Abstract: Systems and methods are described for extending the dynamic range of imaging systems, and more particularly fluorescence or luminescence imaging systems, having low optical background and a linear detector response. Images of a sample at each of a set of exposure times are acquired, a system-level dark estimate for each exposure time is subtracted from each image to form dark-corrected images, and the different exposures (dark-corrected images) are merged into a wider dynamic-range image. Typically merging is performed on a pixel-by pixel basis.

Abstract: Systems, devices, and methods for accurately imaging chemiluminescence and other luminescence are disclosed. A compact, flat-bed scanner having a light-tight enclosure, one or more detector bars of linear charge-coupled device (CCD) or complementary metal oxide semiconductor (CMOS) imaging chips, and high working numerical aperture (NA) optics scans closely over a sample in one direction and then the opposite direction. Averages or other combinations of intensity readings for each pixel location (x, y) between the two or more passes are averaged together in order to compensate for luminescence that varies over time. On-chip pixel binning and multiple clock frequencies can be used to maximize the signal to noise ratio in a CCD-based scanner.

Abstract: Cavity enhanced absorption spectroscopy systems and methods for detecting trace gases using a resonance optical cavity, which contains a gas mixture to be analyzed, and a laser coupled to the cavity by optical feedback. The cavity has any of a variety of configurations with two or more mirrors, including for example a linear cavity, a v-shaped cavity and a ring optical cavity. The cavity will have multiple cavity resonant modes, or a comb of frequencies spaced apart, as determined by the parameters of the cavity, including the length of the cavity, as is well known. Systems and methods herein also allow for optimization of the cavity modes excited during a scan and/or the repetition rate.

Abstract: Cavity enhanced absorption spectroscopy systems and methods for detecting trace gases using a resonance optical cavity, which contains a gas mixture to be analyzed, and a laser coupled to the cavity by optical feedback. The cavity has any of a variety of configurations with two or more mirrors, including for example a linear cavity, a v-shaped cavity and a ring optical cavity. The cavity will have multiple cavity resonant modes, or a comb of frequencies spaced apart, as determined by the parameters of the cavity, including the length of the cavity, as is well known. Systems and methods herein also allow for optimization of the cavity modes excited during a scan and/or the repetition rate.

Abstract: System flow path designs that minimize the impact of gas diffusion sources and sinks. By reducing the magnitude of parasitic sources and sinks, lower rates of photosynthesis and transpiration can be more accurately measured, e.g., without the need for extensive empirical compensation. The gas exchange analysis system includes a sample chamber having an inlet and an outlet, wherein the internal surface(s) of the chamber defining the measurement volume are metal plated. The system also typically includes a source of gas coupled with the inlet of the sample chamber, and a gas analyzer coupled with the outlet of the sample chamber and configured to measure a concentration of one or more gases exiting the chamber, whereby the metal plated internal surface(s) of the chamber reduces sorption of the one or more gases within the chamber.

Abstract: Systems and methods for flattening the image across the entire field by correcting the image for both the fluorescence and scatter spatial variations. Images of a stable fluorescence target and a scattering target are separately acquired in an imaging system. From these target images, a pixel remapping function, e.g., including two correcting pixel slopes, is calculated for subsequent image pixel remapping. An image of a sample under investigation is then acquired by the imaging system and the sample image is remapped based on the pixel remapping function for the imaging system to form a corrected (field flattened) image. Which correction pixel slope to be used is determined based on whether a sample image pixel value is higher or lower than a threshold value.

Abstract: Systems and methods for measuring the isotope ratio of one or more trace gases and/or components of gas mixtures such as different gas species present in a gas mixture. The system includes a resonant optical cavity having two or more mirrors and containing a gas, the cavity having a free spectral range that equals the difference between frequencies of two measured absorption lines of different gas species in the gas, or of two different isotopes, divided onto an integer number. The system includes a continuous-wave tunable laser optically coupled with the resonant optical cavity and a detector system for measuring an absorption of laser light by the gas in the cavity. The detector system includes a photo-detector to measure an intensity of the intra-cavity light, or both a photo-acoustic sensor to measure photo-acoustic waves generated in the cavity and a photo-detector to measure an intensity of the intra-cavity light.

Abstract: Cavity enhanced absorption spectroscopy systems and methods for detecting trace gases. When the frequency of laser light approaches the frequency of a resonance cavity mode, the laser begins to fill the cavity to that mode. Optical intensity inside the cavity reflects total cavity loss when the laser light frequency coincides with the cavity mode transmission peak. The intra-cavity optical power also depends on the coupling efficiency of the laser beam to the particular cavity mode. Measurement of intensities of three optical signals, namely, intensity of the light incident on to the cavity, intensity of the light reflected from the cavity, and intensity of the intra-cavity optical power, with their appropriate normalization advantageously significantly reduce effects of baseline calibration and drift as the normalized signal only depends on total cavity loss, and not the coupling efficiency, as in traditional approaches.

Abstract: Optical feedback assisted cavity enhanced absorption spectroscopy systems and methods for measuring trace gases with improved long-term stability and reproducibility include a laser coupled with a resonant optical cavity containing a gaseous medium and having at least two cavity mirrors and a plurality of optical resonance cavity modes. The laser emits continuous wave laser light with a mean optical frequency of the laser being adjustable over a range of frequencies, and the laser is responsive to optical feedback light emerging from the cavity. The transmissivity of at least one of the cavity mirrors is selected such that the intensity of the optical feedback light impinging on the laser is below a threshold intensity value so as to ensure that a frequency hold interval range of the optical frequency of the laser is smaller than a free spectral range of the cavity.

Abstract: An optical mirror element includes an optically transmissive element having a first surface and a second surface, and a reflective coating layer on the first surface that defines a mirror surface. A first portion of the first surface does not include the reflective coating layer such that the first portion defines an optically transmissive window in the mirror surface. Q method of forming an optical mirror element having a window portion includes providing an optical element, masking a first portion of a first surface of the optical element, and thereafter applying a reflective coating to the first surface so as to define a reflective surface, wherein the masked portion defines a transmissive region in the reflective surface. The exposed portion of the first surface may be coated with an anti-reflective coating, either before or after the reflective coating is applied.

Abstract: System flow path designs that minimize the impact of gas diffusion sources and sinks. By reducing the magnitude of parasitic sources and sinks, lower rates of photosynthesis and transpiration can be more accurately measured, e.g., without the need for extensive empirical compensation. According to one aspect, a sensor head for use in a gas exchange analysis system includes a sample chamber defining a measurement volume for analysis of a sample, the sample chamber having an inlet and an outlet, and a flow splitting mechanism located proximal to the sample chamber, the mechanism configured to split a gas flow received at an input port from a remote source to a first output port and to a second output port, wherein the first output port is coupled with the inlet of the sample chamber.

Abstract: A gas flux measurement system comprises gas collection means, operable to collect gas for analysis, and gas analysing means, operable to analyse the collected gas. The gas collection means has at least one elongate tube. The, or each, tube has one or more gas collection openings to provide gaseous communication from outside of the tube to the inside of the tube.

Abstract: Systems, devices, and methods for accurately imaging chemiluminescence and other luminescence are disclosed. A compact, flat-bed scanner having a light-tight enclosure, one or more detector bars of linear charge-coupled device (CCD) or complementary metal oxide semiconductor (CMOS) imaging chips, and high working numerical aperture (NA) optics scans closely over a sample in one direction and then the opposite direction. Averages or other combinations of intensity readings for each pixel location (x, y) between the two or more passes are averaged together in order to compensate for luminescence that varies over time. On-chip pixel binning and multiple clock frequencies can be used to maximize the signal to noise ratio in a CCD-based scanner.

Abstract: Systems and methods for measuring turbulent gas flux using high-speed vertical wind speed measurements (e.g., on the order of 5-10 Hz or more frequently) and low-speed gas content measurements (e.g., on the order of 5 Hz or less frequently), without the need for the sophisticated and expensive high-speed hardware to separate gas samples (e.g., into accumulation bags) according to updrafts and downdrafts. A time series of high-speed vertical wind speed data is used as a guide to distinguish between updrafts and downdrafts. When vertical wind speed is upward (updraft), the low-speed gas content is recorded into a data structure in one location, or marked with one flag. When vertical wind speed is downward (downdraft), the low-speed gas content is recorded into a different location, or marked with a different flag. Eddy Accumulation or Relaxed Eddy Accumulation computations can be performed using the stored gas content data to determine gas flux.

Abstract: A gas analyzer includes a detector section including a detector, a source section including a light source, and a support structure coupling the detector section with the source section and forming a flow channel defining an optical path measuring region. The gas analyzer also includes an air flow device configured to pull air through the flow channel from an intake region in the support structure to an exhaust region. Sampling is done by pulling air into the sampling cell via an intake opening or tube of wide diameter and short to medium at very fast flow rates (e.g., 10-3000 lpm or more) enabling rapid gas sampling. Fast flow rates enable the use of large volume cell for rapid gas sampling, which in turn, enables rapid measurements of many low-concentration trace gases and sticky/reactive gases (e.g., methane, ammonia, isotopes of CO2, H2O, nitrous oxide, etc.).

Abstract: A system for locking a laser with a resonant optical cavity includes a laser that emits a laser beam, a resonant optical cavity having at least two cavity mirrors, one of which is a cavity coupling mirror, mode matching optics configured to couple the laser beam to the cavity via the cavity coupling mirror, means for applying a periodic dither or modulation waveform signal to the optical frequency of the incident laser beam or to the laser itself to thereby induce modulation of the intracavity optical power, and means for enabling a portion of the light emerging from the cavity coupling mirror to enter a cavity of the laser while maintaining an optical phase that results in periodic optical feedback locking whereby a mean optical frequency of the laser matches a resonance peak of the cavity.

Abstract: An optical mirror element includes an optically transmissive element having a first surface and a second surface, and a reflective coating layer on the first surface that defines a mirror surface. A first portion of the first surface does not include the reflective coating layer such that the first portion defines an optically transmissive window in the mirror surface. Q method of forming an optical mirror element having a window portion includes providing an optical element, masking a first portion of a first surface of the optical element, and thereafter applying a reflective coating to the first surface so as to define a reflective surface, wherein the masked portion defines a transmissive region in the reflective surface. The exposed portion of the first surface may be coated with an anti-reflective coating, either before or after the reflective coating is applied.

Abstract: Systems, devices, and methods for accurately imaging chemiluminescence and other luminescence are disclosed. A compact, flat-bed scanner having a light-tight enclosure, one or more detector bars of linear charge-coupled device (CCD) or complementary metal oxide semiconductor (CMOS) imaging chips, and high working numerical aperture (NA) optics scans closely over a sample in one direction and then the opposite direction. Averages or other combinations of intensity readings for each pixel location (x, y) between the two or more passes are averaged together in order to compensate for luminescence that varies over time. On-chip pixel binning and multiple clock frequencies can be used to maximize the signal to noise ratio in a CCD-based scanner.

Abstract: Compounds and methods are disclosed that are useful for noninvasive imaging in the near-infrared spectral range. The cyanine compounds of Formula I are presented: wherein Q is a portion of a polymethine bridge selected from the group consisting of: Also included are bioconjugates of the compounds of Formula I, methods of labeling biomolecules with the compounds, and methods of imaging.

Abstract: Systems, devices, and methods for accurately imaging chemiluminescence and other luminescence are disclosed. A compact, flat-bed scanner having a light-tight enclosure, one or more detector bars of linear charge-coupled device (CCD) or complementary metal oxide semiconductor (CMOS) imaging chips, and high working numerical aperture (NA) optics scans closely over a sample in one direction and then the opposite direction. Averages or other combinations of intensity readings for each pixel location (x, y) between the two or more passes are averaged together in order to compensate for luminescence that varies over time. On-chip pixel binning and multiple clock frequencies can be used to maximize the signal to noise ratio in a CCD-based scanner.