The theory, design, implementation and evaluation of a three-dimensional surface detection algorithm, Computer Graphics and Image Processing, vol.15, pp.1-24, 1981. ,
Automated cell lineage tracing in Caenorhabditis elegans, Proceedings of the National Academy of Sciences, vol.103, issue.8, pp.2707-2719, 2006. ,
DOI : 10.1073/pnas.0511111103
A protocol to analyse cellular dynamics during plant development, The Plant Journal, vol.59, issue.6, pp.1045-53, 2005. ,
DOI : 10.1111/j.1365-313X.2005.02576.x
URL : https://hal.archives-ouvertes.fr/hal-00016123
A new characterization of three-dimensional simple points, Pattern Recognition Letters, vol.15, issue.2, pp.169-175, 1994. ,
DOI : 10.1016/0167-8655(94)90046-9
URL : https://hal.archives-ouvertes.fr/inria-00615050
A method for registration of 3-D shapes, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.14, issue.2, pp.239-256, 1992. ,
DOI : 10.1109/34.121791
Adaptive Spatio-Temporal Restoration for 4D Fluorescence Microscopic Imaging, International Conference on Medical Robotics, Imaging And Computer Assisted Surgery (MICCAI'05), pp.893-901, 2005. ,
DOI : 10.1007/11566465_110
Patch-Based Nonlocal Functional for Denoising Fluorescence Microscopy Image Sequences, IEEE Transactions on Medical Imaging, vol.29, issue.2, pp.442-54, 2010. ,
DOI : 10.1109/TMI.2009.2033991
URL : https://hal.archives-ouvertes.fr/inria-00541082
4d embryogenesis image analysis using pde methods of image processing, Kybernetika, vol.46, issue.2, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00723331
A survey of image registration techniques, ACM Computing Surveys, vol.24, issue.4, pp.325-376, 1992. ,
DOI : 10.1145/146370.146374
root meristem, The Plant Journal, vol.123, issue.4, pp.619-627, 2006. ,
DOI : 10.1111/j.1365-313X.2006.02892.x
A Novel Three-Dimensional Computer-Assisted Method for a Quantitative Study of Microvascular Networks of the Human Cerebral Cortex, Microcirculation, vol.17, issue.1, pp.1-18, 2006. ,
DOI : 10.1080/10739680500383407
URL : https://hal.archives-ouvertes.fr/hal-00308888
Création et Utilisation d'Atlas Anatomiques Numériques pour la Radiothérapie (Design and Use of Anatomical Atlases for Radiotherapy ), Thèse de sciences, 2007. ,
Watershed Cuts: Minimum Spanning Forests and the Drop of Water Principle, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.31, issue.8, pp.311362-74, 2009. ,
DOI : 10.1109/TPAMI.2008.173
URL : https://hal.archives-ouvertes.fr/hal-00622410
Watershed Cuts: Thinnings, Shortest Path Forests, and Topological Watersheds, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.32, issue.5, pp.925-964, 2010. ,
DOI : 10.1109/TPAMI.2009.71
URL : https://hal.archives-ouvertes.fr/hal-00729346
Image denoising by sparse 3d transform-domain collaborative filtering, IEEE Trans. Image Process, issue.8, pp.162080-2095, 2007. ,
Floral stem cell termination involves the direct regulation of AGAMOUS by PERIANTHIA, Development, vol.136, issue.10, pp.1361605-1611, 2009. ,
DOI : 10.1242/dev.035436
URL : https://hal.archives-ouvertes.fr/hal-00412931
The fluorescent protein palette: tools for cellular imaging, Chemical Society Reviews, vol.90, issue.10, pp.2887-921, 2009. ,
DOI : 10.1039/b901966a
Les nouvelles techniques de microscopie, 2000. ,
Recursively implementing the gaussian and its derivatives, Proceedings of the 2nd International Conference On Image Processing, pp.263-267, 1992. ,
Iterative algorithms, European Symp. Quantitative Analysis of Microstructures in Material Science, 1977. ,
