Reconstructing embryonic development

Profiling by Image Registration Reveals Common Origin of Annelid Mushroom Bodies and Vertebrate Pallium

(2010) Raju Tomer et al.   CELL

Cell morphodynamics visualization from images of zebrafish embryogenesis

(2010) Matteo Campana et al.   COMPUTERIZED MEDICAL IMAGING AND GRAPHICS

Cellular dynamics in the early mouse embryo: from axis formation to gastrulation

(2010) Sonja Nowotschin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Evolving generalized Voronoi diagrams for accurate cellular image segmentation

(2010) Weimiao Yu et al.   CYTOMETRY PART A

Lighting up developmental mechanisms: how fluorescence imaging heralded a new era

(2010) M. Mavrakis et al.   DEVELOPMENT

Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection

(2010) Jerome Mertz et al.   JOURNAL OF BIOMEDICAL OPTICS

3D early embryogenesis image filtering by nonlinear partial differential equations

(2010) Z. Krivá et al.   MEDICAL IMAGE ANALYSIS

Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape

(2010) Erwin Frise et al.   Molecular Systems Biology

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

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Visualization of image data from cells to organisms

(2010) Thomas Walter et al.   NATURE METHODS

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

(2010) Stephan Preibisch et al.   NATURE METHODS

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging

(2010) Michael Held et al.   NATURE METHODS

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

(2010) Romain Fernandez et al.   NATURE METHODS

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

(2010) Philipp J Keller et al.   NATURE METHODS

A simple scanless two-photon fluorescence microscope using selective plane illumination

(2010) Jonathan Palero et al.   OPTICS EXPRESS

Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy

(2010) N. Olivier et al.   SCIENCE

Photomodulatable fluorescent proteins for imaging cell dynamics and cell fate

(2010) Sonja Nowotschin et al.   Organogenesis

VANO: a volume-object image annotation system

(2009) Hanchuan Peng et al.   BIOINFORMATICS

Segmentation of Fluorescence Microscopy Images for Quantitative Analysis of Cell Nuclear Architecture

(2009) Richard A. Russell et al.   BIOPHYSICAL JOURNAL

Use of KikGR a photoconvertible green-to-red fluorescent protein for cell labeling and lineage analysis in ES cells and mouse embryos

(2009) Sonja Nowotschin et al.   BMC DEVELOPMENTAL BIOLOGY

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

(2009) Xiao Liu et al.   CELL

Pulsed Forces Timed by a Ratchet-like Mechanism Drive Directed Tissue Movement during Dorsal Closure

(2009) Jerome Solon et al.   CELL

Methods toward in vivo measurement of zebrafish epithelial and deep cell proliferation

(2009) Matteo Campana et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Biology and Physics of Cell Shape Changes in Development

(2009) Ewa Paluch et al.   CURRENT BIOLOGY

Regulation of cell migration during chick gastrulation

(2009) Manli Chuai et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Quantitative in vivo imaging of entire embryos with Digital Scanned Laser Light Sheet Fluorescence Microscopy

(2009) Philipp J Keller et al.   CURRENT OPINION IN NEUROBIOLOGY

Selective plane illumination microscopy techniques in developmental biology

(2009) J. Huisken et al.   DEVELOPMENT

Fate map and morphogenesis of presumptive neural crest and dorsal neural tube

(2009) Akouavi M. Ezin et al.   DEVELOPMENTAL BIOLOGY

Nlcam modulates midline convergence during anterior neural plate morphogenesis

(2009) Katherine E. Brown et al.   DEVELOPMENTAL BIOLOGY

Cells Segmentation From 3-D Confocal Images of Early Zebrafish Embryogenesis

(2009) C. Zanella et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Visual Exploration of Three-Dimensional Gene Expression Using Physical Views and Linked Abstract Views

(2009) G.H. Weber et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

An automatic system forin vitrocell migration studies

(2009) J. DEGERMAN et al.   JOURNAL OF MICROSCOPY

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

(2009) Fuhui Long et al.   NATURE METHODS

Quantitative imaging of collective cell migration during Drosophila gastrulation: multiphoton microscopy and computational analysis

(2009) Willy Supatto et al.   Nature Protocols

Quantitative approaches in developmental biology

(2009) Andrew C. Oates et al.   NATURE REVIEWS GENETICS

Artifacts resulting from imaging in scattering media: a theoretical prediction

(2009) Alexander Rohrbach   OPTICS LETTERS

Imaging cell signalling and movement in development

(2009) Manli Chuai et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Live-imaging fluorescent proteins in mouse embryos: multi-dimensional, multi-spectral perspectives

(2009) Sonja Nowotschin et al.   TRENDS IN BIOTECHNOLOGY

LIVE IMAGING OF EARLY DEVELOPMENTAL PROCESSES IN MAMMALIAN EMBRYOS WITH OPTICAL COHERENCE TOMOGRAPHY

(2009) KIRILL V. LARIN et al.   Journal of Innovative Optical Health Sciences

Three-Dimensional Microtubule Behavior in Xenopus Egg Extracts Reveals Four Dynamic States and State-Dependent Elastic Properties

(2008) Philipp J. Keller et al.   BIOPHYSICAL JOURNAL

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

(2008) Charless C. Fowlkes et al.   CELL

Shapes of Red Blood Cells: Comparison of 3D Confocal Images with the Bilayer-Couple Model

(2008) Khaled Khairy et al.   Cellular and Molecular Bioengineering

Quantitative neurite outgrowth measurement based on image segmentation with topological dependence

(2008) Weimiao Yu et al.   CYTOMETRY PART A

High-speed imaging of developing heart valves reveals interplay of morphogenesis and function

(2008) P. J. Scherz et al.   DEVELOPMENT

In vivo long-term continuous observation of gene expression in zebrafish embryo nerve systems by using harmonic generation microscopy and morphant technology

(2008) Cho-Shuen Hsieh et al.   JOURNAL OF BIOMEDICAL OPTICS

Segmentation of touching cell nuclei using gradient flow tracking

(2008) G. LI et al.   JOURNAL OF MICROSCOPY

Cell population tracking and lineage construction with spatiotemporal context

(2008) Kang Li et al.   MEDICAL IMAGE ANALYSIS

Spatio-temporal cell cycle phase analysis using level sets and fast marching methods

(2008) Dirk Padfield et al.   MEDICAL IMAGE ANALYSIS

Tensile forces govern germ-layer organization in zebrafish

(2008) M. Krieg et al.   NATURE CELL BIOLOGY

Robust single-particle tracking in live-cell time-lapse sequences

(2008) Khuloud Jaqaman et al.   NATURE METHODS

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

(2008) John Isaac Murray et al.   NATURE METHODS

An Automated Method for Cell Detection in Zebrafish

(2008) Tianming Liu et al.   NEUROINFORMATICS

Fast Three-Dimensional Fluorescence Imaging of Activity in Neural Populations by Objective-Coupled Planar Illumination Microscopy

(2008) Terrence F. Holekamp et al.   NEURON

Dynamics of anisotropic tissue growth

(2008) Thomas Bittig et al.   NEW JOURNAL OF PHYSICS

Miniaturization and defocus correction for objective-coupled planar illumination microscopy

(2008) Diwakar Turaga et al.   OPTICS LETTERS

Dynamic Analyses of Drosophila Gastrulation Provide Insights into Collective Cell Migration

(2008) A. McMahon et al.   SCIENCE

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE

Spherical harmonics-based parametric deconvolution of 3D surface images using bending energy minimization

(2007) Khaled Khairy et al.   MEDICAL IMAGE ANALYSIS