Dataset: Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI

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.本数据集作为研究论文《利用光与X射线散射解析复杂神经元纤维取向并验证扩散磁共振成像》的补充材料。数据集包含通过散射光成像（Scattered Light Imaging, SLI）、小角X射线散射（small-angle X-ray scattering, SAXS）以及扩散磁共振成像（diffusion magnetic resonance imaging, dMRI）对1例黑长尾猴和1例人类大脑样本（包含放射冠、扣带回及胼胝体区域）进行测量所获得的图像与参数图。有关样本制备、测量设置、各类参数图生成方法，以及更详细的数据分析，请参阅该研究论文。 SLI与SAXS测量分别对每个样本的2个切片进行（黑长尾猴大脑切片编号：501与511；人类大脑切片编号：前部切片20、后部切片18）；而dMRI测量则覆盖整个人类大脑样本（尺寸为3.5 × 3.5 × 1 cm³），并分别在对应前部与后部切片的平面上进行评估。SLI的像素尺寸为3 µm，SAXS的像素尺寸分别为100 µm（黑长尾猴样本）与150 µm（人类样本）；dMRI的体素为各向同性200 µm。 所有文件均采用tif格式，可通过ImageJ等标准图像处理软件打开。标注为“dMRI_ODF”的文件包含每个体素的球谐函数集，用于描述通过dMRI测量获得的对应切片平面内神经纤维的取向分布，可通过MRtrix3软件使用命令`mrview [filename] -odf.load_sh [filename]`进行可视化。 除取向分布函数（ODF）外，数据集还包含以图像栈形式存储的整个人类大脑样本的b0值及基于dMRI的指标：各向异性分数（fractional anisotropy, FA）、轴突水分数（axonal water fraction, AWF）、轴向/平均/径向扩散系数（axial/mean/radial diffusivity, AD/MD/RD）以及轴向/平均/径向峰度（axial/mean/radial kurtosis, AK/MK/RK）。 针对评估所用的人类大脑前部/后部切片，分别通过dMRI与SAXS测量推导得到神经纤维的三维取向：标注为“3D-vectors”的文件包含以X-Y-Z栈形式存储的单位向量；标注为“inclination”的文件包含纤维相对于切片平面的（绝对）面外倾角。 所有测量数据均通过SLIX软件（https://github.com/3d-pli/SLIX）进行进一步处理，以提取平面内纤维方向（每个像素最多可提取3个纤维方向）。数据集包含作为输入的图像栈（Stack）以及各类生成的参数图：信号的平均值/最大值/最小值（avg/max/min）、信号峰的距离/显著性/宽度（peakdistance/peakprominence/peakwidth）、计算得到的平面内纤维方向（direction1,2,3）、以不同颜色编码纤维方向的纤维取向图（fom），以及将多个像素的纤维取向叠加显示的向量图（vectors）。 针对黑长尾猴大脑511号切片，数据集还包含配准至SLI参数图的各类参数图。