E. Adelson and J. Wang, Single lens stereo with a plenoptic camera, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.14, issue.2, pp.99-106, 1992.
DOI : 10.1109/34.121783

M. Ahmad and T. Choi, Application of three dimensional shape from image focus in LCD/TFT displays manufacturing, IEEE Transactions on Consumer Electronics, vol.53, 2007.

M. Ahmad and T. Choi, Optimization technique for three-dimensional shape recovery from image focus, Journal of Electronic Imaging, vol.40, issue.4, 2008.
DOI : 10.1109/34.709612

P. Alcantarilla, A. Bartoli, F. Chadebecq, C. Tilmant, and V. Lepilliez, Enhanced imaging colonoscopy facilitates dense motion-based 3D reconstruction, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp.7346-7349, 2013.
DOI : 10.1109/EMBC.2013.6611255

Y. An, G. Kang, I. Kim, H. Chung, and J. Park, Shape from Focus through Laplacian Using 3D Window, 2008 Second International Conference on Future Generation Communication and Networking, pp.46-50, 2008.
DOI : 10.1109/FGCN.2008.139

A. Anish and T. Jebaseeli, A Survey on Multi-Focus Image Fusion Methods, International Journal of Advanced Research in Computer Engineering & Technology, vol.1, pp.319-324, 2012.

M. Asif, A. Malik, C. , and T. S. , 3D shape recovery from image defocus using wavelet analysis, IEEE International Conference on Image Processing 2005, pp.1025-1033, 2005.
DOI : 10.1109/ICIP.2005.1529928

A. Bartoli and T. Collins, Template-Based Isometric Deformable 3D Reconstruction with Sampling-Based Focal Length Self-Calibration, 2013 IEEE Conference on Computer Vision and Pattern Recognition, pp.1514-1521, 2013.
DOI : 10.1109/CVPR.2013.199

A. Bartoli, V. Gay-bellile, U. Castellani, J. Peyras, S. Olsen et al., Coarse-tofine low-rank structure-from-motion, IEEE Conference on Computer Vision and Pattern Recognition, pp.1-8, 2008.

A. Bartoli, Y. Gérard, F. Chadebecq, and T. Collins, On template-based reconstruction from a single view: Analytical solutions and proofs of well-posedness for developable, isometric and conformal surfaces, 2012 IEEE Conference on Computer Vision and Pattern Recognition, pp.2026-2033, 2012.
DOI : 10.1109/CVPR.2012.6247906

URL : https://hal.archives-ouvertes.fr/hal-02092764

A. Bartoli, Y. Gérard, F. Chadebecq, T. Collins, and D. Pizarro, Shape-from-Template, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.37, issue.10, pp.1-39, 2015.
DOI : 10.1109/TPAMI.2015.2392759

URL : https://hal.archives-ouvertes.fr/hal-01161841

A. Bartoli, M. Perriollat, and S. Chambon, Generalized Thin-Plate Spline Warps, IEEE Conference on Computer Vision and Pattern Recognition, pp.1-8, 2007.
DOI : 10.1007/s11263-009-0303-4

URL : https://hal.archives-ouvertes.fr/hal-00147657

A. Bartoli, D. Pizarro, and T. Collins, A Robust Analytical Solution to Isometric Shape-from-Template with Focal Length Calibration, 2013 IEEE International Conference on Computer Vision, pp.961-968, 2013.
DOI : 10.1109/ICCV.2013.123

R. Ben-ari, A Unified Approach for Registration and Depth in Depth from Defocus, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.36, issue.6, pp.1041-1055, 2014.
DOI : 10.1109/TPAMI.2014.14

S. Bhasin and S. Chaudhuri, Depth from defocus in presence of partial self occlusion, Proceedings Eighth IEEE International Conference on Computer Vision. ICCV 2001, pp.488-493, 2001.
DOI : 10.1109/ICCV.2001.937556

URL : http://dspace.library.iitb.ac.in/xmlui/bitstream/10054/462/3/20293.pdf

K. Bhat, C. Twigg, J. Hodgins, P. Khosla, Z. Popovi? et al., Estimating Cloth Simulation Parameters from Video, ACM Eurographics SIGGRAPH Symposium on Computer Animation, Eurographics Association, pp.37-51, 2003.

J. Bonnans, J. Gilbert, C. Lemaréchal, and C. Sagastizábal, Numerical optimization : theoretical and practical aspects, 2006.
DOI : 10.1007/978-3-662-05078-1

F. L. Bookstein, Principal warps: thin-plate splines and the decomposition of deformations, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.11, issue.6, pp.567-585, 1989.
DOI : 10.1109/34.24792

M. Born and E. Wolf, Principles of optics : electromagnetic theory of propagation, interference and diffraction of light 7th Edition, 1999.
DOI : 10.1017/CBO9781139644181

J. Y. Bouguet, Camera calibration toolbox for matlab, 2008.

S. Boyd and L. Vandenberghe, Convex optimization, 2004.

M. Brand, Morphable 3D models from video, Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001, 2001.
DOI : 10.1109/CVPR.2001.990997

