Abstract: A method for correcting distortion in a coherent electron diffraction imaging (CEDI) image induced by a projection lens makes use of a known secondary material that is imaged together with a sample of interest. Reflections generated from the secondary material are located in the image, and these observed reflections are used to approximate a beam center location. Using a known lattice structure of the secondary material, Friedel pairs are located in the image and unit cell vectors are identified. Predicted positions for each of the secondary material reflections are then determined, and the position differences between the observed reflections and the predicted reflections are used to construct a relocation function applicable to the overall image. The relocation function is then used to adjust the position of image components so as to correct for the distortion.

Abstract: A method for correcting distortion in a coherent electron diffraction imaging (CEDI) image induced by a projection lens makes use of a known secondary material that is imaged together with a sample of interest. Reflections generated from the secondary material are located in the image, and these observed reflections are used to approximate a beam center location. Using a known lattice structure of the secondary material, Friedel pairs are located in the image and unit cell vectors are identified. Predicted positions for each of the secondary material reflections are then determined, and the position differences between the observed reflections and the predicted reflections are used to construct a relocation function applicable to the overall image. The relocation function is then used to adjust the position of image components so as to correct for the distortion.

Abstract: A diffraction system for determining a crystalline structure of a sample collects a series of diffraction frames from a crystal sample illuminated by a beam of photonic or particulate radiation, such as X-rays. A plurality of software modules for processing the detected diffraction frames perform different tasks in refining the collected diffraction data, such as harvesting, indexing, scaling, integration, and structure determination. Output parameters from certain modules are used as input parameters in others, and are exchanged between the modules as they become available. The modules operate simultaneously, and generate successive versions of output parameters as corresponding input parameters are changed until a final result is achieved. This provides a system of structure determination that is fast and efficient.

Abstract: An indirect, photon-counting X-ray detector capable of detecting the low-energy X-rays includes a scintillator screen that is directly coupled to a two-dimensional optical sensor. A signal filter receives an electrical output signal from the optical sensor and removes high intensity signal contributions therefrom that are indicative of direct interaction between said X-ray signal and said optical sensor. The scintillator screen has a sufficient thickness to ensure a high absorption of incident X-ray photons, and uses phosphor grains with a relatively small grain size. A cooling apparatus in thermal communication with the optical sensor may be used to control its temperature. The signal filter maintains a running average of changes in measured pixel output values for consecutive measurements, and replaces a measured value caused by a direct interaction event with a value equal to a previous measured value plus said running average.

Abstract: An indirect, photon-counting X-ray detector capable of detecting the low-energy X-rays includes a scintillator screen that is directly coupled to a two-dimensional optical sensor. A signal filter receives an electrical output signal from the optical sensor and removes high intensity signal contributions therefrom that are indicative of direct interaction between said X-ray signal and said optical sensor. The scintillator screen has a sufficient thickness to ensure a high absorption of incident X-ray photons, and uses phosphor grains with a relatively small grain size. A cooling apparatus in thermal communication with the optical sensor may be used to control its temperature. The signal filter maintains a running average of changes in measured pixel output values for consecutive measurements, and replaces a measured value caused by a direct interaction event with a value equal to a previous measured value plus said running average.

Abstract: In an X-ray detector operating in a rolling shutter read out mode, by precisely synchronizing sample rotation with the detector readout, the effects of timing skew on the image intensities and angular positions caused by the rolling shutter read out can be compensated by interpolation or calculation, thus allowing the data to be accurately integrated with conventional software. In one embodiment, the reflection intensities are interpolated with respect to time to recreate data that is synchronized to a predetermined time. This interpolated data can then be processed by any conventional integration routine to generate a 3D model of the sample. In another embodiment a 3D integration routine is specially adapted to allow the time-skewed data to be processed directly and generate a 3D model of the sample.

Abstract: A method of centering a single crystal sample in the X-ray beam of a diffractometer uses detection of diffraction spots with an active pixel sensor operated in rolling shutter mode. A sample is mounted in the automated goniometer head of the diffractometer and an approximate center of the sample found through which three perpendicular sample axes pass. With a first sample axis perpendicular to a center axis of the X-ray beam, the sample is moved along the first axis from a first position outside of the beam, through the beam and then to a second position outside of the beam. The positions at which first the presence and then the absence of diffraction spots are detected are determined, and the steps repeated for each of the other two perpendicular directions. A precise center may then be found by determining the centroid of the six coordinates thereby obtained.

Abstract: A method of X-ray diffraction-based analysis for determining the structure of a crystal sample is provided. The method comprises conducting pre-experiment to collect a first set of diffraction images including reflections at corresponding intensities. The method also comprises conducting a main experiment to collect a second set of diffraction images, the diffraction images of the second set including the reflections with higher relative intensities than those produced during the first experiment, at least some of the diffraction images of the second set including topped reflections resulting from detector saturation. The method also includes a step of replacing intensities of the topped reflections from the second set of images with intensities obtained for the corresponding reflections from the first set of images.

