Abstract: An embodiment of a module system configured to interface with a microscope is described that comprises an input optical fiber configured to provide an excitation light beam from an external light source; dynamic alignment mirrors configured to adjust the position of the beams paths of the excitation light beam on a first plane; a coupling comprising a first end configured to engage with a complementary end, wherein the excitation light reflects off a turning mirror and travels along a beam path on a second plane through an orifice in the coupling; and an output optical fiber for delivering light from a sample to an external detector, wherein the light from the sample travels along the beam path on the second plane through the orifice in the coupling, reflects off the turning mirror and travels along one of the beam paths on the first plane to the output optical fiber.

Abstract: Provided are systems and methods related to hybrid reflective microscope objectives and lens systems used in a spectroscopy system. The objective lens system includes a primary aspheric mirror having a first R-value; and a secondary aspheric mirror having a second R-value smaller than the first R-value, where in the objective lens system has a working distance of at least 20 mm and a numerical aperture of 0.29-0.65, and wherein surfaces of the primary and secondary aspheric mirrors have a non-zero sixth order aspheric parameter.

Abstract: Methods and apparatuses are disclosed whereby structured illumination microscopy (SIM) is applied to a scanning microscope, such as a confocal laser scanning microscope or sample scanning microscope, in order to improve spatial resolution. Particular aspects of the disclosure relate to the discovery of important advances in the ability to (i) increase light throughput to the sample, thereby increasing the signal/noise ratio and/or decreasing exposure time, as well as (ii) decrease the number of raw images to be processed, thereby decreasing image acquisition time. Both effects give rise to significant improvements in overall performance, to the benefit of users of scanning microscopy.

Abstract: A stray light reducing apparatus includes a light source and an entrance slit positioned to pass through light from the light source. A first monochromator mirror is positioned to reflect light passed through the entrance slit. A diffractive surface is positioned to receive and diffract light reflected by the first monochromator mirror. A second monochromator mirror is positioned to reflect light diffracted by the diffractive surface. An exit slit is positioned to pass through light reflected by the second monochromator mirror. A cuvette is positioned to pass through light passed through the exit slit. A long-pass interference filter is positioned to receive light from the light source, reflect light that has a wavelength below a selected value, and pass through light having a wavelength above the selected value. A first sample detector is positioned to receive light reflected by the long-pass interference filter.

Abstract: An image analysis system includes a video camera that collects YUV color images of a liquid sample disposed between a capital and a pedestal, the color images being collected while a light source shines light through an optical beam path between the capital and the pedestal, and a processor adapted to i) obtain from the YUV color images a grayscale component image and a light scatter component image, and ii) obtain at least one binary image of the grayscale component image and at least one binary image of the light scatter component image.

Abstract: A diffuse reflectance apparatus includes a housing having a window formed therein, and a diffuse reflectance mirror spaced from the window and having an aperture extending therethrough. A light source provides a beam of light. A first mirror assembly is positioned to reflect the beam of light through the aperture such that it passes through the window. A second mirror assembly is positioned to reflect scattered light from the concave mirror to a detector.

Abstract: An embodiment of a calibration element for an analytical microscope is described that comprises a substantially non-periodic pattern of features that exhibit contrast when illuminated by a light beam.

Abstract: An embodiment of a module system configured to interface with a microscope is described that comprises an input optical fiber configured to provide an excitation light beam from an external light source; dynamic alignment mirrors configured to adjust the position of the beams paths of the excitation light beam on a first plane; a coupling comprising a first end configured to engage with a complementary end, wherein the excitation light reflects off a turning mirror and travels along a beam path on a second plane through an orifice in the coupling; and an output optical fiber for delivering light from a sample to an external detector, wherein the light from the sample travels along the beam path on the second plane through the orifice in the coupling, reflects off the turning mirror and travels along one of the beam paths on the first plane to the output optical fiber.

Abstract: Methods and apparatuses are disclosed whereby structured illumination microscopy (SIM) is applied to a scanning microscope, such as a confocal laser scanning microscope or sample scanning microscope, in order to improve spatial resolution. Particular aspects of the disclosure relate to the discovery of important advances in the ability to (i) increase light throughput to the sample, thereby increasing the signal/noise ratio and/or decreasing exposure time, as well as (ii) decrease the number of raw images to be processed, thereby decreasing image acquisition time. Both effects give rise to significant improvements in overall performance, to the benefit of users of scanning microscopy.

Abstract: An image analysis system includes a video camera that collects YUV color images of a liquid sample disposed between a capital and a pedestal, the color images being collected while a light source shines light through an optical beam path between the capital and the pedestal, and a processor adapted to i) obtain from the YUV color images a grayscale component image and a light scatter component image, and ii) obtain at least one binary image of the grayscale component image and at least one binary image of the light scatter component image.

Abstract: An image analysis system includes a video camera that collects YUV color images of a liquid sample disposed between a capital and a pedestal, the color images being collected while a light source shines light through an optical beam path between the capital and the pedestal, and a processor adapted to i) obtain from the YUV color images a grayscale component image and a light scatter component image, and ii) obtain at least one binary image of the grayscale component image and at least one binary image of the light scatter component image.

