Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 1S. Ben Hadj.
  Restauration d'images 3D de microscopie de fluorescence en présence d'aberrations optiques, Université Nice Sophia Antipolis, April 2013.
  http://hal.inria.fr/tel-00847334

Articles in International Peer-Reviewed Journals

• 2M. Breuilly, G. Malandain, J. Guglielmi, R. Marsault, T. Pourcher, P. Franken, J. Darcourt.
  Amplitude-based data selection for optimal retrospective reconstruction in micro-SPECT, in: Physics in Medicine and Biology, April 2013, vol. 58, n^o 8, pp. 2657-2674. [ DOI : 10.1088/0031-9155/58/8/2657 ]
  http://hal.inria.fr/hal-00799381

Invited Conferences

• 3A. Habbal, H. Barelli, G. Malandain.
  Modeling cell sheet wound closure, in: Applied Mathematics, Modeling and Computational Science (AMMCS), Waterloo, Ontario, Canada, Wilfrid Laurier University with AIMS and SIAM, 2013.
  http://hal.inria.fr/hal-00923626

International Conferences with Proceedings

• 4S. Ben Hadj, L. Blanc-Féraud, G. Aubert, G. Engler, E. Maalouf, B. Colicchio, A. Dieterlen.
  Blind depth-variant blur removal in confocal microscopy, in: ISBI - International Symposium on Biomedical Imaging, San Francisco, United States, IEEE, April 2013.
  http://hal.inria.fr/hal-00920191
• 5S. Ben Hadj, L. Blanc-Féraud, G. Aubert, E. Gilbert.
  Blind restoration of confocal microscopy images in presence of a depth-variant blur and Poisson noise, in: ICASSP - International Conference on Acoustics, Speech and Signal Processing, Vancouver, Canada, IEEE, May 2013.
  http://hal.inria.fr/hal-00920192
• 6S. Ben Hadj, L. Blanc-Féraud, E. Gilbert.
  Depth-variant blind restoration with pupil-phase constraints for 3D confocal microscopy, in: 3rd International Workshop on New Computational Methods for Inverse Problems, Paris, France, May 2013.
  http://hal.inria.fr/hal-00920193
• 7T. Benseghir, G. Malandain, R. Vaillant.
  Iterative Closest Curve: a Framework for Curvilinear Structure Registration Application to 2D/3D Coronary Arteries Registration, in: MICCAI - Medical Image Computing and Computer Assisted Intervention, Nagoya, Japan, K. Mori, I. Sakuma, Y. Sato, C. Barillot, N. Navab (editors), Lecture Notes in Computer Science, Springer, 2013, vol. 8149, pp. 179-186. [ DOI : 10.1007/978-3-642-40811-3_23 ]
  http://hal.inria.fr/hal-00833196
• 8M. Breuilly, G. Malandain, N. Ayache, J. Guglielmi, T. Pourcher, P. Franken, J. Darcourt.
  Image-based motion detection in 4D images and application to respiratory motion suppression, in: ISBI - International Symposium on Biomedical Imaging, San Francisco, United States, IEEE, April 2013, pp. 792-795.
  http://hal.inria.fr/hal-00799368
• 9R. Cavicchioli, C. Chaux, L. Blanc-Féraud, L. Zanni.
  ML estimation of wavelet regularization hyperparameters in inverse problems, in: ICASSP - International Conference on Acoustics, Speech, and Signal Processing, Vancouver, Canada, IEEE, May 2013, 5 p.
  http://hal.inria.fr/hal-00825819
• 10X. Descombes, G. Malandain, C. Fonta, L. Negyessy, R. Mosko.
  Automatic dendrite spines detection from X-ray tomography volumes, in: ISBI - International Symposium on Biomedical Imaging, San fancisco, United States, IEEE, 2013.
  http://hal.inria.fr/hal-00793573
• 11A. Gamal Eldin, G. Charpiat, X. Descombes, J. Zerubia.
  An efficient optimizer for simple point process models, in: SPIE, Computational Imaging XI, Burlingame, California, United States, C. A. Bouman, I. Pollak, P. J. Wolfe (editors), SPIE Proceedings, SPIE, February 2013, vol. 8657. [ DOI : 10.1117/12.2009238 ]
  http://hal.inria.fr/hal-00801448
• 12L. Guignard, C. Godin, U.-M. Fiuza, L. Hufnagel, P. Lemaire, G. Malandain.
  Spatio-temporal registration of embryo images, in: ISBI - International Symposium on Biomedical Imaging, Pekin, China, IEEE, April 2014.
  http://hal.inria.fr/hal-00919142
• 13G. Michelin, L. Guignard, U.-M. Fiuza, G. Malandain.
  Embryo Cell Membranes Reconstruction by Tensor Voting, in: ISBI - International Symposium on Biomedical Imaging, Beijing, China, IEEE, April 2014.
  http://hal.inria.fr/hal-00915000
• 14A. Mottini, X. Descombes, F. Besse.
  Tree-like Shapes Distance Using the Elastic Shape Analysis Framework, in: BMVC - British Machine Vision Conference, Bristol, United Kingdom, September 2013.
  http://hal.inria.fr/hal-00875475
• 15A. Mottini, X. Descombes, F. Besse.
  Axonal Tree Classification Using an Elastic Shape Analysis Based Distance, in: ISBI - International Symposium on Biomedical Imaging, Beijing, China, IEEE, April 2014.
  http://hal.inria.fr/hal-00920765
• 16S. Prigent, X. Descombes, D. Zugaj, L. Petit, J. Zerubia.
  Multi-scale analysis of skin hyper-pigmentation evolution, in: ICIP - International Conf. on Image Processing, Melbourne, Australia, IEEE, September 2013.
  http://hal.inria.fr/hal-00841460
• 17E. Soubies, L. Blanc-Féraud, S. Schaub, G. Aubert.
  A 3D model with shape prior information for biological structures reconstruction using Multiple-Angle Total Internal Reflection Fluorescence Microscopy, in: ISBI - International Symposium on Biomedical Imaging, Beijing, China, IEEE, April 2014.
  http://hal.inria.fr/hal-00914998
• 18E. Soubiès, P. Weiss, X. Descombes.
  A 3D segmentation algorithm for ellipsoidal shapes. Application to nuclei extraction., in: ICPRAM - International Conference on Pattern Recognition Applications and Methods, Barcelona, Spain, 2013, pp. 97-105, ISBN 978-989-8565-41-9.
  http://hal.inria.fr/hal-00733187
• 19H.-F. Yang, X. Descombes, S. Prigent, G. Malandain, X. Druart, F. Plouraboué.
  Head Tracking and Flagellum Tracing for Sperm Motility Analysis, in: ISBI - International Symposium on Biomedical Imaging, Beijing, China, IEEE, April 2014.
  http://hal.inria.fr/hal-00909868
• 20A. Zubiolo, B. André, D. Eric, G. Malandain.
  A Recursive Approach For Multiclass Support Vector Machine: Application to Automatic Classification of Endomicroscopic Videos, in: VISAPP - International Conference on Computer Vision Theory and Applications, Lisbon, Portugal, January 2014.
  http://hal.inria.fr/hal-00905382

