ArticleNeuroinformatics2014
VolRoverN: enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function.
Article in Neuroinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 2025Article
- Long-Term Potentiation Produces a Sustained Expansion of Synaptic Information Storage Capacity in Adult Rat Hippocampus.bioRxiv : the preprint server for biology · 2024Article
- Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome.The EMBO journal · 2023Article
- Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome.bioRxiv : the preprint server for biology · 2023Article
- CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations.Neuroinformatics · 2023Article
- Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.Briefings in bioinformatics · 2023Article
- Morphological principles of neuronal mitochondria.The Journal of comparative neurology · 2022Article
- Efficient metadata mining of web-accessible neural morphologies.Progress in biophysics and molecular biology · 2022Article
- Modeling Neurons in 3D at the Nanoscale.Advances in experimental medicine and biology · 2022Article
- Article
- 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries.PLoS computational biology · 2020Article
- Long-term potentiation expands information content of hippocampal dentate gyrus synapses.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Heterogeneous anisotropic magnetic susceptibility of the myelin-water layers causes local magnetic field perturbations in axons.NMR in biomedicine · 2017Article
- Article
- A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development.Scientific data · 2015Article
- Computational reconstitution of spine calcium transients from individual proteins.Frontiers in synaptic neuroscience · 2015Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Establishing meaningful relationships between cellular structure and function requires accurate morphological reconstructions. In particular, there is an unmet need for high quality surface reconstructions to model subcellular and synaptic interactions among neurons and glia at nanometer resolution. We address this need with VolRoverN, a software package that produces accurate, efficient, and automated 3D surface reconstructions from stacked 2D contour tracings. While many techniques and tools have been developed in the past for 3D visualization of cellular structure, the reconstructions from VolRoverN meet specific quality criteria that are important for dynamical simulations. These criteria include manifoldness, water-tightness, lack of self- and object-object-intersections, and geometric accuracy. These enhanced surface reconstructions are readily extensible to any cell type and are used here on spiny dendrites with complex morphology and axons from mature rat hippocampal area CA1. Both spatially realistic surface reconstructions and reduced skeletonizations are produced and formatted by VolRoverN for easy input into analysis software packages for neurophysiological simulations at multiple spatial and temporal scales ranging from ion electro-diffusion to electrical cable models.
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Registered trials
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