Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
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Bibliography

Major publications by the team in recent years
[1]
A. Basset, J. Boulanger, J. Salamero, P. Bouthemy, C. Kervrann.
Adaptive spot detection with optimal scale selection in fluorescence microscopy images, in: IEEE Transactions on Image Processing, November 2015, vol. 24, no 11, 16 p. [ DOI : 10.1109/TIP.2015.2450996 ]
https://hal.inria.fr/hal-01248290
[2]
A. Basset, P. Bouthemy, J. Boulanger, F. Waharte, J. Salamero, C. Kervrann.
An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images, in: BMC Bioinformatics, 2017, vol. 18, no 1, 352 p. [ DOI : 10.1186/s12859-017-1765-y ]
https://hal.inria.fr/hal-01561310
[3]
J. Boulanger, A. Gidon, C. Kervrann, J. Salamero.
A patch-based method for repetitive and transient event detection in fluorescence imaging, in: PLoS ONE, Oct 2010, vol. 5, no 10. [ DOI : 10.1371/journal.pone.0013190 ]
[4]
J. Boulanger, C. Kervrann, P. Bouthemy.
Space-time adaptation for patch based image sequence restoration, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, 2007, vol. 29, no 6, pp. 1096–1102.
[5]
J. Boulanger, C. Kervrann, P. Bouthemy.
A simulation and estimation framework for intracellular dynamics and trafficking in video-microscopy and fluorescence imagery, in: Medical Image Analysis, 2009, vol. 13, pp. 132–142.
[6]
J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero.
Patch-based nonlocal functional for denoising fluorescence microscopy image sequences, in: IEEE Transactions on Medical Imaging, Feb 2010, vol. 29, no 2, pp. 442-453. [ DOI : 10.1109/TMI.2009.2033991 ]
[7]
P.M. Carlton, J. Boulanger, C. Kervrann, J.-B. Sibarita, J. Salamero, S. Gordon-Messer, J. Haber, S. Haase, L. Shao, L. Winoto, A. Matsuda, P. Kner, S. Usawa, Y. Strukov, M. Gustafsson, Z. Kam, D. Agard, J.W. Sedat.
Fast live simultaneous multiwavelength four-dimensional optical microscopy, in: Proc Natl Acad Sci USA, Sep 2010, vol. 107, no 37, pp. 16016-16022. [ DOI : 10.1073/pnas.1004037107 ]
[8]
N. Chenouard, I. Smal, F. De Chaumont, M. Maska, I. F. Sbalzarini, Y. Gon, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. Magnusson, J. Jalden, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.-Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. Van Wezel, H.-W. Dan, Y.-S. Tsai, C. Ortiz De Solorzano, J.-C. Olivo-Marin, E. Meijering.
Objective comparison of particle tracking methods, in: Nature Methods, 2014, vol. 11, no 3, pp. 281–289. [ DOI : 10.1038/nmeth.2808 ]
https://hal.inria.fr/hal-00932869
[9]
T. Crivelli, B. Cernuschi-Frias, P. Bouthemy, J.-F. Yao.
Motion Textures: Modeling, Classification, and Segmentation Using Mixed-State, in: SIAM Journal on Imaging Sciences, December 2013, vol. 6, no 4, pp. 2484-2520. [ DOI : 10.1137/120872048 ]
https://hal.inria.fr/hal-00931667
[10]
A. Gidon, S. Bardin, B. Cinquin, J. Boulanger, F. Waharte, L. Héliot, H. De La Salle, D. Hanau, C. Kervrann, B. Goud, J. Salamero.
A Rab11A/myosin Vb/Rab11-FIP2 complex frames two late recycling steps of langerin from the ERC to the plasma membrane, in: Traffic, April 2012, vol. 13, no 6, pp. 815-833. [ DOI : 10.1111/j.1600-0854.2012.01354.x ]
https://hal.inria.fr/hal-00782005
[11]
C. Kervrann, J. Boulanger.
Optimal spatial adaptation for patch-based image denoising, in: IEEE Transactions on Image Processing, 2006, vol. 15, no 10, pp. 2866–2878.
[12]
C. Kervrann, J. Boulanger.
Local adaptivity to variable smoothness for exemplar-based image denoising and representation, in: International Journal of Computer Vision, August 2008, vol. 79, no 1, pp. 45–69.
[13]
C. Kervrann.
PEWA: Patch-based Exponentially Weighted Aggregation for image denoising, in: NIPS - Neural Information Processing Systems, Montreal, Canada, Neural Information Processing Systems Foundation, December 2014.
https://hal.inria.fr/hal-01103358
[14]
T. Pécot, P. Bouthemy, J. Boulanger, A. Chessel, S. Bardin, J. Salamero, C. Kervrann.
Background Fluorescence Estimation and Vesicle Segmentation in Live Cell Imaging with Conditional Random Fields, in: IEEE Transactions on Image Processing, February 2015, vol. 24, no 2, 14 p. [ DOI : 10.1109/TIP.2014.2380178 ]
https://hal.inria.fr/hal-01103126
Publications of the year

Doctoral Dissertations and Habilitation Theses

[15]
B. M. Toledo Acosta.
Multimodal image registration in 2D and 3D correlative microscopy, Rennes 1, May 2018.
https://tel.archives-ouvertes.fr/tel-01868852

Articles in International Peer-Reviewed Journals

[16]
V. Briane, C. Kervrann, M. Vimond.
Statistical analysis of particle trajectories in living cells, in: Physical Review E , June 2018.
https://hal.inria.fr/hal-01961971
[17]
H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann.
A variational method for dejittering large fluorescence line scanner images, in: IEEE Transactions on Computational Imaging, June 2018, vol. 4, no 2, 16 p.
https://hal.inria.fr/hal-01577139
[18]
H.-N. Nguyen, V. Paveau, C. Cauchois, C. Kervrann.
ATMAD : robust image analysis for Automatic Tissue MicroArray De-arraying, in: BMC Bioinformatics, April 2018, vol. 19, no 148, 23 p.
https://hal.inria.fr/hal-01577238
[19]
T. Pécot, L. Zengzhen, J. Boulanger, J. Salamero, C. Kervrann.
A quantitative approach for analyzing the spatio-temporal distribution of 3D intracellular events in fluorescence microscopy, in: eLife, August 2018.
https://hal.inria.fr/hal-01966817
[20]
J.-M. Pérez-Rúa, O. Miksik, T. Crivelli, P. Bouthemy, P. H. S. Torr, P. Pérez.
ROAM: a Rich Object Appearance Model with Application to Rotoscoping, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, November 2018.
https://hal.inria.fr/hal-01923059

Invited Conferences

[21]
C. Kervrann.
Computational methods for fluorescence microscopy and intracellular dynamics analysis, in: Workshop on "Reverse Mathematical Methods for Reconstructing Molecular Dynamics in Single Cell", Pisa, Italy, October 2018.
https://hal.inria.fr/hal-01962608
[22]
C. Kervrann.
Computational methods for fluorescence microscopy and quantitative bioimaging, in: NEUBIAS - Network of European Bioimage Analysts, Szeged, Hungary, January 2018.
https://hal.inria.fr/hal-01962562
[23]
C. Kervrann.
GcoPS: a fast automatic colocalization method for 3D live cell imaging and super-resolution microscopy, in: SIAM Conference on Imaging Science, Bologna, Italy, June 2018.
https://hal.inria.fr/hal-01962601

International Conferences with Proceedings

[24]
A. Caranfil, Y. Le Cunff, C. Kervrann, J. Pecreaux.
Modelling oscillatory behavior in asymmetric division of C.elegans embryo, in: Mathematical Biology Days, Besancon, France, June 2018.
https://hal.inria.fr/hal-01970360
[25]
C. Kervrann.
GcoPS: a Geo-coPositionning System for live cell imaging and superresolution microscopy, in: Quantitative BioImaging (QBI), Gottingen, Germany, January 2018.
https://hal.inria.fr/hal-01962578
[26]
S. Manandhar, P. Bouthemy, E. Welf, P. Roudot, C. Kervrann.
A sparse-to-dense method for 3D optical flow estimation in 3D light microscopy image sequences, in: IEEE International Symposium on Biomedical Imaging (ISBI), Washington DC, United States, April 2018.
https://hal.inria.fr/hal-01960109
[27]
E. Moebel, C. Kervrann.
A Monte Carlo framework for denoising and missing wedge reconstruction in cryo-electron tomography, in: 4th International Workshop on Patch-based Techniques in Medical Imaging, Grenade, Spain, September 2018.
https://hal.inria.fr/hal-01961938
[28]
B. M. Toledo Acosta, X. Heiligenstein, G. Malandain, P. Bouthemy.
Intensity-based matching and registration for 3D correlative microscopy with large discrepancies, in: ISBI 2018 - IEEE 15th International Symposium on Biomedical Imaging, Washington, United States, IEEE, April 2018, pp. 493-496. [ DOI : 10.1109/ISBI.2018.8363623 ]
https://hal.inria.fr/hal-01930740