National Conferences with Proceedings

• 21S. Ben Hadj, L. Blanc-Féraud, E. Gilbert.
  Restauration aveugle d'image 3D de microscopie de fluorescence avec prise en compte des aberrations sphériques et contrainte de phase, in: Colloque Gretsi, Brest, France, September 2013.
  http://hal.inria.fr/hal-00920194
• 22M. Carlavan, L. Blanc-Féraud, M. Antonini, C. Thiebaut, C. Latry, Y. Bobichon.
  Optimisation jointe de la chaîne codage/débruitage pour les images satellite, in: GRETSI, Brest, France, 2013.
  http://hal.inria.fr/hal-00920794

Conferences without Proceedings

• 23H. Barelli, M. Pinot, T. Ferreira, G. Malandain, X. Descombes, B. Goud, B. Antonny.
  Mechanical properties of the plasma membrane of micropatterned cells incubated with mono or polyunsaturated fatty acids, in: American Society for Cell Biology (ASCB) Annual Meeting, New Orleans, United States, 2013.
  http://hal.inria.fr/hal-00909849

Scientific Books (or Scientific Book chapters)

• 24X. Descombes.
  Markov Models and MCMC Algorithms in Image Processing, in: Academic Press Library in Signal Processing, R. Chelappa (editor), Elsevier Ltd, November 2013, vol. 4.
  http://hal.inria.fr/hal-00904989
• 25P. Pankajakshan, G. Engler, L. Blanc-Féraud, J. Zerubia.
  Deconvolution and denoising for computational microscopy, in: Modeling in Computational Biology and Biomedecine. A Multidisciplinary Endeavor, F. Cazals, P. Kornprobst (editors), Springer, 2013, vol. XXVI, pp. 117-164.
  http://hal.inria.fr/hal-00766226

Internal Reports

• 26M. Carlavan, L. Blanc-Féraud, M. Antonini, C. Thiebaut, C. Latry, Y. Bobichon.
  Joint coding-denoising optimization of noisy images, 2013.
  http://hal.inria.fr/hal-00773604
• 27M. Carlavan, L. Blanc-Féraud, M. Antonini, C. Thiebaut, C. Latry, Y. Bobichon.
  On the optimization of the satellite imaging chain, 2013.
  http://hal.inria.fr/hal-00773606

Other Publications

• 28A. Habbal, H. Barelli, G. Malandain.
  Assessing the ability of the 2D Fisher-KPP equation to model cell-sheet wound closure, 2013.
  http://hal.inria.fr/hal-00923588

References in notes

• 29A. Axelrod, E. Hellen, R. Fulbright.
  Total internal reflection fluorescence, in: Topics in fluorescence spectrometry, Springer, 2002, pp. 289-343.
• 30A. Egner, S. Hell.
  Aberrations in confocal and multi-photon fluorescence microscopy induced by refractive index mismatch, in: Handbook of Biological Confocal Microscopy, 2006, pp. 404–413.
• 31B. Hanser, M. Gustafsson, D. Agard, J. Sedat.
  Phase retrieval for high-numerical-aperture optical systems, in: Optics letters, 2003, vol. 28, n^o 10, pp. 801–803.
• 32K. Mosaliganti, R. Noche, F. Xiong, I. Swinburne, S. Megason.
  Acme: automated cell morphology extractor for comprehensive reconstruction of cell membranes, in: PLoS Comput. Biol., 2012, vol. 8, n^o 12.
• 33A. Mottini, X. Descombes, F. Besse.
  Axon extraction from fluorescent confocal microscopy images, in: Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on, 2012, pp. 764-767. [ DOI : 10.1109/ISBI.2012.6235660 ]
• 34A. Srivastava, E. Klassen, S. Joshi, I. Jermyn.
  Shape Analysis of Elastic Curves in Euclidean Spaces, in: Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2011, vol. 33, n^o 7, pp. 1415-1428. [ DOI : 10.1109/TPAMI.2010.184 ]
• 35P. Stokseth.
  Properties of a defocused optical system, in: JOSA, 1969, vol. 59, n^o 10, pp. 1314–1321.
• 36M. Van Lieshout.
  Markov point processes and Their Applications, Impewrial College Press, 2000.