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, Acknowledgements We thank Patrick Parra and Jean-Yves Tiercelin for custom-made high-precision mechanics

, Amparo Ruiz Vera and Odile Lecquyer for the management of the Embryomics and BioEmergences EC projects

A. Colin, Valérie Lavallée and Simon Agostini for fish care

R. Tsien and R. Harland, DNA constructs (mCherry and eGFP-HRAS, respectively)

, Pascal Abbas for technical assistance; the N&D and ISC-PIF staff for administrative support

N. P. and P. B. , This work was supported by grants EC NEST 'Adventure' 012916, EC NEST 'Measuring the Impossible' 28892, ZF-Health EC project HEALTH-F4-2010-242048, ACI STIC santé, Dominique De Waleffe from DENALI SA for his contribution to the BioEmergences EC project's workflow interface

E. F. , coordinated the workflow development, the manuscript preparation and performed the software comparison

T. S. , developed the visualization interface Mov-IT and the BioEmergences web service

B. R. , developed the Gaussian-based nucleus centre detection method; C.M. developed the cell tracking method and contributed to the workflow development

O. , developed filtering and nucleus centre detection methods

D. F. , contributed to the specification of the Mov-IT functionalities and organization of the BioEmergences database; R.S. developed the embryo shape segmentation method and contributed to the workflow development

M. H. , contributed to the workflow development, in both its standalone and web service versions

R. C. , developed algorithm parallelization tools

G. R. , coordinated the specification of the Mov-IT functionalities and organization of the BioEmergences database

B. L. , worked on the reconstruction validation and standardization of error assessment

L. , conducted imaging experiments, data validation and correction

I. C. , S. D. , B. M. , and A. B. , conducted imaging experiments, data validation and correction; J.K. provided engineering support to the computation

P. ,

M. F. , conducted data validation and correction

G. L. , led the molecular biology of embryo staining; Y.K. co-supervised the design and implementation of the tracking method, and co-wrote the manuscript

P. , custom-designed the MLSM coupling and designed the imaging strategies

M. R. , co-coordinated the project, co-developed nucleus and membrane segmentation methods and co-wrote the manuscript

R. D. , co-coordinated the project, co-designed cell tracking methods and co-wrote the manuscript

A. S. , co-coordinated the project, and led several algorithm designs

K. M. , co-coordinated the project, led several algorithm designs, and co-wrote the manuscript; N.P. co-founded and co-coordinated the project, led the biological relevance and co-wrote the manuscript

P. , co-founded and co-coordinated the project, designed the formal and epistemological framework and co-wrote the manuscript