Neuroinformatics

, Volume 15, Issue 3, pp 247–269 | Cite as

Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph

  • Konstantin Mörschel
  • Markus Breit
  • Gillian Queisser
Original Article
  • 283 Downloads

Abstract

Generating realistic and complex computational domains for numerical simulations is often a challenging task. In neuroscientific research, more and more one-dimensional morphology data is becoming publicly available through databases. This data, however, only contains point and diameter information not suitable for detailed three-dimensional simulations. In this paper, we present a novel framework, AnaMorph, that automatically generates water-tight surface meshes from one-dimensional point-diameter files. These surface triangulations can be used to simulate the electrical and biochemical behavior of the underlying cell. In addition to morphology generation, AnaMorph also performs quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions. This toolset allows an extension from the classical dimension-reduced modeling and simulation of cellular processes to a full three-dimensional and morphology-including method, leading to novel structure-function interplay studies in the medical field. The developed numerical methods can further be employed in other areas where complex geometries are an essential component of numerical simulations.

Keywords

AnaMorph 3D simulation NeuroMorpho.Org Neuron reconstruction Geometric modeling 

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Goethe Center for Scientific ComputingGoethe University FrankfurtFrankfurt am MainGermany
  2. 2.Department of MathematicsTemple UniversityPhiladelphiaUSA

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