DOI: 10.5281/zenodo.7208998
title: Dataset: Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI

description: This dataset supplements the research article "Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI". 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. 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. 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]'. 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). 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. 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.
description: We thank Laura Pisani from the Stanford Center for Innovation in In vivo Imaging (SCi3) and Kristin Garlund from Bruker BioSpin USA for assistance with the dMRI measurements, Roger Woods from the UCLA Brain Research Institute and Donald Born from Stanford Pathology for providing the vervet and human brain samples, and the laboratory team from the Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, for the preparation of the vervet and human brain sections for the SLI measurements. This work was supported by the National Institutes of Health (NIH) under award numbers R01NS088040, P41EB017183, R01AG061120-01, R01MH092311, and 5P40OD010965, by the Helmholtz Association port-folio theme "Supercomputing and Modeling for the Human Brain", by the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No. 945539 ("Human Brain Project" SGA3), and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). The Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). The Pilatus detector at beamline 4-2 at SSRL was funded under National Institutes of Health Grant S10OD021512. M.M. received funding from the Helmholtz Doctoral Prize 2019 and the Klaus Tschira Stiftung gGmbH.
description: {"references": ["Menzel et al. (2022), Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI, bioRxiv, DOI: 10.1101/2022.10.04.509781"]}