Abstract: A stray light reducing apparatus includes a light source and an entrance slit positioned to pass through light from the light source. A first monochromator mirror is positioned to reflect light passed through the entrance slit. A diffractive surface is positioned to receive and diffract light reflected by the first monochromator mirror. A second monochromator mirror is positioned to reflect light diffracted by the diffractive surface. An exit slit is positioned to pass through light reflected by the second monochromator mirror. A cuvette is positioned to pass through light passed through the exit slit. A long-pass interference filter is positioned to receive light from the light source, reflect light that has a wavelength below a selected value, and pass through light having a wavelength above the selected value. A first sample detector is positioned to receive light reflected by the long-pass interference filter.

Abstract: A diffuse reflectance apparatus includes a housing having a window formed therein, and a diffuse reflectance mirror spaced from the window and having an aperture extending therethrough. A light source provides a beam of light. A first mirror assembly is positioned to reflect the beam of light through the aperture such that it passes through the window. A second mirror assembly is positioned to reflect scattered light from the concave mirror to a detector.

Abstract: Devices and methods are disclosed having (a) an exposed semiconducting single walled carbon nanotube channel on the surface of a substrate, wherein the exposed semiconducting single walled carbon nanotube channel is functionalized with a capture moiety cognate to a target analyte, (b) a source electrode and a drain electrode connecting opposite ends of the exposed semiconducting single walled carbon nanotube channel, and (c) wherein the source electrode and the drain electrode are electrically connected in a manner to detect changes in current through the exposed semiconducting single walled carbon nanotube channel in response to analyte in contact therewith,

Abstract: An embodiment of a calibration element for an analytical microscope is described that comprises a substantially non-periodic pattern of features that exhibit contrast when illuminated by a light beam.

Abstract: An image analysis system includes a video camera that collects YUV color images of a liquid sample disposed between a capital and a pedestal, the color images being collected while a light source shines light through an optical beam path between the capital and the pedestal, and a processor adapted to i) obtain from the YUV color images a grayscale component image and a light scatter component image, and ii) obtain at least one binary image of the grayscale component image and at least one binary image of the light scatter component image.

Abstract: An optical device is provided that includes a converging lens device, a transmitting optical fiber, a sample holder, and a receiving optical fiber. The converging lens device focuses light onto the transmitting optical fiber, which receives the focused light through an entrance face and transmits the light from an exit face, through a sample, and onto the receiving optical fiber. The sample holder holds the sample for analysis. The receiving optical fiber receives the light through an entrance face of the receiving optical fiber after transmission through the sample. The converging lens device is positioned to focus the light onto the entrance face of the transmitting optical fiber such that a half-angle of the angular distribution of the focused light that reaches the entrance face of the transmitting optical fiber is selected to underfill an entrance aperture of the entrance face of the receiving optical fiber in both a spatial dimension and an angular dimension.

Abstract: A method and corresponding apparatus provide correction of chemical images collected with a germanium hemisphere ATR microscope. A model is developed for rays passing through a simulated germanium (Ge) hemisphere attenuated total reflection (ATR) microscope. The model determines a data set for rays reaching the detector plane. Movement of the hemisphere is simulated along a first axis between each data set determination. A calculated background spectrum is produced by multiplying the percentage of rays by a background spectrum to produce a calculated background spectrum. A real Ge hemisphere ATR microscope having parameters that substantially match those of the simulated Ge hemisphere microscope is then used to collect a chemical image of a sample that is in contact with the Ge hemisphere. The collected image is then corrected to produce a corrected chemical image.

Abstract: An optical device is provided that includes a converging lens device, a transmitting optical fiber, a sample holder, and a receiving optical fiber. The converging lens device focuses light onto the transmitting optical fiber, which receives the focused light through an entrance face and transmits the light from an exit face, through a sample, and onto the receiving optical fiber. The sample holder holds the sample for analysis. The receiving optical fiber receives the light through an entrance face of the receiving optical fiber after transmission through the sample. The converging lens device is positioned to focus the light onto the entrance face of the transmitting optical fiber such that a half-angle of the angular distribution of the focused light that reaches the entrance face of the transmitting optical fiber is selected to underfill an entrance aperture of the entrance face of the receiving optical fiber in both a spatial dimension and an angular dimension.

Abstract: A method and corresponding apparatus provide correction of chemical images collected with a germanium hemisphere ATR microscope. A modeled is developed for rays passing through a simulated germanium (Ge) hemisphere attenuated total reflection (ATR) microscope. The model determines a data set for rays reaching the detector plane. Movement of the hemisphere is simulated along a first axis between each data set determination. A calculated background spectrum is produced by multiplying the percentage of rays by a background spectrum to produce a calculated background spectrum. A real Ge hemisphere ATR microscope having parameters that substantially match those of the simulated Ge hemisphere microscope is then used to collect a chemical image of a sample that is in contact with the Ge hemisphere. The collected image is then corrected to produce a corrected chemical image.