WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration

A semi-local neighborhood-based framework for probabilistic cell lineage tracing

(2014) Anthony Santella et al.   BMC BIOINFORMATICS

De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis

(2014) Zhuo Du et al.   CELL

Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience

(2014) E. S. Heckscher et al.   DEVELOPMENT

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

(2014) Fernando Amat et al.   NATURE METHODS

Dual-view plane illumination microscopy for rapid and spatially isotropic imaging

(2014) Abhishek Kumar et al.   Nature Protocols

OpenWorm: an open-science approach to modeling Caenorhabditis elegans

(2014) Balázs Szigeti et al.   Frontiers in Computational Neuroscience

Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis

(2013) J. L. Moore et al.   DEVELOPMENT

Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy

(2013) Yicong Wu et al.   NATURE BIOTECHNOLOGY

Endrov: an integrated platform for image analysis

(2013) Johan Henriksson et al.   NATURE METHODS

WormBase 2014: new views of curated biology

(2013) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

A High-Fidelity Cell Lineage Tracing Method for Obtaining Systematic Spatiotemporal Gene Expression Patterns in Caenorhabditis elegans

(2013) Daniel L Mace et al.   G3-Genes Genomes Genetics

Actomyosin-based Self-organization of cell internalization during C. elegans gastrulation

(2012) Christian Pohl et al.   BMC BIOLOGY

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos

(2012) C. A. Giurumescu et al.   DEVELOPMENT

Multidimensional regulation of gene expression in the C. elegans embryo

(2012) J. I. Murray et al.   GENOME RESEARCH

Triggering a Cell Shape Change by Exploiting Preexisting Actomyosin Contractions

(2012) Minna Roh-Johnson et al.   SCIENCE

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

(2012) Kishore R. Mosaliganti et al.   PLoS Computational Biology

BrainAligner: 3D registration atlases of Drosophila brains

(2011) Hanchuan Peng et al.   NATURE METHODS

Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans

(2011) Y. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

CATMAID: collaborative annotation toolkit for massive amounts of image data

(2009) S. Saalfeld et al.   BIOINFORMATICS

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

(2009) Fuhui Long et al.   NATURE METHODS

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE