Supplementary Data Supplementary Data 1 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. Supplementary Data 2 contains a set of 20 non-watertight meshes that were randomly selected from the block shown in Supplementary Figure S54 and another set of the their watertight counterparts. Supplementary Data 3 contains a set of 25 neuronal morphologies with different morphological types and their corresponding watertight meshes. Supplementary Data 4 contains a set of 25 synthetic astroglial morphologies 15 and their corresponding watertight meshes. Supplementary Data 5 contains the vascular morphology (shown in Supplementary Fig. S83) and a corresponding multi-partitioned watertight mesh. Supplementary Data 6 contains the datasets used for the comparative analysis shown in Supplementary Section 13. 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). Data Sources 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).

This digital record contains all the datasets used and/or generated by Ultraliser that are cited in the paper: Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience