TrakEM2 Software for Neural Circuit Reconstruction

Elastic volume reconstruction from series of ultra-thin microscopy sections

(2012) Stephan Saalfeld et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

(2011) M. H. Longair et al.   BIOINFORMATICS

The convergence of Notch and MAPK signaling specifies the blood progenitor fate in the Drosophila mesoderm

(2011) Melina Grigorian et al.   DEVELOPMENTAL BIOLOGY

How Thalamus Connects to Spiny Stellate Cells in the Cat's Visual Cortex

(2011) N. M. da Costa 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

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

(2010) S. Saalfeld et al.   BIOINFORMATICS

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

(2010) Benjamin Schmid et al.   BMC BIOINFORMATICS

Semi-automated reconstruction of neural circuits using electron microscopy

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

Machines that learn to segment images: a crucial technology for connectomics

(2010) Viren Jain et al.   CURRENT OPINION IN NEUROBIOLOGY

Metadata matters: access to image data in the real world

(2010) Melissa Linkert et al.   JOURNAL OF CELL BIOLOGY

Identifying Neuronal Lineages of Drosophila by Sequence Analysis of Axon Tracts

(2010) A. Cardona et al.   JOURNAL OF NEUROSCIENCE

Fully automatic stitching and distortion correction of transmission electron microscope images

(2010) Verena Kaynig et al.   JOURNAL OF STRUCTURAL BIOLOGY

An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy

(2010) Albert Cardona et al.   PLOS BIOLOGY

NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail

(2010) Padraig Gleeson et al.   PLoS Computational Biology

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

3D structural imaging of the brain with photons and electrons

(2009) Moritz Helmstaedter et al.   CURRENT OPINION IN NEUROBIOLOGY

A Computational Framework for Ultrastructural Mapping of Neural Circuitry

(2009) James R Anderson et al.   PLOS BIOLOGY

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

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