Abstract: Disclosed is a method for monitoring cell density during cell expansion resulting from a cell culture process in a bioreactor comprising the steps of: a) cultivating cells in a bioreactor culture chamber according to a cell culture process having cell culture parameters; b) during said process, introducing cell culture fluid inputs and generating waste materials; c) determining the intensity of volatile organic compounds (VOCs) and their chemical species in the waste materials; and d) estimating the density or population of cells in the bioreactor based on said determination.

Abstract: Disclosed is a cell culture microscopy slide comprising an optically transparent generally flat supporting surface (20) including upper and lower opposed substrate surfaces (27,28). A peripheral frame (40) surrounds the substrate (20), the frame (40) having a lower frame surface (44) and an upper frame surface (42). The lower frame surface (44) and the lower substrate surface (28) are generally flush. The upper frame surface (42) lies above the upper substrate surface (27), to form a well (32), and the upper and lower frame surfaces (42,44) are continuously flat and generally parallel. The substrate is preferably glass having a thickness of 1.7 mm.

Abstract: Disclosed is a method for monitoring cell density during cell expansion resulting from a cell culture process in a bioreactor comprising the steps of: a) cultivating cells in a bioreactor culture chamber according to a cell culture process having cell culture parameters; b) during said process, introducing cell culture fluid inputs and generating waste materials; c) determining the amount of volatile organic compounds (VOCs) and their chemical species in the waste materials; and d) estimating the density or population of cells in the bioreactor based on said determination.

Abstract: Systems and methods for executing super-resolution microscopy of a specimen with most of the image processing performed in a camera of a fluorescence microscopy instrument are described. In one aspect, the camera includes one or more processors to execute machine-readable instructions that control excitation light output from a multi-channel light source, control capture of intermediate images of the specimen, and perform image processing of the intermediate images to produce a final super-resolution image of the specimen.

Abstract: Methods and apparatus are described for delivering index-matching immersion liquid in high numerical-aperture optical microscopy and lithography. An array of immersion liquid droplets is delivered to a specimen substrate or specimen substrate cover by an immersion liquid printing apparatus. An immersion liquid reservoir provides immersion liquid to the printer by a precision pump. The printer delivers immersion liquid to the substrate or substrate cover in arrays of immersion liquid droplets of defined volumes and array patterns. The volumes and patterns of array droplets delivered to the substrate or substrate cover are optimized to maintain adequate immersion liquid between the substrate or substrate cover and an immersion objective while avoiding the formation of air bubbles in the immersion liquid and the accumulation of excess volumes of immersion liquid.

Abstract: Example embodiments relate to systems and methods for processing an image in optical microscopy, such as for a CMOS camera used as an optical detector in a line confocal fluorescent imager. The method includes acquiring a raw image with a microscope, and asymmetrically deconvolving at least a portion of the raw image using a point-spread function that is different in an X-direction than in a Y-direction in order to generate an asymmetrically deconvolved image. When the image is a monochromatic fluorescence image, the method also includes compressing CMOS camera noise. Also provided is a system for processing an image in optical microscopy and an image processing system for processing a monochromatic image from a CMOS camera-based line-scan confocal fluorescent microscope.

Abstract: Embodiments of the present invention are directed to imaging technologies, and, in particular, to an imaging system that detects relatively weak signals, over time, and that uses the detected signals to determine the positions of signal emitters. Particular embodiments of the present invention are directed to methods and systems for imaging fluorophore-labeled samples in order to produce images of the sample at resolutions significantly greater than the diffraction-limited resolution associated with optical microscopy. Embodiments of the present invention employ overlapping-emitter-image disambiguation to allow data to be collected from densely arranged emitters, which significantly decreases the data-collection time for producing intermediate images as well as the number of intermediate images needed to computationally construct high-resolution final images. Additional embodiments of the present invention employ hierarchical image-processing techniques to further resolve and interpret disambiguated images.

Abstract: Systems and methods for executing super-resolution microscopy of a specimen with most of the image processing performed in a camera of a fluorescence microscopy instrument are described. In one aspect, the camera includes one or more processors to execute machine-readable instructions that control excitation light output from a multi-channel light source, control capture of intermediate images of the specimen, and perform image processing of the intermediate images to produce a final super-resolution image of the specimen.

Abstract: This disclosure is directed to optical microscope calibration devices that can be used with optical microscopes to adjust the microscope imaging parameters so that images of samples can be obtained below the diffraction limit. The microscope calibration devices include at least one calibration target. Each calibration target includes a number of features with dimensions below the diffraction limit of a microscope objective. Separate color component diffraction limited images of one of the calibration targets are obtained for a particular magnification. The color component images can be combined and image processed to obtain a focused and non-distorted image of the calibration target. The parameters used to obtain the focused and non-distorted image of the calibration target can be used to obtain focused and non-distorted images of a sample for the same magnification by using the same parameters.

Abstract: Systems and methods for executing super-resolution microscopy of a specimen with most of the image processing performed in a camera of a fluorescence microscopy instrument are described. In one aspect, the camera includes one or more processors to execute machine-readable instructions that control excitation light output from a multi-channel light source, control capture of intermediate images of the specimen, and perform image processing of the intermediate images to produce a final super-resolution image of the specimen.

Abstract: Example embodiments relate to systems and methods for processing an image in optical microscopy, such as for a CMOS camera used as an optical detector in a line confocal fluorescent imager. The method includes acquiring a raw image with a microscope, and asymmetrically deconvolving at least a portion of the raw image using a point-spread function that is different in an X-direction than in a Y-direction in order to generate an asymmetrically deconvolved image. When the image is a monochromatic fluorescence image, the method also includes compressing CMOS camera noise. Also provided is a system for processing an image in optical microscopy and an image processing system for processing a monochromatic image from a CMOS camera-based line-scan confocal fluorescent microscope.

Abstract: Methods and apparatus are described for delivering index-matching immersion liquid in high numerical-aperture optical microscopy and lithography. An array of immersion liquid droplets is delivered to a specimen substrate or specimen substrate cover by an immersion liquid printing apparatus. An immersion liquid reservoir provides immersion liquid to the printer by a precision pump. The printer delivers immersion liquid to the substrate or substrate cover in arrays of immersion liquid droplets of defined volumes and array patterns. The volumes and patterns of array droplets delivered to the substrate or substrate cover are optimized to maintain adequate immersion liquid between the substrate or substrate cover and an immersion objective while avoiding the formation of air bubbles in the immersion liquid and the accumulation of excess volumes of immersion liquid.

Abstract: Methods and apparatus are described for delivering index-matching immersion liquid in high numerical-aperture optical microscopy and lithography. An array of immersion liquid droplets is delivered to a specimen substrate or specimen substrate cover by an immersion liquid printing apparatus. An immersion liquid reservoir provides immersion liquid to the printer by a precision pump. The printer delivers immersion liquid to the substrate or substrate cover in arrays of immersion liquid droplets of defined volumes and array patterns. The volumes and patterns of array droplets delivered to the substrate or substrate cover are optimized to maintain adequate immersion liquid between the substrate or substrate cover and an immersion objective while avoiding the formation of air bubbles in the immersion liquid and the accumulation of excess volumes of immersion liquid.

Abstract: Embodiments of the present invention are directed to imaging technologies, and, in particular, to an imaging system that detects relatively weak signals, over time, and that uses the detected signals to determine the positions of signal emitters. Particular embodiments of the present invention are directed to methods and systems for imaging fluorophore-labeled samples in order to produce images of the sample at resolutions significantly greater than the diffraction-limited resolution associated with optical microscopy. Embodiments of the present invention employ overlapping-emitter-image disambiguation to allow data to be collected from densely arranged emitters, which significantly decreases the data-collection time for producing intermediate images as well as the number of intermediate images needed to computationally construct high-resolution final images. Additional embodiments of the present invention employ hierarchical image-processing techniques to further resolve and interpret disambiguated images.

Abstract: Embodiments of the present invention are directed to imaging technologies, and, in particular, to an imaging system that detects relatively weak signals, over time, and that uses the detected signals to determine the positions of signal emitters. Particular embodiments of the present invention are directed to methods and systems for imaging fluorophore-labeled samples in order to produce images of the sample at resolutions significantly greater than the diffraction-limited resolution associated with optical microscopy. Embodiments of the present invention employ overlapping-emitter-image disambiguation to allow data to be collected from densely arranged emitters, which significantly decreases the data-collection time for producing intermediate images as well as the number of intermediate images needed to computationally construct high-resolution final images. Additional embodiments of the present invention employ hierarchical image-processing techniques to further resolve and interpret disambiguated images.

Abstract: Embodiments of the present invention are directed to autofocus subsystems within optical instruments that continuously monitor the focus of the optical instruments and adjust distances within the optical instrument along the optical axis in order to maintain a precise and stable optical-instrument focus at a particular point or surface on, within, or near a sample. Certain embodiments of the present invention operate asynchronously with respect to operation of other components and subsystems of the optical instrument in which they are embedded.

Abstract: Systems and methods for executing super-resolution microscopy of a specimen with most of the image processing performed in a camera of a fluorescence microscopy instrument are described. In one aspect, the camera includes one or more processors to execute machine-readable instructions that control excitation light output from a multi-channel light source, control capture of intermediate images of the specimen, and perform image processing of the intermediate images to produce a final super-resolution image of the specimen.

Abstract: This disclosure is directed to optical microscope calibration devices that can be used with optical microscopes to adjust the microscope imaging parameters so that images of samples can be obtained below the diffraction limit. The microscope calibration devices include at least one calibration target. Each calibration target includes a number of features with dimensions below the diffraction limit of a microscope objective. Separate color component diffraction limited images of one of the calibration targets are obtained for a particular magnification. The color component images can be combined and image processed to obtain a focused and non-distorted image of the calibration target. The parameters used to obtain the focused and non-distorted image of the calibration target can be used to obtain focused and non-distorted images of a sample for the same magnification by using the same parameters.

Abstract: Tube and float systems and methods for isolating, enumerating, and harvesting target materials of a suspension are described. In one aspect, a tube and float system includes a filter embedded in a tube cap. The filter enables the passage of fluids but prevents the passage of the target materials. The tube and float system can be used to isolate and enumerate the target materials by centrifuging the tube and float system with the suspension to trap the target materials between the float and inner wall of the tube. Fluids above and below the float are poured off and a second fluid can be introduced to the tube to re-suspend the trapped target material. The second fluid can be poured through the filter in the cap to trap the target material against the filter. The target material can be enumerated and analyzed.

Abstract: Embodiments of the present invention are directed to imaging technologies, and, in particular, to an imaging system that detects relatively weak signals, over time, and that uses the detected signals to determine the positions of signal emitters. Particular embodiments of the present invention are directed to methods and systems for imaging fluorophore-labeled samples in order to produce images of the sample at resolutions significantly greater than the diffraction-limited resolution associated with optical microscopy. Embodiments of the present invention employ overlapping-emitter-image disambiguation to allow data to be collected from densely arranged emitters, which significantly decreases the data-collection time for producing intermediate images as well as the number of intermediate images needed to computationally construct high-resolution final images. Additional embodiments of the present invention employ hierarchical image-processing techniques to further resolve and interpret disambiguated images.