title: REMOD: A Tool for Analyzing and Remodeling the Dendritic Architecture of Neural Cells.
abstract: Dendritic morphology is a key determinant of how individual neurons acquire a unique signal processing profile. The highly branched dendritic structure that originates from the cell body, explores the surrounding 3D space in a fractal-like manner, until it reaches a certain amount of complexity. Its shape undergoes significant alterations under various physiological or neuropathological conditions. Yet, despite the profound effect that these alterations can have on neuronal function, the causal relationship between the two remains largely elusive. The lack of a systematic approach for remodeling neural cells and their dendritic trees is a key limitation that contributes to this problem. Such causal relationships can be inferred via the use of large-scale neuronal models whereby the anatomical plasticity of neurons is accounted for, in order to enhance their biological relevance and hence their predictive performance. To facilitate this effort, we developed a computational tool named REMOD that allows the structural remodeling of any type of virtual neuron. REMOD is written in Python and can be accessed through a dedicated web interface that guides the user through various options to manipulate selected neuronal morphologies. REMOD can also be used to extract meaningful morphology statistics for one or multiple reconstructions, including features such as sholl analysis, total dendritic length and area, path length to the soma, centrifugal branch order, diameter tapering and more. As such, the tool can be used both for the analysis and/or the remodeling of neuronal morphologies of any type.
authors.affiliation: Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH)Crete, Greece; Department of Molecular Biology and Genetics, Democritus University of ThraceCrete, Greece.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Bozelos
authors.affiliation: Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH)Crete, Greece; Department of Biology, University of CreteCrete, Greece.
authors.forename: Stefanos S
authors.initials: SS
authors.lastname: Stefanou
authors.affiliation: Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH)Crete, Greece; Computer Science Department, University of CreteCrete, Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Bouloukakis
authors.affiliation: Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH) Crete, Greece.
authors.forename: Constantinos
authors.initials: C
authors.lastname: Melachrinos
authors.affiliation: Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH) Crete, Greece.
authors.forename: Panayiota
authors.initials: P
authors.lastname: Poirazi
keywords: computational tool; dendrite; dendritic remodeling; neuron; statistical analysis