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: This disclosure is directed to tube and float systems that can be used to detect target materials in a variety of different suspensions. The tube is filled with a suspension suspected of containing a target material. When the tube, a float, and suspension are centrifuged, and the various materials suspended in the suspension are separated into different material layers along the axial length of the tube according to associated specific gravities. The float includes an insert and a float exterior that can be combined so that the float is to be positions at approximately the same level as the layer containing the target material. The float is to be positioned in, and expand the axial length of, the target material layer so that nearly the entire quantity of target material is to be positioned between the float outer surface and the inner surface of the tube.

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: This disclosure is directed to methods for isolating target materials from non-target materials of a suspension that have a similar density to that of the target material. A suspension suspected of containing a target material is added to a tube and float system. A solution containing molecules that interact specifically with the non-target materials to change the density of the non-target materials in also added. A float is also added to the tube, and the tube, float, and suspension are centrifuged together. The float has a specific gravity that positions the float at approximately the same level as a layer containing the target material when the tube, float and suspension are centrifuged. During centrifugation, the non-target material/molecules complexes are drawn either below the float or above float, leaving the target material between the outer surface of the float and the inner surface of the tube.

Abstract: A system and method employing photokinetic techniques in cell biology imaging applications are disclosed. Systems and methods of acquiring image data of an object may comprise: selectively inducing photoactivation of material at a site on the object; performing an optical axis integration scan; simultaneously executing a time delay integration scan sequence; and processing acquired image data in accordance with one or more desired analyses. Various methodologies and applications may include, inter alia, selective photobleaching of a site on the object, diffusion rate, velocity, and wave-front propagation analyses, multi-dimensional analyses of dispersion characteristics, biomolecular binding in cellular organelles, and photoactivation assisted systematic image segmentation for the study of cellular components.

Abstract: A system and method employing photokinetic techniques in cell biology imaging applications are disclosed. Systems and methods of acquiring image data of an object may comprise: selectively inducing photoactivation of material at a site on the object; performing an optical axis integration scan; simultaneously executing a time delay integration scan sequence; and processing acquired image data in accordance with one or more desired analyses. Various methodologies and applications may include, inter alia, selective photobleaching of a site on the object, diffusion rate, velocity, and wave-front propagation analyses, multi-dimensional analyses of dispersion characteristics, biomolecular binding in cellular organelles, and photoactivation assisted systematic image segmentation for the study of cellular components.

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: A system and method of generating and acquiring phase contrast microscope images while minimizing interference with the intensity and optical quality of other microscopy modalities employing polarization and attenuation strategies for phase microscopy applications. A plane polarizing objective phase ring may be used in conjunction with a phase microscopy apparatus. Attenuated light may be controlled such that transparency may be selectively provided with respect to light in a predetermined plane. Illumination outside of the predetermined plane may be selected for phase microscopy applications. Accordingly, a polarizing objective phase ring effective for enabling polarized phase microscopy may reduce interfere with normal usage of the microscope for other applications such as, for example, fluorescence microscopy.

Abstract: A system and method employing photokinetic techniques in cell biology imaging applications are disclosed. Systems and methods of acquiring image data of an object may comprise: selectively inducing photoactivation of material at a site on the object; performing an optical axis integration scan; simultaneously executing a time delay integration scan sequence; and processing acquired image data in accordance with one or more desired analyses. Various methodologies and applications may include, inter alia, selective photobleaching of a site on the object, diffusion rate, velocity, and wave-front propagation analyses, multi-dimensional analyses of dispersion characteristics, biomolecular binding in cellular organelles, and photoactivation assisted systematic image segmentation for the study of cellular components.

Abstract: A system and method employing photokinetic techniques in cell biology imaging applications are disclosed. Systems and methods of acquiring image data of an object may comprise: selectively inducing photoactivation of material at a site on the object; performing an optical axis integration scan; simultaneously executing a time delay integration scan sequence; and processing acquired image data in accordance with one or more desired analyses. Various methodologies and applications may include, inter alia, selective photobleaching of a site on the object, diffusion rate, velocity, and wave-front propagation analyses, multi-dimensional analyses of dispersion characteristics, biomolecular binding in cellular organelles, and photoactivation assisted systematic image segmentation for the study of cellular components.

Abstract: An image acquisition system and method employing multi-axis integration (MAI) may incorporate both optical axis integration (OAI) and time-delay integration (TDI) techniques. Disclosed MAI systems and methods may integrate image data in the z direction as the data are acquired, projecting the image data prior to deconvolution. Lateral translation of the image plane during the scan in the z direction may allow large areas to be imaged in a single scan sequence.

Abstract: A system and method employing photokinetic techniques in cell biology imaging applications are disclosed. Systems and methods of acquiring image data of an object may comprise: selectively inducing photoactivation of material at a site on the object; performing an optical axis integration scan; simultaneously executing a time delay integration scan sequence; and processing acquired image data in accordance with one or more desired analyses. Various methodologies and applications may include, inter alia, selective photobleaching of a site on the object, diffusion rate, velocity, and wave-front propagation analyses, multi-dimensional analyses of dispersion characteristics, biomolecular binding in cellular organelles, and photoactivation assisted systematic image segmentation for the study of cellular components.

Abstract: Expression profiling using DNA microarrays is an important new method for analyzing cellular physiology. In “spotted” microarrays, fluorescently labeled cDNA from experimental and control cells is hybridized to arrayed target DNA and the arrays imaged at two or more wavelengths. Statistical analysis is performed on microarray images and show that non-additive background, high intensity fluctuations across spots, and fabrication artifacts interfere with the accurate determination of intensity information. The probability density distributions generated by pixel-by-pixel analysis of images can be used to measure the precision with which spot intensities are determined. Simple weighting schemes based on these probability distributions are effective in improving significantly the quality of microarray data as it accumulates in a multi-experiment database. Error estimates from image-based metrics should be one component in an explicitly probabilistic scheme for the analysis of DNA microarray data.

Abstract: An image acquisition system and method employing multi-axis integration (MAI) may incorporate both optical axis integration (OAI) and time-delay integration (TDI) techniques. Disclosed MAI systems and methods may integrate image data in the z direction as the data are acquired, projecting the image data prior to deconvolution. Lateral translation of the image plane during the scan in the z direction may allow large areas to be imaged in a single scan sequence.

Abstract: A system and method of providing illumination for a cell imaging system delivering modulated light for illumination of a sample. Modulation of illumination intensity may be effectuated by pulsing the output of a light source, for example, or by selectively interrupting light provided by the source. Such modulated illumination may have particular utility in applications where reducing the number of electrons in a super-excited state may minimize the rate of photobleaching and photodamage in the molecules being studied.

Abstract: Expression profiling using DNA microarrays is an important new method for analyzing cellular physiology. In “spotted” microarrays, fluorescently labeled cDNA from experimental and control cells is hybridized to arrayed target DNA and the arrays imaged at two or more wavelengths. Statistical analysis is performed on microarray images and show that non-additive background, high intensity fluctuations across spots, and fabrication artifacts interfere with the accurate determination of intensity information. The probability density distributions generated by pixel-by-pixel analysis of images can be used to measure the precision with which spot intensities are determined. Simple weighting schemes based on these probability distributions are effective in improving significantly the quality of microarray data as it accumulates in a multi-experiment database. Error estimates from image-based metrics should be one component in an explicitly probabilistic scheme for the analysis of DNA microarray data.

Abstract: A system and method of generating and acquiring phase contrast microscope images without interfering with the intensity and optical quality of other microscopy modalities employ wavelength-specific illumination and attenuation strategies for phase microscopy applications. A wavelength-specific objective phase ring that is opaque only at specific wavelengths may be used in conjunction with a phase microscopy apparatus. Attenuated wavelengths may be controlled such that opacity may be selectively provided only with respect to wavelengths that are outside of the desired range for the fluorescence signals being monitored. Illumination within the opaque wavelength range for the objective phase ring may be selected for phase microscopy applications. Accordingly, an objective phase ring effective for enabling wavelength-specific phase microscopy may not interfere with normal usage of the microscope for other applications such as, for example, fluorescence microscopy.

Abstract: A system and method of providing illumination for a live-cell imaging system deliver modulated light for illumination of a sample. Modulation of illumination intensity may be effectuated by pulsing the output of a light source, for example, or by selectively interrupting light provided by the source. Such modulated illumination may have particular utility in applications where reducing the number of electrons in a super-excited state may minimize the rate of photobleaching and photodamage in the molecules being studied.

Abstract: A system and method of selectively fastening a substrate to a limited travel staging system are disclosed. In accordance with one aspect of a substrate holder, a securing mechanism may be manually or automatically moved in a repeatable manner such that a selected region of a substrate can be moved into the precision travel range of a highly accurate staging system. Some embodiments of a substrate holder may comprise an indexing system enabling referenced movements such that one or more selected substrate regions may be moved relative to the stage.