Abstract: A method of X-ray diffraction-based analysis for determining the structure of a crystal sample is provided. The method comprises conducting pre-experiment to collect a first set of diffraction images including reflections at corresponding intensities. The method also comprises conducting a main experiment to collect a second set of diffraction images, the diffraction images of the second set including the reflections with higher relative intensities than those produced during the first experiment, at least some of the diffraction images of the second set including topped reflections resulting from detector saturation. The method also includes a step of replacing intensities of the topped reflections from the second set of images with intensities obtained for the corresponding reflections from the first set of images.

Abstract: A method for correcting erroneous intensity measurements caused by defective pixels of the detector for a single-crystal X-ray diffraction system uses collected diffraction images and a defective pixel list to modify three-dimensional reflection profiles by replacing profile elements affected by the defective pixels with corresponding profile elements from a model profile. Reflection positions on the detector are predicted using an orientation matrix for the crystal and a three-dimensional observed profile is constructed for each reflection. A model profile is constructed using normalized profile data from multiple reflection profiles. The observed profiles are compared with the defective pixel list to determine which profile elements are affected by defective pixels, and those elements are replaced by corresponding elements from the model profile.

Abstract: A method of centering a single crystal sample in the X-ray beam of a diffractometer uses detection of diffraction spots with an active pixel sensor operated in rolling shutter mode. A sample is mounted in the automated goniometer head of the diffractometer and an approximate center of the sample found through which three perpendicular sample axes pass. With a first sample axis perpendicular to a center axis of the X-ray beam, the sample is moved along the first axis from a first position outside of the beam, through the beam and then to a second position outside of the beam. The positions at which first the presence and then the absence of diffraction spots are detected are determined, and the steps repeated for each of the other two perpendicular directions. A precise center may then be found by determining the centroid of the six coordinates thereby obtained.

Abstract: In an X-ray detector operating in a rolling shutter read out mode, by precisely synchronizing sample rotation with the detector readout, the effects of timing skew on the image intensities and angular positions caused by the rolling shutter read out can be compensated by interpolation or calculation, thus allowing the data to be accurately integrated with conventional software. In one embodiment, the reflection intensities are interpolated with respect to time to recreate data that is synchronized to a predetermined time. This interpolated data can then be processed by any conventional integration routine to generate a 3D model of the sample. In another embodiment a 3D integration routine is specially adapted to allow the time-skewed data to be processed directly and generate a 3D model of the sample.

Abstract: A method for correcting erroneous intensity measurements caused by defective pixels of the detector for a single-crystal X-ray diffraction system uses collected diffraction images and a defective pixel list to modify three-dimensional reflection profiles by replacing profile elements affected by the defective pixels with corresponding profile elements from a model profile. Reflection positions on the detector are predicted using an orientation matrix for the crystal and a three-dimensional observed profile is constructed for each reflection. A model profile is constructed using normalized profile data from multiple reflection profiles. The observed profiles are compared with the defective pixel list to determine which profile elements are affected by defective pixels, and those elements are replaced by corresponding elements from the model profile.

Abstract: In an X-ray detector operating in a rolling shutter read out mode, by precisely synchronizing sample rotation with the detector readout, the effects of timing skew on the image intensities and angular positions caused by the rolling shutter read out can be compensated by interpolation or calculation, thus allowing the data to be accurately integrated with conventional software. In one embodiment, the reflection intensities are interpolated with respect to time to recreate data that is synchronized to a predetermined time. This interpolated data can then be processed by any conventional integration routine to generate a 3D model of the sample. In another embodiment a 3D integration routine is specially adapted to allow the time-skewed data to be processed directly and generate a 3D model of the sample.

Abstract: Readout noise for each pixel in a CMOS Active Pixel Sensor is reduced by a five step process in which the pixel charge data from the sensor is non-destructively sampled at a plurality of times during a sensor frame time period and corrected for gain variation and nonlinearity. Then fixed pattern and dark current noise is estimated and subtracted from the corrected pixel charge data. Next, reset noise is estimated and subtracted from the pixel charge data. In step four, a model function of charge versus time is fit to the corrected pixel charge data samples. Finally, the fitted model function is evaluated at frame boundary times.

Abstract: Readout noise for each pixel in a CMOS Active Pixel Sensor is reduced by a five step process in which the pixel charge data from the sensor is non-destructively sampled at a plurality of times during a sensor frame time period and corrected for gain variation and nonlinearity. Then fixed pattern and dark current noise is estimated and subtracted from the corrected pixel charge data. Next, reset noise is estimated and subtracted from the pixel charge data. In step four, a model function of charge versus time is fit to the corrected pixel charge data samples. Finally, the fitted model function is evaluated at frame boundary times.

Abstract: In an X-ray detector operating in a rolling shutter read out mode, by precisely synchronizing sample rotation with the detector readout, the effects of timing skew on the image intensities and angular positions caused by the rolling shutter read out can be compensated by interpolation or calculation, thus allowing the data to be accurately integrated with conventional software. In one embodiment, the reflection intensities are interpolated with respect to time to recreate data that is synchronized to a predetermined time. This interpolated data can then be processed by any conventional integration routine to generate a 3D model of the sample. In another embodiment a 3D integration routine is specially adapted to allow the time-skewed data to be processed directly and generate a 3D model of the sample.