and development, and for clinical pathology and diagnosis. In alternative embodiments, provided are compositions, including products of manufacture and kits, and methods, for spatially determining, visualizing or quantifying target biological materials comprising in situ staining of a biological sample with one or a plurality of probes that are labeled with light-emitting moieties that exhibit or are encoded with distinct luminescence lifetime (and, optionally, spectrum) characteristics; followed by time-resolved luminescence imaging, measurement and analysis.

Abstract: An imaging system comprises an excitation light source, a directing element positioned to direct light from the excitation light source toward a sample, a detector configured to measure incoming light from the sample, a filter cavity positioned between the sample and the detector, a first filter configured to be inserted into the filter cavity, a sine filter configured to be inserted into the filter cavity, and a processing unit communicatively connected to the detector, configured to receive image data from the detector to form an image. Methods of constructing a hyperspectral image of a sample are also described.

Abstract: An imaging system comprises an excitation light source, a directing element positioned to direct light from the excitation light source toward a sample, a detector configured to measure incoming light from the sample, a filter cavity positioned between the sample and the detector, a first filter configured to be inserted into the filter cavity, a sine filter configured to be inserted into the filter cavity, and a processing unit communicatively connected to the detector, configured to receive image data from the detector to form an image. Methods of constructing a hyperspectral image of a sample are also described.

Abstract: An imaging system comprises an excitation light source, a directing element positioned to direct light from the excitation light source toward a sample, a detector configured to measure incoming light from the sample, a filter cavity positioned between the sample and the detector, a first filter configured to be inserted into the filter cavity, a sine filter configured to be inserted into the filter cavity, and a processing unit communicatively connected to the detector, configured to receive image data from the detector to form an image. Methods of constructing a hyperspectral image of a sample are also described.

Abstract: A label-free imaging method to monitor stem cell metabolism discriminates different states of stem cell as they differentiate in a living tissues. We use intrinsic fluorescence biomarkers and the phasor approach to Fluorescence Lifetime Imaging Microscopy (FLIM). We identify and map intrinsic fluorophores such as collagen, retinol, retinoic acid, flavins, nicotinamide adenine dinucleotide (NADH) and porphyrin. We measure the phasor values of germ cells in C. Elegans germ line. Their metabolic fingerprint cluster according to their differentiation state, reflecting changes in FAD concentration and NADH binding during the differentiation pathway. The phasor approach to lifetime imaging provides a label-free, fit-free and sensitive method to identify different metabolic state of cells during differentiation, to sense small changes in the redox state of cells and may identify symmetric and asymmetric divisions and predict cell fate.

Abstract: An apparatus for inclined single plane Illumination microscopy of a sample includes a laser for launching excitation light beams at a plurality of wavelengths, a laser beam expander, an injection arm optically coupled to the laser beam expander, a conventional back-to-back microscope system, a universal dichroic mirror optically coupled to the injection arm to direct the excitation light beams into the conventional back-to-back microscope onto a sample plane in an imaging plane, and to receive fluorescence light from the sample, a universal optical adaptor optically coupled to the universal dichroic mirror, a re-imaging component optically coupled to the universal optical adaptor; and a camera output connector optically coupled to the re-imaging component, where the laser beam expander, injection arm, universal optical adapter, re-imaging component, and camera are combined in a modular unit which is arranged and configured to be coupled to the conventional back-to-back microscope.

Abstract: In alternative embodiments, the invention provides high throughput, multiplexed systems or methods for detecting a biological, a physiological or a pathological maker, or a single molecule or a single cell using a droplet microfluidics system integrated with use of a sensor or a sensing system, an aptamer, or a DNAzyme. In alternative embodiments, the sensor or sensing system comprises a nucleic acid based, an antibody based, an enzyme based or a chemical based sensor or sensing system. In alternative embodiments, the invention provides methods for detecting a biological, a physiological or a pathological marker, or a single molecule or a single cell using a droplet system integrated with rapid and sensitive fluorescence detection systems including, for example, a 3D Particle Detector. In alternative embodiments, the invention provides systems comprising Integrated Comprehensive Droplet Digitial Detection (IC 3D).

Abstract: An optical imaging method based on a feedback principle in which the specific scan pattern is adapted according to the shape of the sample. The feedback approach produces nanometer-resolved three dimensional images of very small and moving features in live cells and in a matter of seconds. Images of microvilli in live cultured opossum kidney cells expressing NaPi co-transporter proteins with different GFP constructs and images of cell protrusions in a collagen matrix are produced with a resolution of about 20 nm. Along cell protrusions in three dimensional cellular adhesions could be identified to the extracellular matrix.

Abstract: An apparatus for inclined single plane Illumination microscopy of a sample includes a laser for launching excitation light beams at a plurality of wavelengths, a laser beam expander, an injection arm optically coupled to the laser beam expander, a conventional back-to-back microscope system, a universal dichroic mirror optically coupled to the injection arm to direct the excitation light beams into the conventional back-to-back microscope onto a sample plane in an imaging plane, and to receive fluorescence light from the sample, a universal optical adaptor optically coupled to the universal dichroic mirror, a re-imaging component optically coupled to the universal optical adaptor; and a camera output connector optically coupled to the re-imaging component, where the laser beam expander, injection arm, universal optical adapter, re-imaging component, and camera are combined in a modular unit which is arranged and configured to be coupled to the conventional back-to-back microscope.

