D. Ballard, Generalizing the Hough transform to detect arbitrary shapes, Pattern Recognition, vol.13, issue.2, pp.111-122, 1981.
DOI : 10.1016/0031-3203(81)90009-1

L. A. Baena-lopez, The Orientation of Cell Divisions Determines the Shape of Drosophila Organs, Current Biology, vol.15, issue.18, pp.1640-1644, 2005.
DOI : 10.1016/j.cub.2005.07.062

B. Boehm, The Role of Spatially Controlled Cell Proliferation in Limb Bud Morphogenesis, PLoS Biology, vol.5, issue.7, p.1000420, 2010.
DOI : 10.1371/journal.pbio.1000420.s012

M. Bornens, The Centrosome in Cells and Organisms, Science, vol.108, issue.2, pp.422-426, 2012.
DOI : 10.1016/1047-8477(92)90011-X

F. Bosveld, Mechanical Control of Morphogenesis by Fat/Dachsous/Four-Jointed Planar Cell Polarity Pathway, Science, vol.27, issue.1, pp.724-727, 2012.
DOI : 10.1016/j.devcel.2010.11.007

T. Brox, Adaptive structure tensors and their applications Visualization and Processing of Tensor Fields, pp.17-47, 2006.

T. Chan and L. A. Vese, Active contours without edges, IEEE Transactions on Image Processing, vol.10, issue.2, pp.266-277, 2001.
DOI : 10.1109/83.902291

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.2.1828

F. De-chaumont, Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, vol.9, issue.7, pp.690-696, 2012.
DOI : 10.1038/nmeth.1924

O. Drblikova, The Nonlinear Tensor Diffusion in Segmentation of Meaningful Biological Structures from Image Sequences of Zebrafish Embryogenesis, Lect. Notes Comput. Sci. LNCS, vol.31, issue.97, pp.63-74, 2009.
DOI : 10.1023/A:1008009714131

URL : https://hal.archives-ouvertes.fr/hal-00723371

A. Dufour, Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces, IEEE Transactions on Image Processing, vol.14, issue.9, pp.1396-1410, 2005.
DOI : 10.1109/TIP.2005.852790

URL : https://hal.archives-ouvertes.fr/hal-00014483

A. Dufour, 3-D Active Meshes: Fast Discrete Deformable Models for Cell Tracking in 3-D Time-Lapse Microscopy, IEEE Transactions on Image Processing, vol.20, issue.7, pp.1925-1937, 2011.
DOI : 10.1109/TIP.2010.2099125

R. Fernandez, Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution, Nature Methods, vol.19, issue.7, pp.547-553, 2010.
DOI : 10.1145/321694.321699

URL : https://hal.archives-ouvertes.fr/hal-00521491

Y. Gong, Planar cell polarity signaling controls cell division orientation during zebrafish gastrulation, PLoS Biol, vol.430, pp.689-693, 2004.
DOI : 10.1038/nature02796

J. Huisken, Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy, Science, vol.305, issue.5686, pp.1007-1009, 2004.
DOI : 10.1126/science.1100035

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.456.2250

Z. Kriva, 3D early embryogenesis image filtering by nonlinear partial differential equations, Medical Image Analysis, vol.14, issue.4, pp.510-526, 2010.
DOI : 10.1016/j.media.2010.03.003

URL : https://hal.archives-ouvertes.fr/hal-00502622

S. Lankton and A. Tannenbaum, Localizing Region-Based Active Contours, IEEE Transactions on Image Processing, vol.17, issue.11, pp.2029-2039, 2008.
DOI : 10.1109/TIP.2008.2004611

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796112

L. Garrec and J. F. , Quantitative analysis of polarity in 3D reveals local cell coordination in the embryonic mouse heart, Development, vol.140, issue.2, pp.395-404, 2013.
DOI : 10.1242/dev.087940

G. Lin, A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images, Cytometry Part A, vol.69, issue.9, pp.724-736, 2007.
DOI : 10.1007/978-0-387-45524-2_36

M. Matsuyama, Sfrp Controls Apicobasal Polarity and Oriented Cell Division in Developing Gut Epithelium, PLoS Genetics, vol.39, issue.3, p.1000427, 2009.
DOI : 10.1371/journal.pgen.1000427.s013

URL : http://doi.org/10.1371/journal.pgen.1000427

M. Mavrakis, Lighting up developmental mechanisms: how fluorescence imaging heralded a new era, Development, vol.137, issue.3, pp.373-387, 2010.
DOI : 10.1242/dev.031690

URL : https://hal.archives-ouvertes.fr/hal-00567137

S. Megason, In Toto Imaging of Embryogenesis with Confocal Time-Lapse Microscopy, Methods Mol. Biol, vol.546, pp.317-332, 2010.
DOI : 10.1007/978-1-60327-977-2_19

S. Meilhac and M. Buckingham, The behaviour of cells that form the myocardial compartments of the vertebrate heart (eds) Heart Development and Regeneration, 2010.

