A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage

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

(2014) Fernando Amat et al.   NATURE METHODS

OpenMOLE, a workflow engine specifically tailored for the distributed exploration of simulation models

(2013) Romain Reuillon et al.   Future Generation Computer Systems-The International Journal of eScience

Fast and robust optical flow for time-lapse microscopy using super-voxels

(2012) Fernando Amat et al.   BIOINFORMATICS

Biological imaging software tools

(2012) Kevin W Eliceiri et al.   NATURE METHODS

Segmentation of 3D cell membrane images by PDE methods and its applications

(2011) K. Mikula et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Image analysis for understanding embryo development: a bridge from microscopy to biological insights

(2011) MA Luengo-Oroz et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tracing Cells for Tracking Cell Lineage and Clonal Behavior

(2011) Margaret E. Buckingham et al.   DEVELOPMENTAL CELL

Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination

(2011) Thomas A Planchon et al.   NATURE METHODS

Microscopy in 3D: a biologist's toolbox

(2011) Robert S. Fischer et al.   TRENDS IN CELL BIOLOGY

Reconstructing embryonic development

(2010) Khaled Khairy et al.   GENESIS

3D early embryogenesis image filtering by nonlinear partial differential equations

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

Automated sorting of live C. elegans using laFACS

(2010) Anita G Fernandez et al.   NATURE METHODS

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

(2010) Dmitriy M. Chudakov et al.   PHYSIOLOGICAL REVIEWS

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

(2010) N. Olivier et al.   SCIENCE

Unfolding a chordate developmental program, one cell at a time: Invariant cell lineages, short-range inductions and evolutionary plasticity in ascidians

(2009) Patrick Lemaire   DEVELOPMENTAL BIOLOGY

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

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

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

Tracking in cell and developmental biology

(2009) Erik Meijering et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE