Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience

<strong>Supplementary Data</strong> <strong>Supplementary Data 1</strong> contains the input (non-watertight) surface meshes of the block (shown in Figure 2a) reconstructed within the context of the EPFL-KAUST collaboration, and the corresponding output (watertight) meshes generated by Ultraliser. <strong>Supplementary Data 2 </strong>contains a set of 20 non-watertight meshes that were randomly selected from the block shown in <strong>Supplementary Figure S54</strong> and another set of the their watertight counterparts. <strong>Supplementary Data 3</strong> contains a set of 25 neuronal morphologies with different morphological types and their corresponding watertight meshes. <strong>Supplementary Data 4</strong> contains a set of 25 synthetic astroglial morphologies 15 and their corresponding watertight meshes. <strong>Supplementary Data 5</strong> contains the vascular morphology (shown in <strong>Supplementary Fig. S83</strong>) and a corresponding multi-partitioned watertight mesh. <strong>Supplementary Data 6</strong> contains the datasets used for the comparative analysis shown in <strong>Supplementary Section 13</strong>.<br> <br> Neuronal, astrocytic and vascular morphologies are stored in SWC, H5 and VMV file formats respectively. The file structures of the SWC and VMV formats are publicly available online. The H5 files of the complete astrocyte cells can be made available from corresponding authors upon request. All the surface meshes are stored in Wavefront OBJ files. Additional STL meshes are generated to be used for TetGen to create corresponding tetrahedral meshes. All the input and generated data files are publicly available on Zenodo (10.5281/zenodo.7105941). <strong>Data Sources</strong> Cellular and subcellular NGV meshes segmented from the volume shown in Figure 2 are provided by the collaborating co-authors affiliated with KAUST. Neuronal meshes shown in Figure 3, Supplementary Figures S55 - S75 and Supplementary Figures S85 are publicly available from the MICrONS program. Neuronal morphologies shown in Figure 4, Supplementary Figures S80 - S81 and Supplementary Figure S86 are publicly available from NeuroMorpho.Org. Astrocytic morphologies (Figure 5 and Supplementary Figure S82) are provided by Eleftherios Zisis. Vascular morphologies (rat’s cerebral microvasculature) shown in Figure 6 and Supplementary Figures S83 - S84 are courtesy of Bruno Weber, University of Zürich (UZH). The vascular morphology of the arterial arborizations shown in Supplementary Figure S88 is available from the Brain Vasculature (BraVa) database (cng.gmu.edu/brava).<strong>补充数据</strong> <strong>补充数据1</strong> 包含了在洛桑联邦理工学院（EPFL）-阿卜杜拉国王科技大学（KAUST）合作框架下重建的区块（见图2a）的输入非水密（non-watertight）表面网格，以及由Ultraliser生成的对应输出水密（watertight）网格。<strong>补充数据2</strong> 包含从<strong>补充图S54</strong>所示区块中随机选取的20个非水密网格，以及与其对应的另一组水密网格副本。<strong>补充数据3</strong> 包含25种具有不同形态类型的神经元形态数据，以及与其对应的水密网格。<strong>补充数据4</strong> 包含25个合成的星形胶质细胞形态数据15，以及与其对应的水密网格。<strong>补充数据5</strong> 包含血管形态数据（见<strong>补充图S83</strong>），以及对应的多分区水密网格。<strong>补充数据6</strong> 包含用于<strong>补充章节13</strong>所示对比分析的数据集。<br><br>神经元、星形胶质细胞与血管形态数据分别以SWC、H5及VMV文件格式存储。SWC与VMV格式的文件结构可在线公开获取。完整星形胶质细胞的H5文件可根据需求向通讯作者申请获取。所有表面网格均以Wavefront OBJ文件格式存储。额外生成的STL网格用于TetGen生成对应的四面体网格。所有输入及生成的数据文件均可在Zenodo平台（10.5281/zenodo.7105941）公开获取。<strong>数据来源</strong> 从图2所示体积中分割得到的细胞及亚细胞NGV网格由隶属于阿卜杜拉国王科技大学的合作共同作者提供。图3、补充图S55至S75以及补充图S85所示的神经元网格可从MICrONS项目公开获取。图4、补充图S80至S81以及补充图S86所示的神经元形态数据可从NeuroMorpho.Org公开获取。星形胶质细胞形态数据（图5及补充图S82）由Eleftherios Zisis提供。图6及补充图S83至S84所示的血管形态数据（大鼠脑微血管系统）由苏黎世大学（UZH）的Bruno Weber提供。补充图S88所示的动脉分支血管形态数据可从脑血管（BraVa）数据库（cng.gmu.edu/brava）获取。