Abstract: Described herein are methods and compositions for genomic editing. Endonucleases for genomic editing involve inducing breaks in double stranded DNA, for which knock-ins are notoriously inefficient for relying on random integration of homologous DNA sequences into the break site by repair proteins. To address these issues, described herein are novel recombinant fusion proteins that actively recruit linear DNA inserts in closer proximity to the genomic cleavage site, increasing integration efficiency of large DNA fragments into the genome. Such improvements to genomic editing technology allow one to use lower linear DNA concentrations without sacrificing efficiency and can be further combined with other features, such as fluorescent protein reporting systems.

Abstract: Described herein is a method to create dendritic biocompatible polymers from pairs of complementary dendritic nucleic acid monomers in a controlled manner, using polymerization triggers. The dendritic monomers are constituted of nucleic acids and an organic polymer capable of self-assembly. Each polymer contains approximately 200 dendrites that can be used to attach labels and constitute a biologically compatible signal amplification technology. Depending on the context this technology could be used to reveal the presence of a large variety of analytes such as specific nucleic acid molecules, small molecules, proteins, and peptides.

Abstract: A new DNA knock-in approach is provided based on the usage of three single guide RNA (sgRNA) to increase the integration efficiency of donor DNA based on the CRISRP-Cas system. The approach uses a pair of universal sgRNAs complementary to the donor DNA and a single sgRNA that targets the locus of interest. In various embodiments, targeting is achieved by pre-forming a DNA:RNA:protein (DNA:RNP) complex in vitro and introducing the complex into the embryo or cells of interest either by microinjection or transfection.

Abstract: Systems and methods are provided for increasing photon collection during imaging with a light-sheet fluorescence microscope. In one example, one or more adaptive optical elements may be positioned in a detection light path between a detection objective and an imaging sensor. A depth of field of the detection objective is adjusted as a function of a thickness of an excitation light-sheet used to illuminate a sample during imaging. As a result, the detection objective captures more fluorescence photons generated by light-sheet excitation.

Abstract: Systems and methods are provided for multi-spectral or hyper-spectral fluorescence imaging. In one example, a spectral encoding device may be positioned in a detection light path between a detection objective and an imaging sensor of a microscope. In one example, the spectral encoding device includes a first dichroic mirror having a sine transmittance profile and a second dichroic mirror having a cosine transmittance profile. In addition to collecting transmitted light, reflected light from each dichroic mirror is collected and used for total intensity normalization and image analysis.

Abstract: Described herein are methods and compositions for genomic editing. Endonucleases for genomic editing involve inducing breaks in double stranded DNA, for which knock-ins are notoriously inefficient for relying on random integration of homologous DNA sequences into the break site by repair proteins. To address these issues, described herein are novel recombinant fusion proteins that actively recruit linear DNA inserts in closer proximity to the genomic cleavage site, increasing integration efficiency of large DNA fragments into the genome. Such improvements to genomic editing technology allow one to use lower linear DNA concentrations without sacrificing efficiency and can be further combined with other features, such as fluorescent protein reporting systems.

Abstract: Described herein is a method to create dendritic biocompatible polymers from pairs of complementary dendritic nucleic acid monomers in a controlled manner, using polymerization triggers. The dendritic monomers are constituted of nucleic acids and an organic polymer capable of self-assembly. Each polymer contains approximately 200 dendrites that can be used to attach labels and constitute a biologically compatible signal amplification technology. Depending on the context this technology could be used to reveal the presence of a large variety of analytes such as specific nucleic acid molecules, small molecules, proteins, and peptides.

Abstract: Volumetric imaging with selective volume illumination (SVI) using light field detection is provided using various systems and techniques. A volumetric imaging apparatus includes a light source configured to emit an illumination light that propagates via an illumination light path to illuminate a three-dimensional (3D) sample; and an optical system arranged with respect to the light source to receive a light field, which comes from the illuminated 3D sample. The light field propagates via a detection light path, and the light source, the optical system, or both, are configurable to perform SVI, which selects a volume of a 3D-confined illumination of the 3D sample based on the 3D sample to be illuminated and a light field detection (LFD) process to be applied. Further, the volume of the 3D-confined illumination is a selected 3D volume of the 3D sample to be particularly excited by the 3D-confined illumination for imaging.

Abstract: Described herein is a method to create dendritic biocompatible polymers from pairs of complementary dendritic nucleic acid monomers in a controlled manner, using polymerization triggers. The dendritic monomers are constituted of nucleic acids and an organic polymer capable of self-assembly. A variety of additional improvements are described herein, including processes not requiring snap cooling, “wobble clamp” designs to confer a transitory measure of hairpin stability prior to branch migration, and multiple assemblies of amplifying systems. Depending on the context this technology could be used to reveal the presence of a large variety of analytes such as specific nucleic acid molecules, small molecules, proteins, and peptides.

Abstract: This invention relates to a hyperspectral imaging system for denoising and/or color unmixing multiple overlapping spectra in a low signal-to-noise regime with a fast analysis time. This system may carry out Hyper-Spectral Phasors (HySP) calculations to effectively analyze hyper-spectral time-lapse data. For example, this system may carry out Hyper-Spectral Phasors (HySP) calculations to effectively analyze five-dimensional (5D) hyper-spectral time-lapse data. Advantages of this imaging system may include: (a) fast computational speed, (b) the ease of phasor analysis, and (c) a denoising algorithm to obtain the minimally-acceptable signal-to-noise ratio (SNR). An unmixed color image of a target may be generated. These images may be used in diagnosis of a health condition, which may enhance a patient's clinical outcome and evolution of the patient's health.

Abstract: Volumetric imaging with selective volume illumination (SVI) using light field detection is provided using various systems and techniques. A volumetric imaging apparatus includes a light source configured to emit an illumination light that propagates via an illumination light path to illuminate a three-dimensional (3D) sample; and an optical system arranged with respect to the light source to receive a light field, which comes from the illuminated 3D sample. The light field propagates via a detection light path, and the light source, the optical system, or both, are configurable to perform SVI, which selects a volume of a 3D-confined illumination of the 3D sample based on the 3D sample to be illuminated and a light field detection (LFD) process to be applied. Further, the volume of the 3D-confined illumination is a selected 3D volume of the 3D sample to be particularly excited by the 3D-confined illumination for imaging.

Abstract: Methods for fabricating flexible substrate nanostructured devices are disclosed. The nanostructures comprise nano-pillars and metallic bulbs or nano-apertures. The nanostructures can be functionalized to detect biological entities. The flexible substrates can be rolled into cylindrical tubes for detection of fluidic samples.

Abstract: Volumetric imaging with selective volume illumination (SVI) using light field detection is provided using various systems and techniques. A volumetric imaging apparatus includes a light source configured to emit an illumination light that propagates via an illumination light path to illuminate a three-dimensional (3D) sample; and an optical system arranged with respect to the light source to receive a light field, which comes from the illuminated 3D sample. The light field propagates via a detection light path, and the light source, the optical system, or both; are configurable to perform SVI, which selects a volume of a 3D-confined illumination of the 3D sample based on the 3D sample to be illuminated and a light field detection (LFD) process to be applied. Further, the volume of the 3D-confined illumination is a selected 3D volume of the 3D sample to be particularly excited by the 3D-confined illumination for imaging.

Abstract: Implementations of the present disclosure include methods, systems, and computer-readable storage mediums for image reconstruction. Actions include receiving an image acquired by an endoscopic system including an optical fiber bundle with multiple optical fibers, each optical fiber being surrounded by cladding, determining in the image fiber core locations corresponding to the optical fibers, reconstructing missing information from the image using interpolation performed in accordance with the fiber core locations, the missing information corresponding to artifacts in the acquired image that result from the cladding, and providing a fiber-pattern removed image, in which the artifacts in the acquired image are removed using the missing information.

Abstract: Implementations of the present disclosure include methods, systems, and computer-readable storage mediums for image reconstruction. Actions include receiving an image acquired by an endoscopic system including an optical fiber bundle with multiple optical fibers, each optical fiber being surrounded by cladding, determining in the image fiber core locations corresponding to the optical fibers, reconstructing missing information from the image using interpolation performed in accordance with the fiber core locations, the missing information corresponding to artifacts in the acquired image that result from the cladding, and providing a fiber-pattern removed image, in which the artifacts in the acquired image are removed using the missing information.

Abstract: This disclosure relates to the field of Optical Coherence Tomography (OCT). This disclosure particularly relates to an OCT system that generates an image with improved quality. In one example, the OCT system may generate an improved Bscan image by using multiple shaping functions to shape the raw A-scans. In another example, the OCT system may generate the improved B-scan image by forming multiple apodization patterns on a detector and acquiring raw A-scans by using the apodization patterns. A better diagnosis of a health condition may be reached by using the improved images generated by the OCT system of this disclosure.

Abstract: This invention relates to a hyperspectral imaging system for denoising and/or color unmixing multiple overlapping spectra in a low signal-to-noise regime with a fast analysis time. This system may be configured to carry out Hyper-Spectral Phasors (HySP) calculations to effectively analyze hyper-spectral time-lapse data. For example, this system may be configured to carry out Hyper-Spectral Phasors (HySP) calculations to effectively analyze five-dimensional (5D) hyper-spectral time-lapse data. Advantages of this imaging system may include: (a) fast computational speed, (b) the ease of phasor analysis, and (c) a denoising algorithm to obtain the minimally-acceptable signal-to-noise ratio (SNR). An unmixed color image of a target may be generated. These images may be used in diagnosis of a health condition, which may enhance a patient's clinical outcome and evolution of the patient's health.

Abstract: Described herein is a method to create dendritic biocompatible polymers from pairs of complementary dendritic nucleic acid monomers in a controlled manner, using polymerization triggers. The dendritic monomers are constituted of nucleic acids and an organic polymer capable of self-assembly. Each polymer contains approximately 200 dendrites that can be used to attach labels and constitute a biologically compatible signal amplification technology. Depending on the context this technology could be used to reveal the presence of a large variety of analytes such as specific nucleic acid molecules, small molecules, proteins, and peptides.

Abstract: A sclera or contact lens with an image of an eye that is fenestrated, or uniformly speckled with many sub-millimeter sized transparent regions or holes, is disclosed. The micro fenestrated contact lens can be worn on a strabismic, or misaligned, eye so that its image is aligned with the wearer's dominant eye. The fenestrations allow the wearer to see through the opaque or translucent image printed on the contact lens, thus allowing binocular vision even though his or her strabismic eye is covered.

Abstract: This disclosure relates to the field of Optical Coherence Tomography (OCT). This disclosure particularly relates to an OCT system that generates an image with improved quality. In one example, the OCT system may generate an improved Bscan image by using multiple shaping functions to shape the raw A-scans. In another example, the OCT system may generate the improved B-scan image by forming multiple apodization patterns on a detector and acquiring raw A-scans by using the apodization patterns. A better diagnosis of a health condition may be reached by using the improved images generated by the OCT system of this disclosure.