An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution

Information Fusion of Image Analysis, Video Object Tracking, and Data Mining of Biological Images using the Open Source MATLAB Toolbox Gait-CAD

(2014) J. Stegmaier et al.   Biomedical Engineering-Biomedizinische Technik

Mapping brain activity at scale with cluster computing

(2014) Jeremy Freeman et al.   NATURE METHODS

High-resolution reconstruction of the beating zebrafish heart

(2014) Michaela Mickoleit et al.   NATURE METHODS

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

(2014) Fernando Amat et al.   NATURE METHODS

Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks

(2014) Johannes Stegmaier et al.   PLoS One

Towards comprehensive cell lineage reconstructions in complex organisms using light-sheet microscopy

(2013) Fernando Amat et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

A systematic genome-wide analysis of zebrafish protein-coding gene function

(2013) Ross N. W. Kettleborough et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Whole-brain functional imaging at cellular resolution using light-sheet microscopy

(2013) Misha B Ahrens et al.   NATURE METHODS

Live Imaging of Whole Mouse Embryos during Gastrulation: Migration Analyses of Epiblast and Mesodermal Cells

(2013) Takehiko Ichikawa et al.   PLoS One

Imaging Morphogenesis: Technological Advances and Biological Insights

(2013) P. J. Keller   SCIENCE

The CRISPR System—Keeping Zebrafish Gene Targeting Fresh

(2013) Patrick R. Blackburn et al.   Zebrafish

High-throughput hyperdimensional vertebrate phenotyping

(2013) Carlos Pardo-Martin et al.   Nature Communications

High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics

(2013) Benjamin Schmid et al.   Nature Communications

Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope

(2012) A. Kaufmann et al.   DEVELOPMENT

Multiview light-sheet microscope for rapid in toto imaging

(2012) Uros Krzic et al.   NATURE METHODS

Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy

(2012) Raju Tomer et al.   NATURE METHODS

Gastrulation: Making and Shaping Germ Layers

(2011) Lila Solnica-Krezel et al.   Annual Review of Cell and Developmental Biology

Reconstructing embryonic development

(2010) Khaled Khairy et al.   GENESIS

Zebrafish epiboly: mechanics and mechanisms

(2010) Stephanie E. Lepage et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Metadata matters: access to image data in the real world

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

Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy

(2010) Philipp J Keller et al.   NATURE METHODS

Visualizing enveloping layer glycans during zebrafish early embryogenesis

(2010) J. M. Baskin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE