Ultraliser: 3D Neuronal, Astrocytic, and Vascular Morphology Meshes
by Marwan Abdellah / École Polytechnique Fédérale de Lausanne
Available on 1 platform
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Description
Supplementary Data 1 contains input and output surface meshes for a reconstructed tissue block from an EPFL-KAUST collaboration. The collection includes 25 neuronal morphologies, 25 synthetic astroglial morphologies, and a vascular morphology, all with corresponding watertight meshes generated by the Ultraliser framework. Neuronal, astrocytic, and vascular data are stored in SWC, H5, and VMV file formats respectively, with surface meshes provided as Wavefront OBJ and STL files.
Use Cases
Benchmarking watertight mesh generation algorithms based on the provided non-watertight and watertight mesh pairs.
Simulating electrophysiological activity in neurons using the 25 SWC-format neuronal morphologies.
Creating tetrahedral meshes for finite element analysis using the provided STL surface meshes with TetGen.
Developing multiscale brain tissue models by integrating the neuronal, astrocytic, and vascular morphology datasets.
Validating computational geometry tools for neuroscience using the set of 20 randomly selected non-watertight meshes and their counterparts.
Strengths
Includes paired non-watertight and watertight meshes for direct algorithm comparison, as described in Supplementary Data 1 and 2.
Provides morphologies for multiple, specific cell types: 25 neuronal, 25 astroglial, and 1 vascular.
Data originates from a collaboration between EPFL and KAUST, suggesting a research-grade source.
Files are publicly available on Zenodo with a DOI (10.5281/zenodo.7105941), ensuring persistent access.
Limitations
Critical metadata is missing from all platform entries, including row/record counts, total file size, and last update date.
The H5 files for complete astrocyte cells are noted as available only upon request, creating an access barrier for part of the dataset.
The dataset's structure and the exact content of 'Supplementary Data 6' for comparative analysis are not detailed.
Provenance
Source
Collaborating co-authors affiliated with KAUST provided cellular and subcellular meshes segmented from a volume. Neuronal meshes are from publicly available sources.
Collection Method
Meshes were reconstructed within the context of the EPFL-KAUST collaboration and processed by the Ultraliser framework.
The H5 files containing complete astrocyte cell morphologies are not directly publicly available and require a request to the corresponding authors.