Alimentation et nutrition humaines, 1992. ,
Coordination of plant cell division and expansion in a simple morphogenetic system, Proceedings of the National Academy of Sciences, vol.107, issue.6, pp.2711-2717, 2010. ,
DOI : 10.1073/pnas.0906322107
A System for Modelling Cell-Cell Interactions during Plant Morphogenesis, Annals of Botany, vol.101, issue.8, pp.1255-65, 2008. ,
DOI : 10.1093/aob/mcm235
Sample Preparation for Fluorescence Imaging of the Cytoskeleton in Fixed and Living Plant Roots, Methods Mol Biol, vol.586, pp.157-69, 2009. ,
DOI : 10.1007/978-1-60761-376-3_8
The Representation, Recognition, and Locating of 3-D Objects, The International Journal of Robotics Research, vol.5, issue.3, pp.27-49, 1986. ,
DOI : 10.1177/027836498600500302
Imaging plant cells by two-photon excitation, Protoplasma, vol.223, issue.1, pp.1-32, 2004. ,
DOI : 10.1007/s00709-003-0026-2
An Analysis of Histogram-Based Thresholding Algorithms, Computer Vision, Graphics, and Image Processing : Graphical Models and Image Processing, pp.532-537, 1993. ,
DOI : 10.1006/cgip.1993.1040
WatershedCounting3D: A New Method for Segmenting and Counting Punctate Structures from Confocal Image Data, Traffic, vol.120, issue.4, pp.339-385, 2007. ,
DOI : 10.1111/j.1600-0854.2007.00538.x
Modéliser le vivant : créer des plantes virtuelles pour comprendre, simuler, tester, 2005. ,
Finding minimum-cost circulations by canceling negative cycles, Journal of the ACM, vol.36, issue.4, pp.873-886, 1989. ,
DOI : 10.1145/76359.76368
Graphes et Algorithmes . Eyrolles, 1990. ,
Tracking Cell Signals in Fluorescent Images, 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05), Workshops, p.142, 2005. ,
DOI : 10.1109/CVPR.2005.544
Fast surface tracking in three-dimensional binary images, Computer Vision, Graphics, and Image Processing, vol.45, issue.2, pp.196-241, 1989. ,
DOI : 10.1016/0734-189X(89)90132-1
In Vivo Analysis of Cell Division, Cell Growth, and Differentiation at the Shoot Apical Meristem in Arabidopsis, THE PLANT CELL ONLINE, vol.16, issue.1, pp.74-87, 2004. ,
DOI : 10.1105/tpc.017962
Average Brain Models: A Convergence Study, Computer Vision and Image Understanding, vol.77, issue.2, pp.192-210, 2000. ,
DOI : 10.1006/cviu.1999.0815
URL : https://hal.archives-ouvertes.fr/inria-00615030
Dynamic in vivo imaging and cell tracking using a histone fluorescent protein fusion in mice, BMC Biotechnology, vol.4, issue.1, p.33, 2004. ,
DOI : 10.1186/1472-6750-4-33
Developmental Patterning by Mechanical Signals in Arabidopsis, Science, vol.322, issue.5908, pp.3221650-1655, 2008. ,
DOI : 10.1126/science.1165594
URL : https://hal.archives-ouvertes.fr/hal-00412612
A topological proof of a surface tracking algorithm, Computer Vision, Graphics, and Image Processing, pp.162-177, 1983. ,
Insight into the basis of root growth in Arabidopsis thaliana provided by a simple mathematical model, Journal of Plant Research, vol.132, issue.2, pp.85-93, 2006. ,
DOI : 10.1007/s10265-005-0247-x
Why Do Plant Cells Divide?, THE PLANT CELL ONLINE, vol.9, issue.7, pp.1021-1029, 1997. ,
DOI : 10.1105/tpc.9.7.1021
Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem, Bioinformatics, vol.21, issue.Suppl 1, 2005. ,
DOI : 10.1093/bioinformatics/bti1036
An auxin-driven polarized transport model for phyllotaxis, Proceedings of the National Academy of Sciences, vol.103, issue.5, pp.1633-1641, 2006. ,
DOI : 10.1073/pnas.0509839103
Super-resolution in PET imaging, IEEE Transactions on Medical Imaging, vol.25, issue.2, pp.137-184, 2006. ,
