NETMORPH: A Framework for the Stochastic Generation of Large Scale Neuronal Networks With Realistic Neuron Morphologies

No abstract is available for this paper.

• Publication year

  2009

• Venue

  Neuroinformatics

• Publication date

  2009-08-12

• Fields of study

  Medicine, Computer Science

• Identifiers
  DOI 10.1007/s12021-009-9052-3PMID 19672726
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• CX3D: a java package for simulation of cortical development in 3D

  2008cited by this paper
• Synaptic alterations in CA1 in mild Alzheimer disease and mild cognitive impairment

  2007cited by this paper
• Morphological, electrophysiological, and synaptic properties of corticocallosal pyramidal cells in the neonatal rat neocortex.

  2007cited by this paper
• Modeling biology : structures, behaviors, evolution

  2007cited by this paper
• neuroConstruct: A Tool for Modeling Networks of Neurons in 3D Space

  2007cited by this paper
• Development of multi-cluster cortical networks by time windows for spatial growth

  2007cited by this paper
• Spatial embedding of neuronal trees modeled by diffusive growth.

  2006cited by this paper
• Fragile X syndrome and autism at the intersection of genetic and neural networks

  2006cited by this paper
• Morphology, electrophysiology and functional input connectivity of pyramidal neurons characterizes a genuine layer va in the primary somatosensory cortex.

  2006cited by this paper
• NeuGen: A tool for the generation of realistic morphology of cortical neurons and neural networks in 3D

  2006cited by this paper
• A theoretical network model to analyse neurogenesis and synaptogenesis in the dentate gyrus

  2006cited by this paper
• Laminar and Columnar Organization of Ascending Excitatory Projections to Layer 2/3 Pyramidal Neurons in Rat Barrel Cortex

  2005cited by this paper
• Natural Variability in the Geometry of Dendritic Branching Patterns

  2005cited by this paper
• Modeling in the neurosciences : from biological systems to neuromimetic robotics

  2005cited by this paper
• Neurogeometry and potential synaptic connectivity.

  2005cited by this paper
• Biologically plausible models of neurite outgrowth.

  2005cited by this paper
• MinireviewCalcium Signaling and the Control of Dendritic Development

  2005cited by this paper
• Class-Specific Features of Neuronal Wiring distal dendrite ) of PCs ( Freund and Buzsaki

  2004cited by this paper
• Class-specific features of neuronal wiring.

  2004cited by this paper
• Neuronal circuits of the neocortex.

  2004cited by this paper
• Organization, development and function of complex brain networks.

  2004cited by this paper
• Growth Cone Pathfinding: a competition between deterministic and stochastic events

  2004cited by this paper
• Transport limited effects in a model of dendritic branching.

  2004cited by this paper
• Introduction to Cytoskeletal Dynamics and Pathfinding of Neuronal Growth Cones1

  2003cited by this paper
• The control of dendrite development.

  2003cited by this paper
• Modeling neural development

  2003cited by this paper
• Formation of dendritic branching patterns

  2003cited by this paper
• Growth Functions in Dendritic Outgrowth

  2003influential reference
• Branching rates and growth functions in the outgrowth of dendritic branching patterns

  2002cited by this paper
• Measures for quantifying dendritic arborizations

  2002cited by this paper
• Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex.

  2002influential reference
• A shape analysis framework for neuromorphometry

  2002cited by this paper
• Competition for tubulin between growing neurites during development

  2001cited by this paper
• Computer generation and quantitative morphometric analysis of virtual neurons

  2001cited by this paper
• A computational model of dendrite elongation and branching based on MAP2 phosphorylation.

  2001cited by this paper
• Generation, description and storage of dendritic morphology data.

  2001cited by this paper
• The need for integrating neuronal morphology databases and computational environments in exploring neuronal structure and function

  2001cited by this paper
• Biophysical model of axonal pathfinding

  2001cited by this paper
• Modeling dendritic morphological complexity of deep layer cat superior colliculus neurons

  2001cited by this paper
• Modeling Dendritic Geometry and the Development of Nerve Connections

  2000cited by this paper
• L-neuron: A modeling tool for the efficient generation and parsimonious description of dendritic morphology

  2000cited by this paper
• Phosphorylation of microtubule-associated protein 2 (MAP2) and its relevance for the regulation of the neuronal cytoskeleton function.

  2000cited by this paper
• Phenotypic Knockout of Nerve Growth Factor in Adult Transgenic Mice Reveals Severe Deficits in Basal Forebrain Cholinergic Neurons, Cell Death in the Spleen, and Skeletal Muscle Dystrophy

  2000cited by this paper
• Identification of an Invariant Response: Stable Contact with Schwann Cells Induces Veil Extension in Sensory Growth Cones

  2000cited by this paper
• A quantitative analysis of the local connectivity between pyramidal neurons in layers 2/3 of the rat visual cortex

  2000cited by this paper
• Filopodial Adhesion Does Not Predict Growth Cone Steering Events In Vivo

  1999cited by this paper
• Modeling the natural variability in the shape of dendritic trees: Application to basal dendrites of small rat cortical layer 5 pyramidal neurons

  1999cited by this paper
• Models of axon guidance and bundling during development

  1999cited by this paper
• Reconstruction of Brain Networks by Algorithmic Amplification of Morphometry Data

  1999cited by this paper
• Depolarization stimulates lamellipodia formation and axonal but not dendritic branching in cultured rat cerebral cortex neurons.

  1998cited by this paper
• Cortex: Statistics and Geometry of Neuronal Connectivity

  1998cited by this paper
• Mathematical guidance for axons.

  1998cited by this paper
• Axonal outgrowth of cultured neurons is not limited by growth cone competition.

  1998cited by this paper
• Generic modeling of chemotactic based self-wiring of neural networks

  1998cited by this paper
• Natural variability in the number of dendritic segments: Model‐based inferences about branching during neurite outgrowth

  1997cited by this paper
• The NEURON Simulation Environment

  1997cited by this paper
• Complex periodic behaviour in a neural network model with activity-dependent neurite outgrowth.

  1996cited by this paper
• Neural cell adhesion molecules in activity-dependent development and synaptic plasticity.

  1996cited by this paper
• Network connectivity changes through activity-dependent neurite outgrowth

  1996cited by this paper
• Comparison of the topology and growth rules of motoneuronal dendrites

  1995cited by this paper
• Implications of activity dependent neurite outgrowth for neuronal morphology and network development.

  1995cited by this paper
• Geometrical and topological characteristics in the dendritic development of cortical pyramidal and non-pyramidal neurons.

  1994cited by this paper
• Activity-dependent outgrowth of neurons and overshoot phenomena in developing neural networks

  1994cited by this paper
• The Neuron Simulation Program

  1994cited by this paper
• Microtubule-associated protein 2 alters the dynamic properties of microtubule assembly and disassembly.

  1993cited by this paper
• Terminal and intermediate segment lengths in neuronal trees with finite length.

  1993cited by this paper
• Tree asymmetry--a sensitive and practical measure for binary topological trees.

  1992cited by this paper
• Competitive interactions during dendritic growth: a simple stochastic growth algorithm.

  1992cited by this paper
• Dendritic morphology of pyramidal neurones of the visual cortex of the rat. IV: Electrical geometry

  1992cited by this paper
• Dendritic morphology of pyramidal neurones of the visual cortex of the rat: I. Branching patterns

  1991cited by this paper
• The Nerve Growth Cone

  1991cited by this paper
• Neuronal growth cone as an integrator of complex environmental information.

  1990cited by this paper
• Cold Spring Harbor Symposia on Quantitative Biology.: Vol. LII. Evolution of Catalytic Functions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1987, ISBN 0-87969-054-2, xix + 955 pp., US $150.00.

  1989cited by this paper
• Looking into growth cones.

  1989cited by this paper
• Intrinsic determinants of neuronal form and function: edited by R. J. Lasek and M. M. Black, Alan R. Liss, 1988. US$120.00 (xvii + 591 pages) ISBN 0 8451 2739 X

  1989cited by this paper
• Quantitative morphological analysis of deep superior colliculus neurons stained intracellularly with HRP in the cat.

  1986cited by this paper
• Neuronal growth cones.

  1983cited by this paper
• Thalamic input to the cerebral cortex

  1979cited by this paper
• Environmental influences on the neocortex in later life.

  1978cited by this paper
• Three-dimensional branching structure of pyramidal cell dendrites.

  1975cited by this paper
• Emerging synaptic connectivity in simulated networks of outgrowing neurons with realistic morphologies using NETMORPH

  1970cited by this paper
• [MATURATION OF THE NERVOUS SYSTEM].

  1964cited by this paper
• Branching dendritic trees and motoneuron membrane resistivity.

  1959cited by this paper
• Complex Periodic Behaviour in a Neural Network Model with Activity-Dependent Neurite Outgrowth

  year unknowncited by this paper

• Synthetic Data Generation for Classifying Electrophysiological and Morpho-Electrophysiological Neurons from Mouse Visual Cortex

  2025cites this paper
• Neurons exploit stochastic growth to rapidly and economically build dense dendritic arbors

  2025cites this paper
• Role of connectivity anisotropies in the dynamics of cultured neuronal networks

  2025cites this paper
• Neurons exploit stochastic growth to rapidly and economically build dense radially oriented dendritic arbors

  2025cites this paper
• Astrocyte morphology: complex or trivial?

  2025cites this paper
• DendroTweaks, an interactive approach for unraveling dendritic dynamics

  2025cites this paper
• MorphGrower: A Synchronized Layer-by-layer Growing Approach for Plausible Neuronal Morphology Generation

  2024cites this paper
• DendroTweaks: An interactive approach for unraveling dendritic dynamics

  2024cites this paper
• Dendritic growth and synaptic organization from activity-independent cues and local activity-dependent plasticity

  2024cites this paper
• Generating brain-wide connectome using synthetic axonal morphologies

  2024cites this paper
• Neurodevelopmental disorders modeling using isogeometric analysis, dynamic domain expansion and local refinement

  2024cites this paper
• Computational Generation of Long-range Axonal Morphologies

  2024cites this paper
• Biomimetic IGA neuron growth modeling with neurite morphometric features and CNN-based prediction

  2023cites this paper
• Deep learning-based neuron segmentation in quantitative phase images trained on procedurally generated data

  2023cites this paper
• High-Performance and Scalable Agent-Based Simulation with BioDynaMo

  2023cites this paper
• Scaling Properties of a Random Yule Tree Embedded in R^D

  2023cites this paper
• Neurorosettes: a novel computational modelling framework to investigate the Homer-Wright rosette formation in neuroblastoma

  2023cites this paper
• Tissues as networks of cells: towards generative rules of complex organ development

  2023cites this paper
• Models of Purkinje cell dendritic tree selection during early cerebellar development

  2023cites this paper
• Comparing the segmentation of quantitative phase images of neurons using convolutional neural networks trained on simulated and augmented imagery

  2023cites this paper
• A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites

  2023cites this paper
• Brain-wide dendrites in a near-optimal performance of dynamic range and information transmission

  2023cites this paper
• Controlling morpho-electrophysiological variability of neurons with detailed biophysical models

  2023cites this paper
• Segmenting quantitative phase images of neurons using a deep learning model trained on images generated from a neuronal growth model

  2022cites this paper
• The branching code: A model of actin-driven dendrite arborization.

  2022cites this paper
• Efficient simulation of neural development using shared memory parallelization

  2022cites this paper
• Computational Models of Typical and Atypical Brain Network Development.

  2022cites this paper
• Active Dendrites and LFPs: Biophysical Mechanisms and Computational Explorations

  2021cites this paper
• Prediction of Neural Diameter From Morphology to Enable Accurate Simulation

  2021cites this paper
• Efficient metadata mining of web-accessible neural morphologies.

  2021cites this paper
• Architecture of the Neuro-Glia-Vascular System

  2021cites this paper
• Active Dendrites and Local Field Potentials: Biophysical Mechanisms and Computational Explorations

  2021cites this paper
• Generation of Granule Cell Dendritic Morphologies by Estimating the Spatial Heterogeneity of Dendritic Branching

  2020cites this paper
• Achieving functional neuronal dendrite structure through sequential stochastic growth and retraction

  2020cites this paper
• Biological network growth in complex environments: A computational framework

  2020cites this paper
• The microcircuits of striatum in silico

  2020cites this paper
• Computational synthesis of cortical dendritic morphologies

  2020influential citation
• A developmental stretch-and-fill process that optimises dendritic wiring

  2020cites this paper
• Creative Destruction: A Basic Computational Model of Cortical Layer Formation

  2020cites this paper
• Reproducibility and Rigour in Computational Neuroscience

  2020influential citation
• BioDynaMo: a modular platform for high-performance agent-based simulation

  2020influential citation
• Local CPG Self Growing Network Model with Multiple Physical Properties

  2020cites this paper
• From trees to barcodes and back again: theoretical and statistical perspectives

  2020cites this paper
• The branching code: a model of actin-driven dendrite arborisation

  2020cites this paper
• Networks of random trees as a model of neuronal connectivity

  2019cites this paper
• Image-derived Models of Cell Organization Changes During Differentiation of PC12 Cells

  2019cites this paper
• Image-derived models of cell organization changes during differentiation and drug treatments

  2019cites this paper
• Generating High Fidelity Surface Meshes of Neocortical Neurons using Skin Modifiers

  2019cites this paper
• Dissecting Sholl Analysis into Its Functional Components.

