VolRoverN: Enhancing Surface and Volumetric Reconstruction for Realistic Dynamical Simulation of Cellular and Subcellular Function

Automated Transmission-Mode Scanning Electron Microscopy (tSEM) for Large Volume Analysis at Nanoscale Resolution

(2013) Masaaki Kuwajima et al.   PLoS One

Macromolecular structure modeling from 3D EM using VolRover 2.0

(2012) Qin Zhang et al.   BIOPOLYMERS

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

(2012) Iain Hepburn et al.   BMC Systems Biology

Computational methods and challenges for large-scale circuit mapping

(2012) Moritz Helmstaedter et al.   CURRENT OPINION IN NEUROBIOLOGY

Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil

(2012) Justin P. Kinney et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Elastic volume reconstruction from series of ultra-thin microscopy sections

(2012) Stephan Saalfeld et al.   NATURE METHODS

Beyond counts and shapes: Studying pathology of dendritic spines in the context of the surrounding neuropil through serial section electron microscopy

(2012) M. Kuwajima et al.   NEUROSCIENCE

TrakEM2 Software for Neural Circuit Reconstruction

(2012) Albert Cardona et al.   PLoS One

Topologically correct reconstruction of tortuous contour forests

(2011) John Edwards et al.   COMPUTER-AIDED DESIGN

Volume electron microscopy for neuronal circuit reconstruction

(2011) Kevin L Briggman et al.   CURRENT OPINION IN NEUROBIOLOGY

Dendritic changes in visual pathways in glaucoma and other neurodegenerative conditions

(2011) Meng Liu et al.   EXPERIMENTAL EYE RESEARCH

Large-Scale Automated Histology in the Pursuit of Connectomes

(2011) D. Kleinfeld et al.   JOURNAL OF NEUROSCIENCE

Network anatomy and in vivo physiology of visual cortical neurons

(2011) Davi D. Bock et al.   NATURE

Wiring specificity in the direction-selectivity circuit of the retina

(2011) Kevin L. Briggman et al.   NATURE

High-accuracy neurite reconstruction for high-throughput neuroanatomy

(2011) Moritz Helmstaedter et al.   NATURE NEUROSCIENCE

The endoplasmic reticulum and protein trafficking in dendrites and axons

(2011) Omar A. Ramírez et al.   TRENDS IN CELL BIOLOGY

A high-level 3D visualization API for Java and ImageJ

(2010) Benjamin Schmid et al.   BMC BIOINFORMATICS

Synapse Pathology in Psychiatric and Neurologic Disease

(2010) Myrrhe van Spronsen et al.   Current Neurology and Neuroscience Reports

Semi-automated reconstruction of neural circuits using electron microscopy

(2010) Dmitri B Chklovskii et al.   CURRENT OPINION IN NEUROBIOLOGY

Ssecrett and NeuroTrace: Interactive Visualization and Analysis Tools for Large-Scale Neuroscience Data Sets

(2010) Won-Ki Jeong et al.   IEEE COMPUTER GRAPHICS AND APPLICATIONS

Ultrastructural Analysis of Hippocampal Neuropil from the Connectomics Perspective

(2010) Yuriy Mishchenko et al.   NEURON

An automatic 3D mesh generation method for domains with multiple materials

(2009) Yongjie Zhang et al.   COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING

Semi-Automated Reconstruction of Neural Processes from Large Numbers of Fluorescence Images

(2009) Ju Lu et al.   PLoS One

Serial Section Scanning Electron Microscopy of Adult Brain Tissue Using Focused Ion Beam Milling

(2008) G. Knott et al.   JOURNAL OF NEUROSCIENCE

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Surface smoothing and quality improvement of quadrilateral/hexahedral meshes with geometric flow

(2007) Yongjie Zhang et al.   Communications in numerical methods in engineering