DOI : 10.1109/TMI.2005.861705
Intensity-Based Image Registration Using Robust Correlation Coefficients, IEEE Transactions on Medical Imaging, vol.23, issue.11, pp.1430-1474, 2004. ,
DOI : 10.1109/TMI.2004.835313
Digital topology : introduction and survey, Computer Vision, Graphics, and Image Processing, pp.357-393, 1989. ,
DOI : 10.1016/0734-189x(89)90127-8
A justification of a fast surface tracking algorithm, Computer Vision, Graphics, and Image Processing : Graphical Models and Image Processing, pp.162-170, 1992. ,
DOI : 10.1016/1049-9652(92)90063-4
Model-Based Detection of Tubular Structures in 3D Images, Computer Vision and Image Understanding, vol.80, issue.2, pp.130-171, 2000. ,
DOI : 10.1006/cviu.2000.0866
URL : https://hal.archives-ouvertes.fr/inria-00615029
3D spatial compounding of ultrasound images using image-based nonrigid registration, Ultrasound in Medicine & Biology, vol.26, issue.9, pp.1475-88, 2000. ,
DOI : 10.1016/S0301-5629(00)00286-6
3D Well-Composed Pictures, Graphical Models and Image Processing, vol.59, issue.3, pp.164-172, 1997. ,
DOI : 10.1006/gmip.1997.0422
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.304.9284
Quelques traitements bas niveau basés sur une analyse du contraste local, Vision Interface '99, pp.598-603, 1999. ,
Croissance racinaire et survie à la sécheresse chez les types de dactylis glomerata l. non dormants en été, Congrès du sous-réseau méditerranéen FAO-CIHEAM sur les pâturages et cultures fourragères, pp.99-102, 2002. ,
Multiple nuclei tracking using integer programming for quantitative cancer cell cycle analysis, IEEE Trans Med Imaging, vol.29, issue.1, pp.96-105, 2010. ,
Online tracking of migrating and proliferating cells imaged with phase-contrast microscopy, Computer Vision and Pattern Recognition Workshop (CVPRW'06, 2006. ,
A hybrid 3D watershed algorithm incorporating gradient cues and object models for automatic segmentation of nuclei in confocal image stacks, Cytometry, vol.20, issue.1, pp.23-36, 2003. ,
DOI : 10.1002/cyto.a.10079
Robust estimation of stem cell lineages using local graph matching, Computer Vision and Pattern Recognition Workshop, pp.194-201, 2009. ,
Automated tracking of stem cell lineages of Arabidopsis shoot apex using local graph matching, The Plant Journal, vol.28, issue.2, pp.135-147, 2010. ,
DOI : 10.1111/j.1365-313X.2009.04117.x
Marching cubes: A high resolution 3D surface construction algorithm, ACM SIGGRAPH Computer Graphics, vol.21, issue.4, pp.163-169, 1987. ,
DOI : 10.1145/37402.37422
Multi-scale line segmentation with automatic estimation of width, contrast and tangential direction in 2D and 3D medical images, Int. Conf. on Computer Vision, Virtual Reality and Robotics in Medicine and Medical Robotics and Computer-Assisted Surgery (CVRMed- MRCAS'97 number 1205 in LNCS, pp.233-242, 1997. ,
DOI : 10.1007/BFb0029242
A survey of medical image registration, Medical Image Analysis, vol.2, issue.1, pp.1-36, 1998. ,
DOI : 10.1016/S1361-8415(01)80026-8
Image processing via level set curvature flow., Proceedings of the National Academy of Sciences, vol.92, issue.15, pp.927046-50, 1995. ,
DOI : 10.1073/pnas.92.15.7046
Applying watershed algorithms to the segmentation of clustered nuclei, Cytometry, vol.1660, issue.4, pp.289-97, 1997. ,
DOI : 10.1002/(SICI)1097-0320(19970801)28:4<289::AID-CYTO3>3.0.CO;2-7
Cell Division Detection on the Arabidopsis Thaliana Root, 4th Iberian Conference on Pattern Recognition and Image Analysis, pp.168-175, 2009. ,
DOI : 10.1007/978-3-642-02172-5_23
Automated Arabidopsis plant root cell segmentation based on SVM classification and region merging, Computers in Biology and Medicine, vol.39, issue.9, pp.785-93, 2009. ,
DOI : 10.1016/j.compbiomed.2009.06.008
A hybrid approach for arabidopsis root cell image segmentation Tracking of arabidopsis thaliana root cells in time-lapse microscopy, 5th Int. Conf. on Image Analysis and Recognition International Conference on Pattern Recognition (ICPR'08), pp.739-749, 2008. ,
Deformable models in medical image analysis: a survey, Medical Image Analysis, vol.1, issue.2, pp.91-108, 1996. ,
DOI : 10.1016/S1361-8415(96)80007-7
Cells tracking in a live zebrafish embryo, 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp.1631-1635, 2007. ,
DOI : 10.1109/IEMBS.2007.4352619
URL : https://hal.archives-ouvertes.fr/hal-00275367
Prehistory and History of Arabidopsis Research, PLANT PHYSIOLOGY, vol.125, issue.1, pp.15-19, 2001. ,
DOI : 10.1104/pp.125.1.15
A review of deformable surfaces: topology, geometry and deformation, Image and Vision Computing, vol.19, issue.14, pp.1023-1040, 2001. ,
DOI : 10.1016/S0262-8856(01)00064-6
URL : https://hal.archives-ouvertes.fr/inria-00615110
Imaging Plant Cells, Handbook of Biological Confocal Microscopy, chapter 44 SpringerScience+Business Media, pp.769-787, 2006. ,
DOI : 10.1007/978-0-387-45524-2_44
Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society, pp.2353-2359, 2006. ,
DOI : 10.1109/IEMBS.2006.259890
Botanique Générale, 1998. ,
Automated three-dimensional detection and counting of neuron somata, Journal of Neuroscience Methods, vol.180, issue.1, pp.147-60, 2009. ,
DOI : 10.1016/j.jneumeth.2009.03.008
Interaction in the segmentation of medical images: A survey, Medical Image Analysis, vol.5, issue.2, pp.127-169, 2001. ,
DOI : 10.1016/S1361-8415(00)00041-4
Segmentation of confocal microscope images of cell nuclei in thick tissue sections, Journal of Microscopy, vol.193, issue.3, pp.193212-193238, 1999. ,
DOI : 10.1046/j.1365-2818.1999.00463.x
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
Recalage d'images médicales par appariement de régions -Application à la construction d'atlas histologiques 3D, Thèse de sciences, 2002. ,
Block matching : A general framework to improve robustness of rigid registration of medical images Image thresholding : Some new techniques, Third International Conference on Medical Robotics, pp.557-566139, 1935. ,
A review on image segmentation techniques, Pattern Recognition, vol.26, issue.9, pp.1277-1294, 1993. ,
DOI : 10.1016/0031-3203(93)90135-J
Blind deconvolution for thin-layered confocal imaging, Applied Optics, vol.48, issue.22, pp.4437-4485, 2009. ,
DOI : 10.1364/AO.48.004437
URL : https://hal.archives-ouvertes.fr/inria-00395523
Super-resolution image reconstruction: a technical overview, IEEE Signal Processing Magazine, vol.20, issue.3, pp.21-36, 2003. ,
DOI : 10.1109/MSP.2003.1203207
The use of super-resolution techniques to reduce slice thickness in functional MRI, Special issue on High Resolution Image Reconstruction, pp.131-138, 2004. ,
DOI : 10.1002/ima.20016
L'incertitude dans les problèmes de reconnaissance et de recalage Application en imagerie médicale et biologie moléculaire, Thèse de doctorat, 1996. ,
Current Methods in Medical Image Segmentation, Annual Review of Biomedical Engineering, vol.2, issue.1, pp.315-352, 2000. ,
DOI : 10.1146/annurev.bioeng.2.1.315
Seeded watersheds for combined segmentation and tracking of cells An adjustablethreshold algorithm for the identification of objects in three-dimensional images, Int. Conf. on Image Analysis and Processing, pp.336-343, 2003. ,
Three-dimensional extended field-of-view ultrasound, Ultrasound in Medicine & Biology, vol.32, issue.3, pp.357-69, 2006. ,
DOI : 10.1016/j.ultrasmedbio.2005.11.003
Software for bead-based registration of selective plane illumination microscopy data, Nature Methods, vol.7, issue.6, pp.418-427, 2010. ,
DOI : 10.1364/OE.15.008029
Vers une polyédrisation des objets discrets bruités 3D, 2009. ,
Automatic real-time three-dimensional cell tracking by fluorescence microscopy, Journal of Microscopy, vol.216, issue.2, pp.131-138, 2004. ,
DOI : 10.1111/j.0022-2720.2004.01404.x
Molecular Genetics of Rice Root Development, Rice, vol.33, issue.Spec No, 2009. ,
DOI : 10.1007/s12284-008-9016-5
Real-time lineage analysis reveals oriented cell divisions associated with morphogenesis at the shoot apex of Arabidopsis thaliana, Development, vol.131, issue.17, pp.1314225-1314262, 2004. ,
DOI : 10.1242/dev.01261
Détection et quantification de processus évolutifs dans des images médicales tridimensionnelles : application à la sclérose en plaques, Thèse de sciences, 2002. ,
Performance of Low-Level Motion Estimation Methods for Confocal Microscopy of Plant Cells in vivo, 2007 IEEE Workshop on Motion and Video Computing (WMVC'07), p.13, 2007. ,
DOI : 10.1109/WMVC.2007.32
Unifying maximum likelihood approaches in medical image registration, International Journal of Imaging Systems and Technology, vol.17, issue.1, pp.71-80, 2000. ,
DOI : 10.1002/(SICI)1098-1098(2000)11:1<71::AID-IMA8>3.0.CO;2-5
URL : https://hal.archives-ouvertes.fr/cea-00333642
Imaging and modeling the patterning of arabidopsis sepal cells, 2009. ,
Three-dimensional spatial compounding of ultrasound images, Medical Image Analysis, vol.1, issue.3, pp.177-93, 1997. ,
DOI : 10.1016/S1361-8415(97)85009-8
Registration-Based Approach for Reconstruction of High-Resolution In Utero Fetal MR Brain Images, Academic Radiology, vol.13, issue.9, pp.1072-81, 2006. ,
DOI : 10.1016/j.acra.2006.05.003
URL : https://hal.archives-ouvertes.fr/hal-00257196
Robust Regression and Outlier Detection, 1987. ,
DOI : 10.1002/0471725382
New stereoscopic reconstruction protocol for scanning electron microscope images and its application to in vivo replicas of the shoot apical meristem, Functional Plant Biology, issue.10, pp.351034-1046, 2008. ,
A Computational Model of Cellular Morphogenesis in Plants, European Conference on Advances in Artificial Life (ECAL'05), pp.78-87, 2005. ,
DOI : 10.1007/11553090_9
Nonrigid registration using free-form deformations: application to breast MR images, IEEE Transactions on Medical Imaging, vol.18, issue.8, pp.18712-721, 1999. ,
DOI : 10.1109/42.796284
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.126.4732
A survey of thresholding techniques, Computer Vision, Graphics, and Image Processing, pp.233-260, 1988. ,
DOI : 10.1016/0734-189X(88)90022-9
Raman imaging of cell wall polymers in Arabidopsis thaliana, Biochemical and Biophysical Research Communications, vol.395, issue.4, 2010. ,
DOI : 10.1016/j.bbrc.2010.04.055
Image Analysis and Mathematical Morphology, 1982. ,
Image analysis and mathematical morphology : theoretical advances, 1988. ,
Survey over image thresholding techniques and quantitative performance evaluation, Journal of Electronic Imaging, vol.13, issue.1, pp.146-165, 2004. ,