  2019cites this paper
• Reconstructive Quantitation of Neuron Morphology: Potential Insights into Development, Synaptic Organization, and Disease

  2019cites this paper
• Decay of connection probabilities with distance in 2D and 3D neuronal networks

  2019cites this paper
• Stochastic Modeling of Radiation-induced Dendritic Damage on in silico Mouse Hippocampal Neurons

  2018cites this paper
• Modelling and characterizing axon growth from in vivo data

  2018cites this paper
• Neuroinformatics and Computational Modelling as Complementary Tools for Neurotoxicology Studies

  2018cites this paper
• Theoretical Models of Neural Development

  2018influential citation
• Modelling brain-wide neuronal morphology via rooted Cayley trees

  2018cites this paper
• Morphological determinants of dendritic arborization neurons in Drosophila larva

  2018cites this paper
• An evolutionary developmental approach for generation of 3D neuronal morphologies using gene regulatory networks

  2018cites this paper
• Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures

  2018influential citation
• Neuronal morphologies: the shapes of thoughts

  2018cites this paper
• A neural network growing algorithm based on Brownian movement and gravity constraint

  2018cites this paper
• Sampling Neuron Morphologies

  2018cites this paper
• Design and implementation of multi-signal and time-varying neural reconstructions

  2018cites this paper
• Research on algorithms of neural network based on self-growing of neuron

  2017cites this paper
• T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells

  2017cites this paper
• Mechanisms of Connectome Development.

  2017cites this paper
• Organisational Principles of Connectomes: Changes During Evolution and Development

  2017cites this paper
• Entwicklung axonaler Dioden zur Untersuchung des gerichteten Informationsflusses in neuronalen Strukturen

  2017cites this paper
• Modular topology emerges from plasticity in a minimalistic excitable network model.

  2017cites this paper
• Impact of Structural Plasticity on Memory Capacity

  2017cites this paper
• Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

  2017cites this paper
• Structural Plasticity in Dendrites: Developmental Neurogenetics, Morphological Reconstructions, and Computational Modeling

  2017cites this paper
• Network Formation Through Activity-Dependent Neurite Outgrowth: A Review of a Simple Model of Homeostatic Structural Plasticity

  2017cites this paper
• Biomaterials and computation: a strategic alliance to investigate emergent responses of neural cells.

  2017cites this paper
• REMOD: A Tool for Analyzing and Remodeling the Dendritic Architecture of Neural Cells

  2016cites this paper
• An Algorithm for Motif-Based Network Design

  2016cites this paper
• Dendrite and Axon Specific Geometrical Transformation in Neurite Development

  2016cites this paper
• Estudo da relação estrutura-dinâmica em redes modulares

  2016cites this paper
• Micro-connectomics: Probing the organizational principles of neuronal networks at the cellular scale

  2016cites this paper
• Neuronal devices: understanding neuronal cultures through percolation helps prepare for the next step

  2016cites this paper
• Framework for efficient synthesis of spatially embedded morphologies.

  2016cites this paper
• Knowledge Representation and Data Mining of Neuronal Morphologies Using Neuroinformatics Tools and Formal Ontologies

  2016cites this paper
• Reconstructing the brain: from image stacks to neuron synthesis

  2016cites this paper
• Structure of a randomly grown 2-d network

  2015cites this paper
• Developmental time windows for axon growth influence neuronal network topology

  2015cites this paper
• Computational model of axon guidance

  2015cites this paper
• Tree Topology Estimation

  2015cites this paper
• Fuzzy-Logic Based Detection and Characterization of Junctions and Terminations in Fluorescence Microscopy Images of Neurons

  2015cites this paper
• BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies

  2015cites this paper
• The effects of neuron morphology on graph theoretic measures of network connectivity: the analysis of a two-level statistical model

  2015influential citation
• Quantitative Investigations of Axonal and Dendritic Arbors

  2015cites this paper
• Comparative Topological Analysis of Neuronal Arbors via Sequence Representation and Alignment

  2015cites this paper
• Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

  2014cites this paper
• Context-aware modeling of neuronal morphologies

  2014cites this paper
• Discrete stochastic model for the generation of axonal trees

  2014cites this paper
• A software tool for the analysis of neuronal morphology data

  2014cites this paper
• The Computing Dendrite

  2014cites this paper
• A study on the structure and dynamics of complex networks

  2014cites this paper
• A Morpho-Density Approach to Estimating Neural Connectivity

  2014influential citation
• Parametric Anatomical Modeling: a method for modeling the anatomical layout of neurons and their projections

  2014cites this paper