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8 results for “diffuse scattering”
Dataset: Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI
<p>This dataset supplements the research article <a href="https://doi.org/10.1101/2022.10.04.509781">"Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI"</a>. It contains images and parameter maps obtained from measurements with Scattered Light Imaging (SLI), small-angle X-ray scattering (SAXS), and diffusion magnetic resonance imaging (dMRI) of a vervet monkey and a human brain sample (containing parts of the corona radiata, the cingulum, and the corpus callosum). Please refer to the research article for more information about the sample preparation, the measurement settings, and the generation of the different parameter maps - as well as for a more detailed analysis of the data.</p> <p>While SLI and SAXS were performed on two sections per sample (vervet monkey brain: sections no. 501 and 511; human brain: anterior section no. 20, posterior section no. 18), dMRI was performed on the entire human brain sample (3.5 x 3.5 x 1 cm³), and evaluated in the corresponding section plane of the anterior and posterior section, respectively. Pixel sizes in SLI are 3 µm, and in SAXS 100 µm (vervet) and 150 µm (human). Voxels in dMRI are 200 µm isotropic.</p> <p>All files are in tif-format and can be opened with standard image processing tools like ImageJ. The files labeled with "dMRI_ODF" contain a set of spherical harmonics for each voxel, describing the orientation distribution of the nerve fibers in the respective section plane obtained from the dMRI measurement, and can be visualized with MRtrix3, using the command 'mrview [filename] -odf.load_sh [filename]'.</p> <p>In addition to the ODFs, the dataset contains the b0-values and the dMRI-based metrics for the whole human brain sample in form of image stacks: fractional anisotropy (FA), axonal water fraction (AWF), axial/mean/radial diffusivity (AD/MD/RD), and axial/mean/radial kurtosis (AK/MK/RK).</p> <p>For the evaluated human brain sections (anterior/posterior), the 3D-orientations of the nerve fibers were derived from the dMRI and SAXS measurements, respectively: The files labeled with "3D-vectors" contain the unit vectors as X-Y-Z stack; the files labeled with "inclination" contain the (absolute) out-of-plane inclination of the fibers with respect to the section plane.</p> <p>All measurements were further evaluated with the software SLIX (https://github.com/3d-pli/SLIX) in order to derive the in-plane fiber directions (up to three fiber directions per pixel). The dataset contains the image stacks used as input (Stack) as well as the resulting parameter maps: average/maximum/minimum of the signal (avg/max/min), distance/prominence/width of peaks in the signal (peakdistance/peakprominence/peakwidth), the computed in-plane fiber directions (direction1,2,3), the fiber orientation map encoding the fiber directions in different colors (fom), as well as the vector maps (vectors) where fiber orientations of several pixels are displayed on top of each other. For the vervet brain section no. 511, the dataset also contains the parameter maps registered onto the SLI parameter maps.</p>
Femtosecond electron diffuse scattering data of black phosphorus
<p>Femtosecond electron diffuse scattering data of black phosphorus measured at the Fritz Haber Institute in Berlin. The dataset contains an experiment at 100 K (measurement _1.h5) .</p>
Electrical Low-Frequency 1/fγ Noise Due to Surface Diffusion of Scatterers on an Ultra-low-Noise Graphene Platform
<p>Experimental dataset for article “Electrical Low-Frequency 1/<em>f<sup>γ</sup></em> Noise Due to Surface Diffusion of Scatterers on an Ultra-low-Noise Graphene Platform”, <em>Nano letters</em>, <strong>21</strong>(18), 7637-7643 (2021), <a href="https://doi.org/10.1021/acs.nanolett.1c02325">doi: 10.1021/acs.nanolett.1c02325</a></p>
Diffusion Coefficient Analysis by Dynamic Light Scattering Enables Determination of Critical Micelle Concentration
<p>This upload contains dynamic light scattering data files obtained from the work described in the manuscript that is published by Lena Nielinger and co-workers in ChemPlusChem (<a href="https://doi.org/10.1002/cplu.202400645">https://doi.org/10.1002/cplu.202400645</a>) (WILEY). The files in this repository contain dynamic light scattering data obtained from the analysis of different detergents series and can be downloaded and analysed with a Zetasizer software according to the instructions procied in the manuscript. For information on how to obtain the the Zetasizer software, we refer to the customer support and/or website of the company Malvern Panalytical.</p>
Precision and bias in dynamic light scattering optical coherence tomography measurements of diffusion and flow