A guide to choosing fluorescent proteins, Nature Methods, vol.102, issue.12, pp.905-914, 2005. ,
DOI : 10.1038/nmeth819
Automated medical image segmentation techniques, Journal of Medical Physics, vol.35, issue.1, pp.3-14, 2010. ,
DOI : 10.4103/0971-6203.58777
Topological Repairing of 3D Digital Images, Journal of Mathematical Imaging and Vision, vol.17, issue.3, pp.249-274, 2008. ,
DOI : 10.1007/s10851-007-0054-1
A plausible model of phyllotaxis, Proceedings of the National Academy of Sciences, vol.103, issue.5, pp.1301-1307, 2006. ,
DOI : 10.1073/pnas.0510457103
Morphological image analysis : principles and applications, 1999. ,
Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development, PLoS Computational Biology, vol.133, issue.11, 2008. ,
DOI : 10.1371/journal.pcbi.1000207.s018
URL : https://hal.archives-ouvertes.fr/hal-00412857
Multiple imaging axis microscopy improves resolution for thick-sample applications, Optics Letters, vol.28, issue.18, pp.281654-281660, 2003. ,
DOI : 10.1364/OL.28.001654
From genes to shape: Understanding the control of morphogenesis at the shoot meristem in higher plants using systems biology, Comptes Rendus Biologies, vol.332, issue.11, pp.332974-85, 2009. ,
DOI : 10.1016/j.crvi.2009.09.008
World population prospects : the 2009 revision, 2009. ,
A New Algorithm for Computational Image Analysis of Deformable Motion at High Spatial and Temporal Resolution Applied to Root Growth. Roughly Uniform Elongation in the Meristem and Also, after an Abrupt Acceleration, in the Elongation Zone, PLANT PHYSIOLOGY, vol.132, issue.3, pp.1138-1186, 2003. ,
DOI : 10.1104/pp.103.021345
Topological considerations in isosurface generation, ACM Transactions on Graphics, vol.13, issue.4, pp.337-375, 1994. ,
DOI : 10.1145/195826.195828
Diffeomorphic demons: Efficient non-parametric image registration, NeuroImage, vol.45, issue.1, pp.61-72, 2009. ,
DOI : 10.1016/j.neuroimage.2008.10.040
URL : https://hal.archives-ouvertes.fr/inserm-00349600
Robust mosaicing with correction of motion distortions and tissue deformations for in vivo fibered microscopy, Medical Image Analysis, vol.10, issue.5, pp.673-692, 2006. ,
DOI : 10.1016/j.media.2006.06.006
Pluripotent versus totipotent plant stem cells : dependence versus autonomy ? Trends in plant science, pp.245-252, 2007. ,
Watersheds in digital spaces: an efficient algorithm based on immersion simulations, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.13, issue.6, pp.583-598, 1991. ,
DOI : 10.1109/34.87344
Alignment by maximization of mutual information, Proceedings of IEEE International Conference on Computer Vision, pp.137-154, 1997. ,
DOI : 10.1109/ICCV.1995.466930
Cells Segmentation From 3-D Confocal Images of Early Zebrafish Embryogenesis, IEEE Transactions on Image Processing, 2010. ,
DOI : 10.1109/TIP.2009.2033629
URL : https://hal.archives-ouvertes.fr/hal-00444516
Hierarchical watershed segmentation of canopy height for multi-scale forest inventory, ISPRS Workshop on Laser Scanning, 2007. ,
Segmentation and tracking of migrating cells in videomicroscopy with parametric active contours: a tool for cell-based drug testing, IEEE Transactions on Medical Imaging, vol.21, issue.10, pp.1212-1233, 2002. ,
DOI : 10.1109/TMI.2002.806292
Nonlinear magic: multiphoton microscopy in the biosciences, Nature Biotechnology, vol.21, issue.11, pp.1369-1377 ,
DOI : 10.1038/nbt899
Image registration methods: a survey, Image and Vision Computing, vol.21, issue.11, pp.977-1000, 2003. ,
DOI : 10.1016/S0262-8856(03)00137-9