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

Basic local alignment search tool

1990 • 87,358 citations

Distinctive Image Features from Scale-Invariant Keypoints

2004 • 52,232 citations

The WEKA data mining software

2009 • 17,798 citations

Snakes: Active contour models

1988 • 17,015 citations

Image processing with ImageJ

2004 • 11,866 citations

CellProfiler: image analysis software for identifying and quantifying cell phenotypes.

2006 • 4,776 citations

Level set methods and fast marching methods : evolving interfaces in computational geometry, fluid mechanics, computer vision, and materials science

1999 • 3,680 citations

Robust wide-baseline stereo from maximally stable extremal regions

2004 • 3,598 citations

Globally optimal stitching of tiled 3D microscopic image acquisitions

2009 • 2,222 citations

Computer Control of Microscopes Using µManager

2010 • 1,700 citations

A Whole-Genome Assembly of Drosophila

2000 • 1,532 citations

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

2008 • 1,479 citations

KNIME: The Konstanz Information Miner

2008 • 1,172 citations

TrakEM2 Software for Neural Circuit Reconstruction

2012 • 984 citations

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

2011 • 960 citations

Network anatomy and in vivo physiology of visual cortical neurons

2011 • 910 citations

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

2010 • 844 citations

The chemical basis of morphogenesis

1990 • 766 citations

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

2010 • 722 citations

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

2010 • 510 citations

Systems survey of endocytosis by multiparametric image analysis

2010 • 451 citations

The chemical basis of morphogenesis

1990 • 397 citations

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

2010 • 376 citations

Automated cell lineage tracing in Caenorhabditis elegans

2006 • 366 citations

Bioimage informatics: a new area of engineering biology

2008 • 349 citations

Elastic volume reconstruction from series of ultra-thin microscopy sections

2012 • 307 citations

Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization

2006 • 303 citations

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

2010 • 298 citations

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

2008 • 273 citations

Imaging in Systems Biology

2007 • 252 citations

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

2008 • 200 citations

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

2009 • 186 citations

BrainAligner: 3D registration atlases of Drosophila brains

2011 • 154 citations

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

2010 • 143 citations

A Computational Framework for Ultrastructural Mapping of Neural Circuitry

2009 • 141 citations

Automated Image Analysis for High-Content Screening and Analysis

2010 • 134 citations

Fully automatic stitching and distortion correction of transmission electron microscope images

2010 • 74 citations

Identifying Neuronal Lineages ofDrosophilaby Sequence Analysis of Axon Tracts

2010 • 59 citations

Open source bioimage informatics for cell biology

2009 • 52 citations

ICY: A new open-source community image processing software

2011 • 47 citations

Geometrical Consistent 3D Tracing of Neuronal Processes in ssTEM Data

2010 • 33 citations