URL : http://www.merl.com/papers/docs/TR2001-37.pdf

C. Brauer-burchardt, M. Heinze, C. Munkelt, P. Kühmstedt, and G. Notni, Distance Dependent Lens Distortion Variation in 3D Measuring Systems Using Fringe Projection, Procedings of the British Machine Vision Conference 2006, pp.34-44, 2006.
DOI : 10.5244/C.20.34

URL : http://www.macs.hw.ac.uk/bmvc2006/papers/150.pdf

C. Bregler, A. Hertzmann, and H. Biermann, Recovering non-rigid 3D shape from image streams, Proceedings IEEE Conference on Computer Vision and Pattern Recognition. CVPR 2000 (Cat. No.PR00662), pp.690-696, 2000.
DOI : 10.1109/CVPR.2000.854941

URL : http://www.mrl.nyu.edu/publications/recovering-nonrigid/bhb-cvpr00.pdf

D. Britton, Generalized Gaussian Decompositions for Image Analysis and Synthesis, 2006.
DOI : 10.1006/dspr.2002.0438

F. Brunet, Contributions to Parametric Image Registration and 3D Surface Reconstruction, 2010.

F. Brunet, A. Bartoli, and R. Hartley, Monocular template-based 3D surface reconstruction: Convex inextensible and nonconvex isometric methods, Computer Vision and Image Understanding, vol.125, pp.138-154, 2014.
DOI : 10.1016/j.cviu.2014.04.003

E. Catmull, A Subdivision Algorithm for Computer Display of Curved Surfaces, 1974.

F. Chadebecq, C. Tilmant, and A. Bartoli, Measuring the size of neoplasia in colonoscopy using depth-from-defocus, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp.1478-1481, 2012.
DOI : 10.1109/EMBC.2012.6346220

F. Chadebecq, C. Tilmant, and A. Bartoli, Estimation de l'échelle des néoplasies en coloscopie par détection de la profondeur de défocalisation, in : ORASIS-Journées francophones des jeunes chercheurs en vision par ordinateur, AFRIF, pp.1-8, 2013.

F. Chadebecq, C. Tilmant, and A. Bartoli, Using the Infocus-Breakpoint to estimate the scale of neoplasia in colonoscopy, 2013 IEEE 10th International Symposium on Biomedical Imaging, pp.354-357, 2013.
DOI : 10.1109/ISBI.2013.6556485

F. Chadebecq, C. Tilmant, and A. Bartoli, How big is this neoplasia? Live colonoscopic size measurement using the Infocus-Breakpoint, Medical Image Analysis, vol.19, issue.1, pp.58-74, 2015.
DOI : 10.1016/j.media.2014.09.002

F. Chadebecq, C. Tilmant, J. Peyras, T. Collins, and A. Bartoli, Estimation de l'échelle en coloscopie monoculaire par quantification du flou optique : étude de faisabilité, Reconnaissance des Formes et Intelligence Artificielle, pp.1-8, 2012.

A. Chakrabarti, T. Zickler, and W. Freeman, Analyzing spatially-varying blur, 2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp.12-19, 2010.
DOI : 10.1109/CVPR.2010.5539954

URL : http://www.eecs.harvard.edu/~zickler/papers/svblur_CVPR2010.pdf

C. Chang, H. Chiu, H. Wang, C. Lee, J. Tai et al., An endoscopic training model to improve accuracy of colonic polyp size measurement, International Journal of Colorectal Disease, vol.21, issue.12, pp.655-660, 2010.
DOI : 10.1067/mge.2001.114328

L. Chaptini, A. Chaaya, F. Depalma, K. Hunter, S. Peikin et al., Variation in polyp size estimation among endoscopists and impact on surveillance intervals, Gastrointestinal Endoscopy, vol.80, issue.4, pp.652-659, 2014.
DOI : 10.1016/j.gie.2014.01.053

A. Chhatkuli, D. Pizarro, and A. Bartoli, Non-Rigid Shape-from-Motion for Isometric Surfaces using Infinitesimal Planarity, Proceedings of the British Machine Vision Conference 2014, pp.1-5, 2014.
DOI : 10.5244/C.28.11

URL : http://www.bmva.org/bmvc/2014/files/abstract041.pdf

A. Chhatkuli, D. Pizarro, and A. Bartoli, Stable Template-Based Isometric 3D Reconstruction in All Imaging Conditions by Linear Least-Squares, 2014 IEEE Conference on Computer Vision and Pattern Recognition, pp.708-715, 2014.
DOI : 10.1109/CVPR.2014.96

T. Choi and J. Yun, Three-dimensional shape recovery from the focused-image surface, Optical Engineering, vol.17, issue.5, pp.1321-1326, 2000.
DOI : 10.1109/34.368191

C. Claxton, Colour depth-from-defocus incorporating experimental point spread function measurements, 2007.

C. Claxton and R. Staunton, Measurement of the point-spread function of a noisy imaging system, Journal of the Optical Society of America A, vol.25, issue.1, 2008.
DOI : 10.1364/JOSAA.25.000159

L. Cohen and I. Cohen, Finite-element methods for active contour models and balloons for 2-D and 3-D images, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.15, issue.11, pp.1131-1147, 1993.
DOI : 10.1109/34.244675

URL : http://www.ceremade.dauphine.fr/~cohen/mypapers/PAMI93.ps.gz

T. Collins and A. Bartoli, Locally affine and planar deformable surface reconstruction from video, in : Workshop on Vision, Modeling and Visualization, Eurographics Association, pp.339-346339, 2010.

R. L. Cook and K. E. Torrance, A Reflectance Model for Computer Graphics, ACM Transactions on Graphics, vol.1, 1982.
DOI : 10.1145/800224.806819

W. Crofts, The Generation of Depth Maps via Depth-from-Defocus, 2007.

I. Daubechies, Ten lectures on wavelets, 1992.

D. Bue, A. Smeraldi, F. Agapito, and L. , Non-Rigid Structure-from-Motion using non- Parametric Tracking and Non-Linear Optimization, IEEE Conference on Computer Vision and Pattern Recognition, pp.1-8, 2004.

F. Deschênes, D. Ziou, and P. Fuchs, An unified approach for a simultaneous and cooperative estimation of defocus blur and spatial shifts, Image and Vision Computing, vol.22, issue.1, 2004.
DOI : 10.1016/j.imavis.2003.08.003

F. Deschênes, D. Ziou, and P. Fuchs, A homotopy-based approach for computing defocus blur and affine transform simultaneously, Pattern Recognition, vol.41, issue.7, 2008.
DOI : 10.1016/j.patcog.2007.12.005

D. Orazio, L. Bartoli, A. Baetz, A. Beorchia, S. Calvary et al., Multimodal and multimedia image analysis and collaborative networking for digestive endoscopy, Innovation and Research in BioMedical engineering, vol.35, pp.88-94, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00953377

J. D. Durou, M. Falcone, and M. Sagona, Numerical methods for shape-from-shading: A new survey with benchmarks, Computer Vision and Image Understanding, vol.109, issue.1, 2008.
DOI : 10.1016/j.cviu.2007.09.003

J. Ens and P. Lawrence, An investigation of methods for determining depth from focus, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.15, issue.2, pp.97-108, 1993.
DOI : 10.1109/34.192482

P. Favaro, Recovering thin structures via nonlocal-means regularization with application to depth from defocus, 2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2010.
DOI : 10.1109/CVPR.2010.5540089

URL : http://lmb.informatik.uni-freiburg.de/lectures/seminar_brox/seminar_ws1011/cvpr10_favaro.pdf

P. Favaro and A. Duci, A theory of defocus via Fourier analysis, 2008 IEEE Conference on Computer Vision and Pattern Recognition, 2008.
DOI : 10.1109/CVPR.2008.4587412

URL : http://mplab.ucsd.edu/wp-content/uploads/cvpr2008/conference/data/papers/072.pdf

P. Favaro and S. Soatto, A geometric approach to shape from defocus, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.27, issue.3, pp.406-417, 2005.
DOI : 10.1109/TPAMI.2005.43

URL : http://emfs1.eps.hw.ac.uk/~pf21/pages/page2/assets/favaro-pami2005.pdf

P. Favaro, S. Soatto, M. Burger, and S. J. Osher, Shape from Defocus via Diffusion, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.30, issue.3, pp.518-531, 2008.
DOI : 10.1109/TPAMI.2007.1175

J. Florczak and M. Petko, Usage of Shape From Focus Method For 3D Shape Recovery And Identification of 3D Object Position, International Journal of Image Processing, vol.8, pp.116-124, 2014.

M. Fusaglia, D. Wallach, M. Peterhans, G. Beldi, and S. Weber, Accuracy evaluation of an image overlay in an instrument guidance system for laparoscopic liver surgery, Computer Assisted Radiology and Surgery, pp.1-6, 2012.

V. Gaganov and A. Ignatenko, Robust Shape from Focus via Markov Random Fields, pp.74-80, 2009.

P. Gargallo, P. Sturm, and S. Pujades, An Occupancy?Depth Generative Model of Multiview Images, Asian Conference on Computer Vision, pp.373-383, 2007.
DOI : 10.1007/978-3-540-76390-1_37

URL : https://hal.archives-ouvertes.fr/inria-00384276

J. Goodman, Physics Today, vol.22, issue.4, 2004.
DOI : 10.1063/1.3035549

P. Gotardo and A. Martinez, Computing Smooth Time Trajectories for Camera and Deformable Shape in Structure from Motion with Occlusion, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.33, issue.10, pp.51-65, 2011.
DOI : 10.1109/TPAMI.2011.50

P. Gotardo and A. Martinez, Non-rigid structure from motion with complementary rank-3 spaces, CVPR 2011, pp.65-72, 2011.
DOI : 10.1109/CVPR.2011.5995560

G. Granlund and H. Knutsson, Signal Processing for Computer Vision, 1995.
DOI : 10.1007/978-1-4757-2377-9

P. Grossmann, Depth from focus, Pattern Recognition Letters, vol.5, issue.1, pp.63-69, 1987.
DOI : 10.1016/0167-8655(87)90026-2

E. C. Group, Update on the Paris classification of superficial neoplastic lesions in the digestive tract, Endoscopy, vol.37, pp.570-578, 2005.