K. Mosaliganti, Anisotropic plate diffusion filtering for detection of cell membranes in 3D microscopy images, 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp.588-591, 2010.
DOI : 10.1109/ISBI.2010.5490110

K. Mosaliganti, ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes, PLoS Computational Biology, vol.7, issue.329, p.1002780, 2012.
DOI : 10.1371/journal.pcbi.1002780.s007

J. C. Olivo-marin, Extraction of spots in biological images using multiscale products, Pattern Recognition, vol.35, issue.9, pp.1989-1996, 2002.
DOI : 10.1016/S0031-3203(01)00127-3

N. Otsu, A Threshold Selection Method from Gray-Level Histograms, IEEE Transactions on Systems, Man, and Cybernetics, vol.9, issue.1, pp.62-66, 1979.
DOI : 10.1109/TSMC.1979.4310076

P. Perona and J. Malik, Scale-space and edge detection using anisotropic diffusion, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.12, issue.7, pp.629-639, 1990.
DOI : 10.1109/34.56205

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.108.2553

P. Pitrone, OpenSPIM: An open access Selective Plane Illumination Microscope for the observation of developing fruitfly and zebrafish embryos, Proceedings of the European Microscopy Congress, 2012.

S. Pop, Image filtering using anisotropic structure tensor for cell membrane enhancement in 3D microscopy, 2011 18th IEEE International Conference on Image Processing, pp.2085-2088, 2011.
DOI : 10.1109/ICIP.2011.6115880

S. Preibisch, Software for bead-based registration of selective plane illumination microscopy data, Nature Methods, vol.7, issue.6, pp.418-419, 2010.
DOI : 10.1364/OE.15.008029

S. Saburi, Loss of Fat4 disrupts PCP signaling and oriented cell division and leads to cystic kidney disease, Nature Genetics, vol.6, issue.8, pp.1010-1015, 2008.
DOI : 10.1038/sj.ki.5001534

A. Sarti, Subjective surfaces: A method for completing missing boundaries, Proceedings of the National Academy of Sciences, vol.18, issue.6, pp.6258-6263, 2000.
DOI : 10.1109/42.781012

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC18589

Y. Sato, Dynamic Analysis of Vascular Morphogenesis Using Transgenic Quail Embryos, PLoS ONE, vol.3, issue.9, p.12674, 2010.
DOI : 10.1371/journal.pone.0012674.s010

J. Sharpe, Two ways to use imaging: focusing directly on mechanism, or indirectly via behaviour?, Current Opinion in Genetics & Development, vol.21, issue.5, pp.523-539, 2011.
DOI : 10.1016/j.gde.2011.08.012

R. Terebes, Flow coherence diffusion. Linear and nonlinear case, Lect. Notes Comput. Sci. LNCS, vol.3708, pp.316-322, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00400130

G. M. Treece, Regularised marching tetrahedra: improved iso-surface extraction, Computers & Graphics, vol.23, issue.4, pp.583-598, 1998.
DOI : 10.1016/S0097-8493(99)00076-X

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.29.9171

G. M. Van-kempen, The application of a local dimensionality estimator to the analysis of 3d microscopic network structures, Proceedings of the Scandinavian Conference on Image Analysis, pp.447-455, 1999.

J. Weickert, Coherence enhancing diffusion, International Journal of Computer Vision, vol.31, issue.2/3, pp.111-127, 1999.
DOI : 10.1023/A:1008009714131

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.35.5217

L. Xinghua, Learning to segment dense cell nuclei with shape prior, 2012 IEEE Conference on Computer Vision and Pattern Recognition, pp.1012-1018, 2012.
DOI : 10.1109/CVPR.2012.6247778

C. Zanella, Cells Segmentation From 3-D Confocal Images of Early Zebrafish Embryogenesis, IEEE Transactions on Image Processing, vol.19, issue.3, pp.770-781, 2010.
DOI : 10.1109/TIP.2009.2033629

URL : https://hal.archives-ouvertes.fr/hal-00444516