<p>This repository contains raw data and analysis routines of the publication <strong>“<em>Precision and bias in dynamic light scattering optical coherence tomography measurements of diffusion and flow</em>”</strong> in Biomedical Optics Express (doi.org/10.1364/BOE.505847<em>). </em>The reader is free to use the scripts and data in this depository if the manuscript is correctly cited in their work. For further questions, feel free to contact the corresponding author. Python 3.7 was used for programming. Kindly note that simulating autocorrelation functions from extensive time series data, especially with a high repetition rate, can be time-consuming, often requiring more than 5-10 minutes. Despite parallelized processing routines for the measurement data, the full analysis may still take up to an hour. Please restart the kernel and run the code again if the parallelization fails.</p> <p>For the diffusion measurement under static conditions, there is only one file. However, for experiments involving both flowing and diffusing particles, the dataset comprises diffusion calibration, focus (beam shape) calibration, and flow measurement files. Due to the upload size limitations of the Zenodo repository, only the flow measurements corresponding to one discharge rate have been uploaded. Furthermore, only the non-dilute flow dataset has been uploaded for the same reason. However, for the dilute flow, the analysis logic remains the same, but users will need to utilize the complete g2 formula outlined in Section 2.2 of our article. All file names are sufficiently descriptive, showing whether it is diffusion, focus (waist) calibration or flow measurement. To conduct the analysis, it's essential to have information regarding the time series length (number of A-scans), the number of repeats (B-scans), and the acquisition rate.</p> <p>The results are plotted at the end of our analysis routines. The parameters are displayed as a function of depth. Users can readily compute the Signal-to-Noise Ratio (SNR) at each depth by utilizing the fitted autocorrelation amplitudes. Occasionally, the fitted amplitudes may surpass unity. In such instances, users can assume an extremely high (even infinite) SNR.</p> <div> <table> <tbody> <tr> <td> <p><strong>Name</strong></p> </td> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Parameters</strong></p> </td> </tr> <tr> <td> <p>Diffusion_03032023.oct</p> </td> <td> <p>Diffusion measurement file.</p> </td> <td> <p>Na=4096, Nb=1100, 5.5 kHz</p> </td> </tr> <tr> <td> <p>Diffusion_07032023.oct</p> </td> <td> <p>Diffusion calibration file for flow measurement.</p> </td> <td> <p>Na=4096, Nb=10, 36 kHz</p> </td> </tr> <tr> <td> <p>Waist_07032023.oct</p> </td> <td> <p>Beam waist calibration file for flow measurement.</p> </td> <td> <p>Na=4096, Nb=40, 36 kHz</p> </td> </tr> <tr> <td> <p>Q=2_07032023.oct</p> </td> <td> <p>Flow measurement file for a discharge rate of 2 ml/min.</p> </td> <td> <p>Na=4096, Nb=1000, 36 kHz</p> </td> </tr> <tr> <td> <p>Chirp.data</p> </td> <td> <p>File containing k-interpolation data.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>ReadOCTFile.py</p> </td> <td> <p>Written by Jos de Wit, this module reads and imports spectra from raw OCT files.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Data_processing.py</p> </td> <td> <p>This module contains all analysis, simulation and processing routines.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Simulation_diffusion.py</p> </td> <td> <p>This script is for simulating and fitting g1 and g2 from diffusive particles.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Simulation_flow.py</p> </td> <td> <p>This script is for simulating and fitting g1 and g2 from flowing and diffusive particles.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Diffusion_parallel.py</p> </td> <td> <p>This script is for analyzing static diffusion measurements performed using Thorlabs Ganymede OCT system.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Flow_parallel.py</p> </td> <td> <p>This script is for analyzing flow measurements performed using Thorlabs Ganymede OCT system.</p> </td> <td> <p> </p> </td> </tr> </tbody> </table> </div> <p> </p>
simlation of Li diffusion via neutron scattering
<p>don't even open</p>
Wavenumber-dependent dynamic light scattering optical coherence tomography measurements of collective and self-diffusion
<p>This repository contains raw data and analysis routines of the publication <strong>“<em>Wavenumber-dependent dynamic light scattering optical coherence tomography measurements of collective and self-diffusion</em>”</strong> in Optics Express (doi.org/10.1364/OE.521702)<em>. </em>The reader is free to use the scripts and data in this depository if the manuscript is correctly cited in their work. For further questions, feel free to contact the corresponding author. Python 3.11 was used for programming. Kindly note that simulating autocorrelation functions from extensive time series data, especially with a high repetition rate, can be time-consuming, often requiring more than 20-30 minutes. Despite parallelized processing routines for the measurement data, the full analysis may still take up to an hour. Please restart the kernel and run the code again if the parallelization fails. Also, keep in mind the significant RAM usage.</p> <p>We've conducted measurements using both a custom-built OCT system and the Thorlabs OCT system. The custom setup specifically focused on measuring diffusion in concentrated suspensions, while the Thorlabs OCT system was used to analyze both concentrated and dilute suspensions. To analyze the data from the custom setup, we require an additional dark measurement file. Conversely, analyzing the Thorlabs measurements necessitates a chirp interpolation file. All filenames, whether for raw data or analysis files, are sufficiently descriptive. Files obtained with the Thorlabs OCT system are easily identifiable as they contain “Thorlabs” in their names. To conduct the analysis of Thorlabs measurements, it's essential to have information regarding the time series length (number of A-scans), the number of repeats (B-scans), and the acquisition rate. The results are plotted at the end of our analysis routines, with the parameters displayed as a function of depth or wavenumber. Raw measurement files and analysis routines are described below.</p> <div> <table> <tbody> <tr> <td> <p><strong>Name</strong></p> </td> <td> <p><strong>Description</strong></p> </td> <td> <p><strong>Parameters</strong></p> </td> </tr> <tr> <td> <p>10050, 10 us.mat</p> </td> <td> <p>Interference intensity from the custom setup for the concentrated Kostrosöl 10050 sample.</p> </td> <td> <p>Na=8192, Nb=20, 4.5 kHz</p> </td> </tr> <tr> <td> <p>CS50-28, 10 us.mat</p> </td> <td> <p>Interference intensity from the custom setup for the concentrated Levasil CS50-28 sample.</p> </td> <td> <p>Na=8192, Nb=20, 4.5 kHz</p> </td> </tr> <tr> <td> <p>Mix, 10 us.mat</p> </td> <td> <p>Interference intensity from the custom setup for the concentrated mixed sample.</p> </td> <td> <p>Na=8192, Nb=20, 4.5 kHz</p> </td> </tr> <tr> <td> <p>Dark, 10 us.mat</p> </td> <td> <p>Background interference intensity from a custom setup.</p> </td> <td> <p>Na=2048, Nb=5, 4.5 kHz</p> </td> </tr> <tr> <td> <p>Concentrated 8050, Thorlabs.oct</p> </td> <td> <p>Interference intensity from the Thorlabs OCT for the concentrated Kostrosöl 8050 sample.</p> </td> <td> <p>Na=65536, Nb=10, 36 Khz</p> </td> </tr> <tr> <td> <p>Concentrated 9550, Thorlabs.oct</p> </td> <td> <p>Interference intensity from the Thorlabs OCT for the concentrated Kostrosöl 9550 sample.</p> </td> <td> <p>Na=65536, Nb=10, 36 Khz</p> </td> </tr> <tr> <td> <p>Concentrated mix, Thorlabs.oct</p> </td> <td> <p>Interference intensity from the Thorlabs OCT for the concentrated mixed sample.</p> </td> <td> <p>Na=65536, Nb=10, 36 Khz</p> </td> </tr> <tr> <td> <p>Dilute 8050, Thorlabs.oct</p> </td> <td> <p>Interference intensity from the Thorlabs OCT for the dilute Kostrosöl 8050 sample.</p> </td> <td> <p>Na=32768, Nb=20, 36 Khz</p> </td> </tr> <tr> <td> <p>Dilute 9550, Thorlabs.oct</p> </td> <td> <p>Interference intensity from the Thorlabs OCT for the dilute Kostrosöl 9550 sample.</p> </td> <td> <p>Na=32768, Nb=20, 36 Khz</p> </td> </tr> <tr> <td> <p>Dilute mix, Thorlabs.oct</p> </td> <td> <p>Interference intensity from the Thorlabs OCT for the dilute mixed sample.</p> </td> <td> <p>Na=32768, Nb=20, 36 Khz</p> </td> </tr> <tr> <td> <p>Chirp.data</p> </td> <td> <p>File containing k-interpolation data for the Thorlabs OCT measurements.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>ReadOCTFile.py</p> </td> <td> <p>Written by Jos de Wit, this module reads and imports spectra from raw Thorlabs OCT files.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Data_processing.py</p> </td> <td> <p>This module contains all analysis functions.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Custom_concentrated.py</p> </td> <td> <p>The script is for analyzing raw concentrated measurement files from the custom setup.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Thorlabs_concentrated.py</p> </td> <td> <p>The script is for analyzing raw concentrated measurement files from the Thorlabs setup.</p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p>Thorlabs_dilute.py</p> </td> <td> <p>The script is for running analysis of raw dilute measurement files from the Thorlabs setup.</p> </td> <td> <p> </p> </td> </tr> </tbody> </table> </div> <p> </p>
simulation of Li diffusion in neutron scattering experiment
<p>Don't even try to open</p>
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