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

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

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

Network anatomy and in vivo physiology of visual cortical neurons

(2011) Davi D. Bock et al.   NATURE

BrainAligner: 3D registration atlases of Drosophila brains

(2011) Hanchuan Peng et al.   NATURE METHODS

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

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

Systems survey of endocytosis by multiparametric image analysis

(2010) Claudio Collinet et al.   NATURE

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Software for bead-based registration of selective plane illumination microscopy data

(2010) Stephan Preibisch et al.   NATURE METHODS

Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution

(2010) Romain Fernandez et al.   NATURE METHODS

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

(2010) Albert Cardona et al.   PLOS BIOLOGY

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

A 3D digital atlas of C. elegans and its application to single-cell analyses

(2009) Fuhui Long et al.   NATURE METHODS

Open source bioimage informatics for cell biology

(2009) Jason R. Swedlow et al.   TRENDS IN CELL BIOLOGY

A Computational Framework for Ultrastructural Mapping of Neural Circuitry

(2009) James R Anderson et al.   PLOS BIOLOGY

Bioimage informatics: a new area of engineering biology

(2008) Hanchuan Peng   BIOINFORMATICS

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

(2008) Charless C. Fowlkes et al.   CELL

Automated analysis of embryonic gene expression with cellular resolution in C. elegans

(2008) John Isaac Murray et al.   NATURE METHODS

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE