L. Heinrich, Reaction wood varieties caused by different experimental treatments, TRACE, Tree Rings in Archaeology Climatology and Ecology, vol.5, pp.224-232, 2007.

. Bastien, Clonal variation of indirect cambium reaction to within-growing season temperature changes in Douglas-fir, Forestry, vol.77, issue.4, pp.257-268, 2004.

E. Nicolini, Y. Caraglio, R. Pélissier, C. Leroy, and J. Roggy, Epicormic Branches: a Growth Indicator for the Tropical Forest Tree, Dicorynia guianensis Amshoff (Caesalpiniaceae), Annals of Botany, vol.92, issue.1, pp.97-105, 2003.
DOI : 10.1093/aob/mcg119

URL : https://hal.archives-ouvertes.fr/hal-01032037

H. Wu, M. Jaeger, M. Wang, B. Li, and B. Zhang, 3D-Reconstruction and Visualization of Xylem Vessels of Wheat Nodal Root, 2010. Proceedings,of Plant growth Modeling, and their Applications (PMA09), pp.384-390, 2009.

P. Quelhas, J. Nieuwland, W. Dewitte, A. M. Mendonça, J. Murray et al., Arabidopsis Thaliana Automatic Cell File Detection and Cell Length Estimation, Image Analysis and Recognition, pp.1-11, 2011.
DOI : 10.1109/TSMC.1979.4310076

M. K. Moëll and L. A. Donaldson, COMPARISON OF SEGMENTATION METHODS FOR DIGITAL IMAGE ANALYSIS OF CONFOCAL MICROSCOPE IMAGES TO MEASURE TRACHEID CELL DIMENSIONS, IAWA Journal, vol.22, issue.3, pp.267-288, 2001.
DOI : 10.1163/22941932-90000284

D. Baggett, M. Nakaya, M. Mcauliffe, T. P. Yamaguchi, and S. Lockett, Whole cell segmentation in solid tissue sections, Cytometry Part A, vol.307, issue.2, pp.137-143, 2005.
DOI : 10.1002/cyto.a.20162

T. Fourcaud, X. Zhang, A. Stokes, H. Lambers, and C. Körner, Plant Growth Modelling and Applications: The Increasing Importance of Plant Architecture in Growth Models, Annals of Botany, vol.101, issue.8, pp.1053-1063, 2008.
DOI : 10.1093/aob/mcn050

URL : https://hal.archives-ouvertes.fr/halsde-00281936

J. Park and J. M. Keller, Snakes on the Watershed, IEEE Trans. Pattern Anal. Mach. Intell, pp.1201-1205, 2001.

L. Vincent and P. Soille, 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

A. Kass, D. Witkin, and . Terzopoulos, Snakes: Active contour models, International Journal of Computer Vision, vol.5, issue.6035, pp.321-331, 1988.
DOI : 10.1007/BF00133570

M. B. Jeacocke and B. C. Lovell, A multi-resolution algorithm for cytological image segmentation, Proceedings of ANZIIS '94, Australian New Zealnd Intelligent Information Systems Conference, pp.322-326, 1994.
DOI : 10.1109/ANZIIS.1994.396981

R. Jones and L. Bischof, A graph?based segmentation of wood micrographs, Computing Science and Statistics, pp.12-20, 1996.

P. Kennel, G. Subsol, M. Guéroult, and P. Borianne, Automatic identification of cell files in light microscopic images of conifer wood, 2010 2nd International Conference on Image Processing Theory, Tools and Applications, pp.98-103, 2010.
DOI : 10.1109/IPTA.2010.5586800

URL : https://hal.archives-ouvertes.fr/lirmm-00804426

G. T. Einevoll and H. E. Plesser, Response of the difference-of-Gaussians model to circular drifting-grating patches, Visual Neuroscience, vol.344, issue.04, pp.437-446, 2005.
DOI : 10.1007/BF00227775

L. Breiman, J. Friedman, C. J. Stone, and R. A. Olshen, Classification and Regression Trees, 1984.

O. M. Hitz, H. Gärtner, I. Heinrich, and M. Monbaron, Wood anatomical changes in roots of European ash (Fraxinus excelsior L.) after exposure, Dendrochronologia, vol.25, issue.3, pp.145-152, 2008.
DOI : 10.1016/j.dendro.2007.03.005

A. J. Travis, D. J. Hirst, and A. Chesson, Automatic Classification of Plant Cells According to Tissue Type using Anatomical Features Obtained by the Distance Transform, Annals of Botany, vol.78, issue.3, pp.325-331, 1996.
DOI : 10.1006/anbo.1996.0127

B. Clair, J. Gril, F. Di-renzo, H. Yamamoto, and F. Quignard, Characterization of a Gel in the Cell Wall To Elucidate the Paradoxical Shrinkage of Tension Wood, Biomacromolecules, vol.9, issue.2, pp.494-498, 2007.
DOI : 10.1021/bm700987q

J. R. Bray and J. T. Curtis, An Ordination of the Upland Forest Communities of Southern Wisconsin, Ecological Monographs, vol.27, issue.4, p.325, 1957.
DOI : 10.2307/1942268

E. Forgy, Cluster analysis of multivariate data: efficiency vs interpretability of classifications, Biometrics, vol.212324, pp.768-769, 1965.

E. Andrès, Discrete circles, rings and spheres, Computers & Graphics, vol.18, issue.5, pp.695-706, 1994.
DOI : 10.1016/0097-8493(94)90164-3

D. Baggett, M. Nakaya, M. Mcauliffe, T. Yamaguchi, and S. Lockett, Whole cell segmentation in solid tissue sections, Cytometry Part A, vol.307, issue.2, pp.137-143, 2005.
DOI : 10.1002/cyto.a.20162

D. Barthélémy and Y. Caraglio, Plant Architecture: A Dynamic, Multilevel and Comprehensive Approach to Plant Form, Structure and Ontogeny, Annals of Botany, vol.99, issue.3, pp.375-407, 2007.
DOI : 10.1093/aob/mcl260

S. Beucher, Towards a unification of waterfalls, standard and P algorithms, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00835016

L. Breiman, J. Friedman, C. Stone, and R. Olshen, Classification and regression trees, 1984.

G. Brunel, P. Borianne, G. Subsol, M. Jaeger, and Y. Caraglio, Automatic characterization of the cell organization in light microscopic images of wood: Application to the identification of the cell file Plant growth modeling, simulation, visualization and applications, The Fourth International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, pp.58-65, 2012.

G. Brunel, P. Borianne, G. Subsol, and M. Jaeger, Simple-graphs fusion in image mosaic: application to automated cell files identification in wood slices Lecture notes in computer science. Image analysis, pp.34-43, 2013.

L. Busin, J. Shi, N. Vandenbroucke, and L. Macaire, Color space selection for color image segmentation by spectral clustering, 2009 IEEE International Conference on Signal and Image Processing Applications, pp.262-267, 2009.
DOI : 10.1109/ICSIPA.2009.5478603

URL : https://hal.archives-ouvertes.fr/hal-00732828

B. Clair, J. Gril, D. Renzo, F. Yamamoto, H. Quignard et al., Characterization of a Gel in the Cell Wall To Elucidate the Paradoxical Shrinkage of Tension Wood, Biomacromolecules, vol.9, issue.2, pp.494-498, 2007.
DOI : 10.1021/bm700987q

T. Cormen, X. Cazin, and G. Kocher, AD. Introduction to algorithms, 2001.

E. Forgy, Cluster analysis of multivariate data: efficiency vs interpretability of classifications, Biometrics, vol.21, pp.768-769, 1965.

T. Fourcaud, X. Zhang, A. Stokes, H. Lambers, and C. Körner, Plant Growth Modelling and Applications: The Increasing Importance of Plant Architecture in Growth Models, Annals of Botany, vol.101, issue.8, pp.1053-1063, 2008.
DOI : 10.1093/aob/mcn050

URL : https://hal.archives-ouvertes.fr/halsde-00281936

P. Gilmore and C. T. Kelley, An Implicit Filtering Algorithm for Optimization of Functions with Many Local Minima, SIAM Journal on Optimization, vol.5, issue.2, pp.269-285, 1995.
DOI : 10.1137/0805015

W. Gindl, CELL-WALL LIGNIN CONTENT RELATED TO TRACHEID DIMENSIONS IN DROUGHT-SENSITIVE AUSTRIAN PINE (PINUS NIGRA), IAWA Journal, vol.22, issue.2, pp.113-120, 2001.
DOI : 10.1163/22941932-90000272

Y. Guédon, O. Taugourdeau, Y. Caraglio, and S. Sabatier, Characterizing the balance between ontogeny and environmental constraints in forest tree development using growth phase duration distributions, Proceedings of the 7th International Conference on Functional Structural Plant Models, pp.237-239, 2013.

. Brunel, Automatic identification of radial cell files in wood Page 11 of 12

R. Haddad and A. Akansu, A class of fast Gaussian binomial filters for speech and image processing, IEEE Transactions on Signal Processing, vol.39, issue.3, pp.723-727, 1991.
DOI : 10.1109/78.80892

L. Heinrich, Reaction wood varieties caused by different experimental treatments. TRACE, Tree Rings in Archaeology, Climatology and Ecology, vol.5, pp.224-232, 2007.

O. Hitz, H. Gärtner, I. Heinrich, and M. Monbaron, Wood anatomical changes in roots of European ash (Fraxinus excelsior L.) after exposure, Dendrochronologia, vol.25, issue.3, pp.145-152, 2008.
DOI : 10.1016/j.dendro.2007.03.005

M. Jeacocke and B. Lovell, A multi-resolution algorithm for cytological image segmentation, Proceedings of ANZIIS '94, Australian New Zealnd Intelligent Information Systems Conference, pp.322-326, 1994.
DOI : 10.1109/ANZIIS.1994.396981

R. Jones and L. Bischof, A graph? based segmentation of wood micrographs. Computing science and statistics 28, Proceedings in Computing Science and Statistics, vol.28, pp.12-20, 1996.

P. Kennel, G. Subsol, M. Guéroult, and P. Borianne, Automatic identification of cell files in light microscopic images of conifer wood, 2010 2nd International Conference on Image Processing Theory, Tools and Applications, pp.98-103, 2010.
DOI : 10.1109/IPTA.2010.5586800

URL : https://hal.archives-ouvertes.fr/lirmm-00804426

C. Krause, S. Rossi, M. Thibeault-martel, and P. Plourde, Relations entre climat et caract??ristiques cellulaires dans la tige et les racines de l?????pinette noire et du sapin baumier, Annals of Forest Science, vol.147, issue.4, pp.402-402, 2010.
DOI : 10.1051/forest/2009122

S. Lachaud, A. Catesson, and J. Bonnemain, Structure and functions of the vascular cambium, Comptes Rendus de l'Académie des Sciences ? Series III. Sciences de la Vie, pp.633-650, 1999.
DOI : 10.1016/S0764-4469(99)80103-6

S. Ladjal, Estimation du flou dans les images naturelles In: Quinziéme congrés francophone Reconnaissance des formes et intelligence artificielle (RFIA). François, 2006.

M. Marcuzzo, P. Quelhas, A. Campilho, A. Mendonça, and A. Campilho, Automated Arabidopsis plant root cell segmentation based on SVM classification and region merging, Computers in Biology and Medicine, vol.39, issue.9, pp.785-793, 2009.
DOI : 10.1016/j.compbiomed.2009.06.008

T. Mcinerney and D. Terzopoulos, T-snakes: Topology adaptive snakes, Medical Image Analysis, vol.4, issue.2, pp.840-845, 1999.
DOI : 10.1016/S1361-8415(00)00008-6

M. Moëll and L. Donaldson, COMPARISON OF SEGMENTATION METHODS FOR DIGITAL IMAGE ANALYSIS OF CONFOCAL MICROSCOPE IMAGES TO MEASURE TRACHEID CELL DIMENSIONS, IAWA Journal, vol.22, issue.3, pp.267-288, 2001.
DOI : 10.1163/22941932-90000284

E. Nicolini, Y. Caraglio, R. Pélissier, C. Leroy, and J. Roggy, Epicormic Branches: a Growth Indicator for the Tropical Forest Tree, Dicorynia guianensis Amshoff (Caesalpiniaceae), Annals of Botany, vol.92, issue.1, pp.97-105, 2003.
DOI : 10.1093/aob/mcg119

URL : https://hal.archives-ouvertes.fr/hal-01032037

J. Park and J. Keller, Snakes on the watershed, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.23, issue.10, pp.1201-1205, 2001.
DOI : 10.1109/34.954609

P. Quelhas, J. Nieuwland, W. Dewitte, A. Mendonça, J. Murray et al., Arabidopsis thaliana automatic cell file detection and cell length estimation Image analysis and recognition, pp.1-11, 2011.

C. Rathgeber, S. Rossi, and J. Bontemps, Cambial activity related to tree size in a mature silver-fir plantation, Annals of Botany, vol.108, issue.3, pp.429-438, 2011.
DOI : 10.1093/aob/mcr168

URL : https://hal.archives-ouvertes.fr/hal-01000480

S. Rossi, A. Deslauriers, and T. Anfodillo, Conifers in cold environments synchronize maximum growth rate of tree-ring formation with day length, New Phytologist, vol.21, issue.2, pp.301-310, 2006.
DOI : 10.1139/x01-208

S. Rossi, S. Simard, C. Rathgeber, A. Deslauriers, and C. Zan, Effects of a 20-day-long dry period on cambial and apical meristem growth in Abies balsamea seedlings, Trees, vol.38, issue.1, pp.85-93, 2009.
DOI : 10.1007/s00468-008-0257-0

URL : https://hal.archives-ouvertes.fr/hal-01195111

P. Rozenberg, G. Schü-te, M. Ivkovich, C. Bastien, and J. Bastien, Clonal variation of indirect cambium reaction to within-growing season temperature changes in Douglas-fir, Forestry, vol.77, issue.4, pp.257-268, 2004.
DOI : 10.1093/forestry/77.4.257

C. Schneider, W. Rasbaand, and K. Eliceiri, NIH Image to ImageJ: 25 years of image analysis, Nature Methods, vol.42, issue.7, pp.671-675, 2012.
DOI : 10.1038/nmeth.2089

M. Thibeault-martel, C. Krause, H. Morin, and S. Rossi, Cambial Activity and Intra-annual Xylem Formation in Roots and Stems of Abies balsamea and Picea mariana, Annals of Botany, vol.102, issue.5, pp.667-674, 2008.
DOI : 10.1093/aob/mcn146

A. Travis, D. Hirst, and A. Chesson, Automatic Classification of Plant Cells According to Tissue Type using Anatomical Features Obtained by the Distance Transform, Annals of Botany, vol.78, issue.3, pp.325-331, 1996.
DOI : 10.1006/anbo.1996.0127

L. Vincent and P. Soille, 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

M. Wang, X. Zhou, F. Li, J. Huckins, R. King et al., Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy, Bioinformatics, vol.24, issue.1, pp.94-101, 2008.
DOI : 10.1093/bioinformatics/btm530

J. Zunic and K. Hirota, Measuring shape circularity Progress in Pattern Recognition, Image Analysis and Applications Lecture Notes, Computer Science, vol.5197, pp.94-101, 2008.

R. 1. Lézoray, O. Grady, and L. , Image processing and Analysis With Graphs, 2012.

J. Cousty, G. Bertrand, M. Couprie, and L. Najman, Fusion Graphs: Merging Properties and Watersheds, Journal of Mathematical Imaging and Vision, vol.147, issue.2???3, pp.87-104, 2008.
DOI : 10.1007/s10851-007-0047-0

URL : https://hal.archives-ouvertes.fr/hal-00622371

P. J. Baldevbhai and R. S. Anand, Review of Graph, Medical and Color Image base Segmentation Techniques, IOSR Journal of Electrical and Electronics Engineering, vol.1, issue.1, pp.1-19, 2012.
DOI : 10.9790/1676-0110119

B. Peng, L. Zhang, D. Zhang, and J. Yang, Image segmentation by iterated region merging with localized graph cuts, Pattern Recognition, vol.44, issue.10-11, pp.10-11, 2013.
DOI : 10.1016/j.patcog.2011.03.024

M. Brown and D. G. Lowe, Automatic Panoramic Image Stitching using Invariant Features, International Journal of Computer Vision, vol.50, issue.1, pp.59-73, 2007.
DOI : 10.1007/s11263-006-0002-3

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.193.2527

D. G. Lowe, Distinctive Image Features from Scale-Invariant Keypoints, International Journal of Computer Vision, vol.60, issue.2, pp.91-110, 2004.
DOI : 10.1023/B:VISI.0000029664.99615.94

C. Clenti, Architectures flot de données dédiées au traitement d'images par Morphologie Mathématique, Thèse de doctorat en morphologie mathématique, In: ENSMP, issue.431, 2009.

C. Sun, R. Beare, V. Hilsenstein, and P. Jackway, Mosaicing of microscope images with global geometric and radiometric corrections, Journal of Microscopy, vol.7, issue.4, pp.158-165, 2006.
DOI : 10.1016/S0895-6111(03)00036-3

T. Vercauteren, A. Perchant, G. Malandain, X. Pennec, and N. Ayache, 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

P. Thévenaz and M. Unser, User-friendly semiautomated assembly of accurate image mosaics in microscopy, Microscopy Research and Technique, vol.15, issue.2, pp.135-146, 2007.
DOI : 10.1002/jemt.20393

C. Liang, L. Filion, and L. Cournoyer, ), Canadian Journal of Forest Research, vol.27, issue.10, pp.1538-1547, 1997.
DOI : 10.1139/x97-117

B. F. Wilson, The Growing Tree. The University of, 1970.

W. Gindl, CELL-WALL LIGNIN CONTENT RELATED TO TRACHEID DIMENSIONS IN DROUGHT-SENSITIVE AUSTRIAN PINE (PINUS NIGRA), IAWA Journal, vol.22, issue.2, pp.113-120, 2001.
DOI : 10.1163/22941932-90000272

G. Brunel, P. Borianne, G. Subsol, M. Jaeger, and Y. Caraglio, Automatic characterization of the cell organization in light microscopic images of wood: Application to the identification of the cell file, 2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, pp.58-65, 2012.
DOI : 10.1109/PMA.2012.6524813

URL : https://hal.archives-ouvertes.fr/tel-01079815

P. Kennel, G. Subsol, M. Guéroult, and P. Borianne, Automatic identification of cell files in light microscopic images of conifer wood, 2010 2nd International Conference on Image Processing Theory, Tools and Applications, pp.98-103, 2010.
DOI : 10.1109/IPTA.2010.5586800

URL : https://hal.archives-ouvertes.fr/lirmm-00804426

M. Sjodahl and B. Oreb, Stitching interferometric measurement data for inspection of large optical components, Optical Engineering, vol.41, issue.2, pp.403-408, 2002.
DOI : 10.1117/1.1430727

J. C. Wyant and J. Schmit, Large field of view, high spatial resolution, surface measurements, International Conference on Metrology and Properties of Engineering Surfaces, pp.691-698, 1998.
DOI : 10.1016/S0890-6955(97)00119-3

L. Vincent and P. Soille, 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

A. Tremeau and P. Colantoni, Regions adjacency graph applied to color image segmentation, IEEE Transactions on Image Processing, vol.9, issue.4, pp.735-744, 2000.
DOI : 10.1109/83.841950

S. Beucher, Watershed, Hierarchical Segmentation and Waterfall Algorithm, Proc. Mathematical Morphology and its Applications to Image Processing, pp.69-76, 1994.
DOI : 10.1007/978-94-011-1040-2_10

S. Ladjal, Blur estimation in Natural Images In: 15e congrès francophone AFRIF-AFIA Reconnaissance des Formes et Intelligence Artificielle, pp.112-124, 2006.

G. Brunel, P. Borianne, G. Subsol, M. Jaeger, and Y. Caraglio, Results reliability of the automated identification of cell files in microscopic images of gymnosperms, 7th International Conference on Fuctional-Structural Plant Models, 2013.