M. Hansard, S. Lee, O. Choi, and R. Horaud, Time-of-flight cameras : principles, methods and applications, 2012.
DOI : 10.1007/978-1-4471-4658-2

URL : https://hal.archives-ouvertes.fr/hal-00725654

R. Hartley and A. Zisserman, Multiple view geometry in computer vision, 2004.
DOI : 10.1017/CBO9780511811685

F. Helmli and S. Scherer, Adaptive shape from focus with an error estimation in light microscopy, ISPA 2001. Proceedings of the 2nd International Symposium on Image and Signal Processing and Analysis. In conjunction with 23rd International Conference on Information Technology Interfaces (IEEE Cat. No.01EX480), pp.188-193, 2001.
DOI : 10.1109/ISPA.2001.938626

K. Hien, P. Tongyan, W. Zhaoyang, L. Minh, N. et al., Accurate 3D shape measurement of multiple separate objects with stereo vision, Measurement Science and Technology, vol.25, pp.1-7, 2014.

B. Horn, Focusing. Artificial Intelligence Memo, vol.160, 1968.

W. Huang and Z. Jing, Evaluation of focus measures in multi-focus image fusion, Pattern Recognition Letters, vol.28, issue.4, pp.493-500, 2007.
DOI : 10.1016/j.patrec.2006.09.005

P. Huber, Robust Estimation of a Location Parameter, The Annals of Mathematical Statistics, vol.35, issue.1, pp.73-101, 1964.
DOI : 10.1214/aoms/1177703732

Y. Hyun, D. Han, J. Bae, H. Park, and C. Eun, Graduated injection needles and snares for polypectomy are useful for measuring colorectal polyp size, Digestive and Liver Disease, vol.43, issue.5, pp.391-394, 2011.
DOI : 10.1016/j.dld.2010.12.015

, Les cancers en France en 2013 Institut National du Cancer, Institut National du Cancer, 2014.

R. Jarvis, A Perspective on Range Finding Techniques for Computer Vision, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.5, issue.2, 1983.
DOI : 10.1109/TPAMI.1983.4767365

A. Kaufman and J. Wang, Visualization in Medicine and Life Sciences, 2008.

D. Kim, P. Pickhardt, A. Taylor, W. Leung, T. Winter et al., CT Colonography versus Colonoscopy for the Detection of Advanced Neoplasia, New England Journal of Medicine, vol.357, issue.14, pp.1403-1412, 2007.
DOI : 10.1056/NEJMoa070543

P. King, P. Comley, and C. Sansom, Parabolic Trough Surface form Mapping Using Photogrammetry and its Validation with a Large Coordinate Measuring Machine, Energy Procedia, vol.49, 2014.
DOI : 10.1016/j.egypro.2014.03.013

E. Krotkov, Exploratory visual sensing with an agile camera, 1987.

S. Kudo, S. Hirota, T. Nakajima, S. Hosobe, H. Kusaka et al., Colorectal tumours and pit pattern., Journal of Clinical Pathology, vol.47, issue.10, pp.880-885, 1994.
DOI : 10.1136/jcp.47.10.880

F. Leberl, A. Irschara, T. Pock, P. Meixner, M. Gruber et al., Point Clouds, Photogrammetric Engineering & Remote Sensing, vol.76, issue.10, pp.1123-11340099, 2010.
DOI : 10.14358/PERS.76.10.1123

K. Levenberg, A method for the solution of certain non-linear problems in least squares, Quarterly of Applied Mathematics, vol.2, issue.2, pp.164-168, 1944.
DOI : 10.1090/qam/10666

A. Levin, R. Fergus, F. Durand, and W. Freeman, Image and Depth from a Conventional Camera with a Coded Aperture, ACM Eurographics SIGGRAPH Symposium on Computer Animation, Eurographics Association, pp.1-9, 2007.

A. Levin, D. Lischinski, and Y. Weiss, A Closed-Form Solution to Natural Image Matting, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.30, issue.2, pp.228-242, 1177.
DOI : 10.1109/TPAMI.2007.1177

A. Li, R. Staunton, and T. Tjahjadi, Rational-operator-based depth-from-defocus approach to scene reconstruction, Journal of the Optical Society of America A, vol.30, issue.9, 2013.
DOI : 10.1364/JOSAA.30.001787

C. Li, S. Su, Y. Matsushita, K. Zhou, and S. Lin, Bayesian Depth-from-Defocus with Shading Constraints, IEEE Conference on Computer Vision and Pattern Recognition, pp.217-224, 2013.

S. Li and B. Yang, Multifocus image fusion by combining curvelet and wavelet transform, Pattern Recognition Letters, vol.29, issue.9, pp.1295-1301, 2008.
DOI : 10.1016/j.patrec.2008.02.002

G. Ligthart and F. Groen, A comparison of different autofocus algorithms, IEEE Pattern Recognition, pp.597-600, 1982.

J. Lin, X. Ji, W. Xu, and Q. Dai, Absolute Depth Estimation From a Single Defocused Image, IEEE Transactions on Image Processing, vol.22, pp.4545-4550, 2013.

J. Lin, C. Zhang, and Q. Shi, Estimating the amount of defocus through a wavelet transform approach, Pattern Recognition Letters, vol.25, issue.4, pp.407-411, 2004.
DOI : 10.1016/j.patrec.2003.11.003

A. Lobay and D. Forsyth, Shape from Texture without Boundaries, International Journal of Computer Vision, vol.17, issue.4, pp.71-91, 2006.
DOI : 10.1109/CVPR.2000.855856

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

URL : http://www.cs.ubc.ca/~lowe/papers/ijcv03.ps

Z. Ma, R. Liao, X. Tao, L. Xu, J. Jia et al., Handling motion blur in multi-frame super-resolution, IEEE Conference on Computer Vision and Pattern Recognition, pp.5224-5232, 2015.

A. Malik and T. Choi, A novel algorithm for estimation of depth map using image focus for 3D shape recovery in the presence of noise, Pattern Recognition, vol.41, issue.7, 2008.
DOI : 10.1016/j.patcog.2007.12.014

S. Mallat, A Wavelet Tour of Signal Processing, 2009.

A. Malti and A. Bartoli, Combining Conformal Deformation and Cook???Torrance Shading for 3-D Reconstruction in Laparoscopy, IEEE Transactions on Biomedical Engineering, vol.61, issue.6, 2014.
DOI : 10.1109/TBME.2014.2300237

A. Malti, A. Bartoli, and T. Collins, Template-based conformal shape-from-motion from registered laparoscopic images, Conference on Medical Image Understanding and Analysis, pp.1-7, 2011.
DOI : 10.1007/978-3-642-30618-1_1

C. Margulies, B. Krevsky, and M. Catalano, How accurate are endoscopic estimates of size?, Gastrointestinal Endoscopy, vol.40, issue.2, pp.174-17610, 1994.
DOI : 10.1016/S0016-5107(94)70162-8

J. Martínez, Algorithms for Solving Nonlinear Systems of Equations, pp.81-108, 1994.
DOI : 10.1007/978-94-009-0369-2_4

T. Mcinerney and D. Terzopoulos, A finite element model for 3D shape reconstruction and nonrigid motion tracking, 1993 (4th) International Conference on Computer Vision, pp.518-523, 1993.
DOI : 10.1109/ICCV.1993.378169

P. Meer and I. Weiss, Smoothed differentiation filters for images, IEEE Conference on Pattern Recognition, pp.121-126, 1990.
DOI : 10.1016/1047-3203(92)90030-w

R. Minhas, A. Mohammed, Q. Wu, and M. Sid-ahmed, 3D Shape from Focus and Depth Map Computation Using Steerable Filters, Lecture Notes in Computer Science, vol.13, issue.9, pp.573-583, 2009.
DOI : 10.1109/34.93808

R. Minhas, A. A. Mohammed, Q. , and J. W. , Shape from focus using fast discrete curvelet transform, Pattern Recognition, vol.44, issue.4, 2011.
DOI : 10.1016/j.patcog.2010.10.015

D. Mirota, M. Ishii, and G. Hager, Vision-Based Navigation in Image-Guided Interventions, Annual Review of Biomedical Engineering, vol.13, issue.1, pp.297-319, 2011.
DOI : 10.1146/annurev-bioeng-071910-124757

F. Moreno-noguer and P. Fua, Stochastic Exploration of Ambiguities for Nonrigid Shape Recovery, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.35, issue.2, 2013.
DOI : 10.1109/TPAMI.2012.102

URL : http://www.iri.upc.edu/people/fmoreno/Publications/PAMI13a/Pami13a.pdf

F. Moreno-noguer, J. M. Porta, and P. Fua, Exploring Ambiguities for Monocular Non-rigid Shape Estimation, pp.370-383, 2010.
DOI : 10.1007/978-3-642-15558-1_27

URL : http://upcommons.upc.edu/bitstream/2117/12544/1/Francesc.pdf

S. Moug, N. Vernall, J. Saldanha, J. Mcgregor, M. Balsitis et al., Endoscopists??? estimation of size should not determine surveillance of colonic polyps, Colorectal Disease, vol.46, issue.Suppl V, 2010.
DOI : 10.1016/S0016-5107(96)70255-9

M. Muhammad and T. Choi, Sampling for Shape from Focus in Optical Microscopy, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.34, issue.3, 2012.
DOI : 10.1109/TPAMI.2011.144

Z. Myles and V. Da-vitoria-lobo, Recovering affine motion and defocus blur simultaneously, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.20, issue.6, pp.652-658, 1998.
DOI : 10.1109/34.683782

URL : http://www.cs.ucf.edu/~vision/papers/defocusPAMI1998.pdf

V. Namboodiri and S. Chaudhuri, On defocus, diffusion and depth estimation, Pattern Recognition Letters, vol.28, issue.3, pp.311-319, 2007.
DOI : 10.1016/j.patrec.2006.04.011

V. Namboodiri and S. Chaudhuri, Recovery of relative depth from a single observation using an uncalibrated (real-aperture) camera, 2008 IEEE Conference on Computer Vision and Pattern Recognition, pp.1-6, 2008.
DOI : 10.1109/CVPR.2008.4587779

S. Nayar and Y. Nakagawa, Shape from focus, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.16, issue.8, pp.824-831, 1994.
DOI : 10.1109/34.308479

K. Ogle, , 1968.

M. Oren and S. Nayar, Generalization of the Lambertian model and implications for machine vision, International Journal of Computer Vision, vol.19, issue.1, pp.227-251, 1995.
DOI : 10.1117/12.7972479

S. Park, E. Choi, S. Lee, J. Byeon, J. Jo et al., Polyp Measurement Reliability, Accuracy, and Discrepancy: Optical Colonoscopy versus CT Colonography with Pig Colonic Specimens, Radiology, vol.244, issue.1, pp.157-164, 2007.
DOI : 10.1148/radiol.2441060794

A. Pentland, Depth of Scene from Depth of Field, in : DARPA Image Understanding Workshop, DARPA, pp.253-259, 1982.

A. Pentland, A New Sense for Depth of Field, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.9, issue.4, pp.523-531, 1987.
DOI : 10.1109/TPAMI.1987.4767940

M. Perriollat, R. Hartley, and A. Bartoli, Monocular Template-based Reconstruction of Inextensible Surfaces, International Journal of Computer Vision, vol.67, issue.2, pp.124-137, 2011.
DOI : 10.1007/s11263-005-3962-9

URL : https://hal.archives-ouvertes.fr/hal-00344576

S. Pertuz, D. Puig, and M. Garcia, Analysis of focus measure operators for shape-from-focus, Pattern Recognition, vol.46, issue.5, pp.1415-1432, 2013.
DOI : 10.1016/j.patcog.2012.11.011

S. Pertuz, D. Puig, and M. Garcia, Reliability measure for shape-from-focus, Image and Vision Computing, vol.31, issue.10, pp.725-734, 2013.
DOI : 10.1016/j.imavis.2013.07.005

D. Pizarro, A. Bartoli, and T. Collins, Isowarp and Conwarp: Warps that Exactly Comply with Weak-Perspective Projection of Deforming Objects, Procedings of the British Machine Vision Conference 2013, pp.1-11, 2013.
DOI : 10.5244/C.27.104

A. N. Pressley, Elementary Differential Geometry 2nd Edition, pp.978-979, 2010.

R. Rahmat, A. Malik, N. Kamel, and H. Nisar, 3D shape from focus using LULU operators and discrete pulse transform in the presence of noise, Journal of Visual Communication and Image Representation, vol.24, issue.3, 2013.
DOI : 10.1016/j.jvcir.2013.01.005

A. Raj, Accurate depth from defocus estimation with video-rate implementation, 2009.

A. Rajagopalan and S. Chaudhuri, An MRF model-based approach to simultaneous recovery of depth and restoration from defocused images, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.21, issue.7, pp.577-589, 1999.
DOI : 10.1109/34.777369

T. Reichl, X. Luo, M. Menzel, H. Hautmann, K. Mori et al., Hybrid electromagnetic and image-based tracking of endoscopes with guaranteed smooth output, International Journal of Computer Assisted Radiology and Surgery, vol.57, issue.3, pp.955-965, 2013.
DOI : 10.1016/j.lungcan.2004.03.005

N. Ren, Digital Light Field Photography, 2006.

F. Rooms, Estimating image blur in the wavelet domain, IEEE Conference on Acoustics , Speech, and Signal Processing, 2002.

C. Rubio, J. Jónasson, G. Nesi, J. Mazur, and E. Olafsdóttir, The Size of Colon Po ps Revisited : Intra-and Inter-observer Variations, Cancer Research and Treatment, vol.30, pp.1-2, 2010.

N. Saitoh, K. Kuroki, and K. Kurosawa, Estimation of out-of-focus blur and its effectiveness for deblurring, Investigative Image Processing, 1997.

M. Salzmann and P. Fua, Reconstructing sharply folding surfaces: A convex formulation, 2009 IEEE Conference on Computer Vision and Pattern Recognition, 2009.
DOI : 10.1109/CVPR.2009.5206759

M. Salzmann and P. Fua, Linear Local Models for Monocular Reconstruction of Deformable Surfaces, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.33, issue.5, 2011.
DOI : 10.1109/TPAMI.2010.158

URL : http://ttic.uchicago.edu/~salzmann/papers/SalzmannFuaPAMI.pdf

M. Salzmann, R. Hartley, and P. Fua, Convex Optimization for Deformable Surface 3-D Tracking, 2007 IEEE 11th International Conference on Computer Vision, pp.1-8, 2007.
DOI : 10.1109/ICCV.2007.4409031

URL : http://cvlab.epfl.ch/publications/publications/2007/SalzmannHF07.pdf

M. Salzmann, R. Urtasun, and P. Fua, Local deformation models for monocular 3D shape recovery, 2008 IEEE Conference on Computer Vision and Pattern Recognition, pp.1-8, 2008.
DOI : 10.1109/CVPR.2008.4587499

URL : http://cvlab.epfl.ch/publications/publications/2008/Salzmann08.pdf

L. Sang-yong, Y. Kumar, C. Ji-man, L. Sang-won, and K. Soo-won, Enhanced Autofocus Algorithm Using Robust Focus Measure and Fuzzy Reasoning, IEEE Transactions on Circuits and Systems for Video Technology, pp.1237-1246, 2008.
DOI : 10.1109/TCSVT.2008.924105

A. Saxena, S. Chung, and A. Ng, 3-D Depth Reconstruction from a Single Still Image, International Journal of Computer Vision, vol.35, issue.8, pp.53-69, 2008.
DOI : 10.1007/s11263-007-0071-y

URL : https://link.springer.com/content/pdf/10.1007%2Fs11263-007-0071-y.pdf

J. Schlag, A. Sanderson, C. P. , N. Wimberly, and F. , Implementation of Automatic Focusing Algorithms for a Computer Vision System with Camera Control, 1983.

C. Schmalz, F. Forster, A. Schick, and E. Angelopoulou, An endoscopic 3D scanner based on structured light, Medical Image Analysis, vol.16, issue.5, 2012.
DOI : 10.1016/j.media.2012.04.001

R. Schoen, The case for population-based screening for colorectal cancer, Nature Reviews Cancer, vol.331, issue.1, pp.65-70, 2002.
DOI : 10.1056/NEJM199412223312501

R. Schoen, L. Gerber, and C. Margulies, The pathologic measurement of polyp size is preferable to the endoscopic estimate, Gastrointestinal Endoscopy, vol.46, issue.6, pp.492-496, 1997.
DOI : 10.1016/S0016-5107(97)70002-6

S. O. Shim and T. S. Choi, A novel iterative shape from focus algorithm based on combinatorial optimization, Pattern Recognition, vol.43, issue.10, pp.3338-3347, 2010.
DOI : 10.1016/j.patcog.2010.05.029

N. Sochen, R. Kimmel, and A. Bruckstein, Diffusions and confusions in signal and image processing, Journal of Mathematical Imaging and Vision, vol.14, issue.3, pp.195-209, 2001.
DOI : 10.1023/A:1011277827470

M. Subbarao, Direct recovery of depth-map I : differential methods, IEEE workshop on computer vision, pp.58-65, 1987.

M. Subbarao, Parallel Depth Recovery By Changing Camera Parameters, [1988 Proceedings] Second International Conference on Computer Vision, pp.149-155, 1988.
DOI : 10.1109/CCV.1988.589986

URL : http://www.ee.sunysb.edu/~cvl/Publications/MSubbarao_ICCV1988.ps

M. Subbarao, Efficient depth recovery through inverse optics. Machine Vision for Inspection and Measurement, pp.101-126, 1989.
DOI : 10.1016/b978-0-12-266719-0.50008-7

URL : http://www.ee.sunysb.edu/~cvl/Publications/MSubbarao_Book1989.ps

M. Subbarao and T. Choi, Accurate recovery of three-dimensional shape from image focus, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.17, issue.3, pp.266-274, 1995.
DOI : 10.1109/34.368191

URL : http://www.ee.sunysb.edu/~cvl/Publications/TSChoi_PAMI1995.ps

M. Subbarao and N. Gurumoorthy, Depth recovery from blurred edges, Proceedings CVPR '88: The Computer Society Conference on Computer Vision and Pattern Recognition, pp.498-503, 1988.
DOI : 10.1109/CVPR.1988.196281

M. Subbarao and G. Surya, Depth from defocus: A spatial domain approach, International Journal of Computer Vision, vol.9, issue.4, pp.271-294, 1994.
DOI : 10.1016/B978-0-12-266719-0.50008-7

URL : http://www.ee.sunysb.edu/~cvl/Publications/Surya_IJCV1994.ps

I. Talbot, Redetection and growth of colorectal polyps., Gut, vol.39, issue.3, 1996.
DOI : 10.1136/gut.39.3.492

URL : http://gut.bmj.com/content/gutjnl/39/3/492.full.pdf

M. Tao, S. Hadap, J. Malik, and R. Ramamoorthi, Depth from Combining Defocus and Correspondence Using Light-Field Cameras, 2013 IEEE International Conference on Computer Vision, pp.673-680, 2013.
DOI : 10.1109/ICCV.2013.89

URL : http://www.eecs.berkeley.edu/~ravir/lightfield_ICCV.pdf

A. Thelen, S. Frey, S. Hirsch, and P. Hering, Improvements in Shape-From-Focus for Holographic Reconstructions With Regard to Focus Operators, Neighborhood-Size, and Height Value Interpolation, IEEE Transactions on Image Processing, vol.18, issue.1, pp.151-157, 2008.
DOI : 10.1109/TIP.2008.2007049

L. Torresani, A. Hertzmann, and C. Bregler, Nonrigid Structure-from-Motion: Estimating Shape and Motion with Hierarchical Priors, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.30, issue.5, pp.878-892, 2007.
DOI : 10.1109/TPAMI.2007.70752

URL : http://research.microsoft.com/~ltorre/Papers/TorrHertzBreg-pami07.pdf

L. Tsap, D. Goldof, and S. Sarkar, Nonrigid motion analysis based on dynamic refinement of finite element models, IEEE Conference on Computer Vision and Pattern Recognition, pp.728-734, 1998.
DOI : 10.1109/34.857007

URL : http://marathon.csee.usf.edu/~tsap/./proj_pami_cvpr2.ps.gz

A. Varol, M. Salzmann, E. Tola, and P. Fua, Template-free monocular reconstruction of deformable surfaces, 2009 IEEE 12th International Conference on Computer Vision, pp.1811-1818, 2009.
DOI : 10.1109/ICCV.2009.5459403

URL : https://infoscience.epfl.ch/record/140284/files/VarolSTF09a.pdf

S. Vicente and L. Agapito, Soft Inextensibility Constraints for Template-Free Non-rigid Reconstruction, European Conference on Computer Vision, pp.426-440, 2012.
DOI : 10.1007/978-3-642-33712-3_31

URL : http://www0.cs.ucl.ac.uk/staff/S.Vicente/papers/ECCV2012.pdf

M. Watanabe and S. Nayar, Rational Filters for Passive Depth from Defocus, International Journal of Computer Vision, vol.27, issue.3, pp.203-225, 1998.
DOI : 10.1023/A:1007905828438

C. Wee and R. Paramesran, Measure of image sharpness using eigenvalues, Information Sciences, vol.177, issue.12, 2007.
DOI : 10.1016/j.ins.2006.12.023

Y. Wei, Z. Dong, and C. Wu, Global depth from defocus with fixed camera parameters, IEEE Conference on Mechatronics and Automation, 2009.

Y. Wei, Z. Dong, and C. Wu, Depth measurement using single camera with fixed camera parameters, IET Computer Vision, vol.6, issue.1, 2012.
DOI : 10.1049/iet-cvi.2010.0017

L. Wenguo, F. Suping, and D. Shaojun, 3D shape measurement based on structured light projection applying polynomial interpolation technique, Optik -Light and Electron Optics, vol.124, 2013.

, World Health Organization World Cancer Report. International Agency for Research on Cancer. URL, 2008.

J. Xiao and T. Kanade, Uncalibrated perspective reconstruction of deformable structures, IEEE Conference on Computer Vision, 2005.

H. Xie, W. Rong, and L. Sun, Wavelet-Based Focus Measure and 3-D Surface Reconstruction Method for Microscopy Images, 2006 IEEE/RSJ International Conference on Intelligent Robots and Systems, pp.229-234, 2006.
DOI : 10.1109/IROS.2006.282641

Y. Xiong and S. Shafer, Moment and Hypergeometric Filters for High Precision Computation of Focus, Stereo and Optical Flow, International Journal of Computer Vision, vol.22, issue.1, pp.25-59, 1997.
DOI : 10.1023/A:1007927810205

G. Yang and B. Nelson, Wavelet-based autofocusing and unsupervised segmentation of microscopic images, IEEE Conference on Intelligent Robots and Systems, 2003.

J. Yang and D. Schonfeld, Virtual Focus and Depth Estimation From Defocused Video Sequences, IEEE Transactions on Image Processing, vol.19, issue.3, pp.668-679, 2009.
DOI : 10.1109/TIP.2009.2036708

X. Zhang, Z. Liu, M. Jiang, and M. Chang, Fast and accurate auto-focusing algorithm based on the combination of depth from focus and improved depth from defocus, Optics Express, vol.22, issue.25, pp.31237-31247, 2014.
DOI : 10.1364/OE.22.031237

C. Zhou, S. Lin, and S. Nayar, Coded Aperture Pairs for Depth-from-Defocus, IEEE Conference on Computer Vision, IEEE, pp.325-332, 2009.

X. Zhu, S. Cohen, S. Schiller, and P. Milanfar, Estimating Spatially Varying Defocus Blur From A Single Image, IEEE Transactions on Image Processing, vol.22, issue.12, 2013.
DOI : 10.1109/TIP.2013.2279316

S. Zhuo and T. Sim, On the Recovery of Depth from a Single Defocused Image, Computer Analysis of Images and Patterns, vol.5702, pp.889-897, 2009.
DOI : 10.1007/978-3-642-03767-2_108

S. Zhuo and T. Sim, Defocus map estimation from a single image, Pattern Recognition, vol.44, issue.9, pp.1852-1858, 2011.
DOI : 10.1016/j.patcog.2011.03.009

D. Ziou, Passive depth from defocus using a spatial domain approach, Sixth International Conference on Computer Vision (IEEE Cat. No.98CH36271), pp.799-804, 1998.
DOI : 10.1109/ICCV.1998.710809

URL : http://www.dmi.usherb.ca/~moivre/files/iccv98.ps.gz

D. Ziou and F. Deschênes, Depth from Defocus Estimation in Spatial Domain, Computer Vision and Image Understanding, vol.81, issue.2, 2001.
DOI : 10.1006/cviu.2000.0899

URL : http://www.dmi.usherb.ca/~moivre/files/rep_dfd99.ps.gz