Abstract: An apparatus and method for in-depth fluorescence imaging using two-photon fluorescence imaging in turbid media. The apparatus includes a detector which can significantly enhance the use of a detection method that allows to efficiently collect scattered fluorescence photons from a wide area of the turbid sample. By using this detector it is possible to perform imaging of turbid samples, simulating brain tissue at depths up to 3 mm, where the two-photon induced fluorescence signal is too weak to be detected by previous means used in conventional two-photon microscopy. The detector separates the excitation and detection optics which allows a more efficient collection of fluorescence and enhancing the possible imaging depth.

Abstract: A system and method is provided for improved fluorescence decay time measurement. A digital heterodyning technique is disclosed in which a photon detector is sampled at a rate slightly faster than a digitally pulsed excitation signal. A resulting cross correlation frequency is low enough to be read by inexpensive electronics such as by a field programmable gate array. Phase information in the signal provides correlation with corresponding photon detections.

Abstract: “A label-free imaging method to monitor stem cell metabolism discriminates different states of stem cell as they differentiate in a living tissues. We use intrinsic fluorescence biomarkers and the phasor approach to Fluorescence Lifetime Imaging Microscopy (FLIM). We identify and map intrinsic fluorophores such as collagen, retinol, retinoic acid, flavins, nicotinamide adenine dinucleotide (NADH) and porphyrin. We measure the phasor values of germ cells in C. Elegans germ line. Their metabolic fingerprint cluster according to their differentiation state, reflecting changes in FAD concentration and NADH binding during the differentiation pathway. The phasor approach to lifetime imaging provides a label-free, fit-free and sensitive method to identify different metabolic state of cells during differentiation, to sense small changes in the redox state of cells and may identify symmetric and asymmetric divisions and predict cell fate.

Abstract: An apparatus and method for in-depth fluorescence imaging using two-photon fluorescence imaging in turbid media. The apparatus includes a detector which can significantly enhance the use of a detection method that allows to efficiently collect scattered fluorescence photons from a wide area of the turbid sample. By using this detector it is possible to perform imaging of turbid samples, simulating brain tissue at depths up to 3 mm, where the two-photon induced fluorescence signal is too weak to be detected by previous means used in conventional two-photon microscopy. The detector separates the excitation and detection optics which allows a more efficient collection of fluorescence and enhancing the possible imaging depth.

Abstract: An optical imaging method based on a feedback principle in which the specific scan pattern is adapted according to the shape of the sample. The feedback approach produces nanometer-resolved three dimensional images of very small and moving features in live cells and in a matter of seconds. Images of microvilli in live cultured opossum kidney cells expressing NaPi co-transporter proteins with different GFP constructs and images of cell protrusions in a collagen matrix are produced with a resolution of about 20 nm. Along cell protrusions in three dimensional cellular adhesions could be identified to the extracellular matrix.

Abstract: Tear film stability has an important role in the quality of vision. A system and method for performing Fluctuation Analysis of Spatial Image Correlation (FASIC) provides for a non-invasive system and method for evaluating the dynamics of the tear film surface using spatial autocorrelation analysis. With FASIC, a series of images are obtained using illumination and a camera. The spatial autocorrelation is calculated for image frames produced by the camera. A sinusoidal background appears in this correlation together with other features. The changes in the sinusoidal background of the spatial autocorrelation is extracted and monitored over time. The spatial period of this sinusoidal background correlates with the thickness of the tear film. In this regard, one is able to derive the tear film thickness from the period of this sinusoidal background.

Abstract: A system and method is provided for improved fluorescence decay time measurement. A digital heterodyning technique is disclosed in which a photon detector is sampled at a rate slightly faster than a digitally pulsed excitation signal. A resulting cross correlation frequency is low enough to be read by inexpensive electronics such as by a field programmable gate array. Phase information in the signal provides correlation with corresponding photon detections.

Abstract: The invention provides methods and devices for detecting, identifying, classifying and characterizing particles in a fluid sample. Optical analyzers are provided having a rotating and/or translating sample container for measuring the concentrations of fluorescent particles present in very low concentrations and for characterizing fluorescent particles on the basis of size, shape, diffusion constant and/or composition. Scanning optical analyzers are provided using pattern recognitions data analysis techniques and multichannel detection.

Abstract: Tear film stability has an important role in the quality of vision. A system and method for performing Fluctuation Analysis of Spatial Image Correlation (FASIC) provides for a non-invasive system and method for evaluating the dynamics of the tear film surface using spatial autocorrelation analysis. With FASIC, a series of images are obtained using illumination and a camera. The spatial autocorrelation is calculated for image frames produced by the camera. A sinusoidal background appears in this correlation together with other features. The changes in the sinusoidal background of the spatial autocorrelation is extracted and monitored over time. The spatial period of this sinusoidal background correlates with the thickness of the tear film. In this regard, one is able to derive the tear film thickness from the period of this sinusoidal background.

Abstract: The invention provides methods and devices for detecting, identifying, classifying and characterizing particles in a fluid sample. Optical analyzers are provided having a rotating and/or translating sample container for measuring the concentrations of fluorescent particles present in very low concentrations and for characterizing fluorescent particles on the basis of size, shape, diffusion constant and/or composition. Scanning optical analyzers are provided using pattern recognitions data analysis techniques and multichannel detection.