National Conferences with Proceedings

[29]
L. Maczyta, P. Bouthemy, O. Le Meur.
Détection temporelle de saillance dynamique dans des vidéos par apprentissage profond, in: RFIAP 2018 - Reconnaissance des Formes, Image, Apprentissage et Perception, Marne-la-Vallée, France, June 2018, pp. 1-8.
https://hal.inria.fr/hal-01926351

Other Publications

[30]
V. Briane, M. Vimond, C. Kervrann.
An overview of diffusion models for intracellular dynamics analysis, December 2018, working paper or preprint.
https://hal.inria.fr/hal-01966825
[31]
V. Briane, M. Vimond, C. A. Valades Cruz, A. Salomon, C. Wunder, C. Kervrann.
A sequential algorithm to detect diffusion switching along intracellular particle trajectories, December 2018, working paper or preprint.
https://hal.inria.fr/hal-01966831
[32]
F. Lavancier, A. Poinas, R. Waagepetersen.
Adaptive estimating function inference for non-stationary determinantal point processes, 2018, working paper or preprint.
https://hal.archives-ouvertes.fr/hal-01816528
[33]
E. Moebel, C. Kervrann.
A Monte Carlo framework for noise removal and missing wedge restoration in cryo-electron tomography, December 2018, working paper or preprint.
https://hal.inria.fr/hal-01966821
[34]
E. Moebel, A. Martinez, D. Larivière, J. Ortiz, W. Baumeister, C. Kervrann.
3D ConvNet improves macromolecule localization in 3D cellular cryo-electron tomograms, December 2018, working paper or preprint.
https://hal.inria.fr/hal-01966819
[35]
J.-M. Pérez-Rúa, T. Crivelli, P. Bouthemy, P. Pérez.
Learning how to be robust: Deep polynomial regression, November 2018, working paper or preprint.
https://hal.inria.fr/hal-01923068
References in notes
[36]
D. Axelrod.
Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
[37]
E. Betzig, G. Patterson, R. Sougrat, O. Lindwasser, S. Olenych, J. Bonifacino, M. Davidson, J. Lippincott-Schwartz, H. Hess.
Imaging intracelluar fluorescent proteins at nanometer resolution, in: Science, 2006, vol. 313, pp. 1642–1645.
[38]
A. Chessel, B. Cinquin, S. Bardin, J. Salamero, C. Kervrann.
Computational geometry-based scale-space and modal image decomposition: application to light video-microscopy imaging, in: Conf. on Scale Space and Variational Methods (SSVM'09), Voss, Norway, June 2009, pp. 770–781.
[39]
T. Crivelli, P. Bouthemy, B. Cernuschi-Frias, J.-F. Yao.
Simultaneous motion detection and background reconstruction with a conditional mixed-state Markov random field, in: International Journal of Computer Vision, 2011, vol. 94, no 3, pp. 295–316.
[40]
M. Gustafsson, L. Shao, P.M. Carlton, R. Wang, I. Golubovskaya, W. Cande, D. Agard, J.W. Sedat.
3D resolution doubling in wide-filed fluorescence microscopy by structured illumination, in: Biophysical J., 2008, vol. 94, pp. 4957–4970.
[41]
N. Hoze, D. Nair, E. Hosy, C. Sieben, S. Manley, A. Herrmann, J.-B. Sibarita, D. Choquet, D. Holcman.
Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging, in: Proc. Natl. Academy Sciences, 2012, vol. 10, no 42, pp. 17052-17057.
[42]
J. Li, F. Luisier, T. Blu.
PURE-LET image deconvolution, in: IEEE Trans. Image Processing, 2018, vol. 27, no 1, pp. 92–105.
[43]
S. Ozere, P. Bouthemy, F. Spindler, P. Paul-Gilloteaux, C. Kervrann.
Robust parametric stabilization of moving cells with intensity correction in light microscopy image sequences, in: 10th International Symposium on Biomedical Imaging (ISBI), IEEE, 2013, pp. 468–471.
[44]
M. Pinot, V. Steiner, B. Dehapiot, B.-K. Yoo, F. Chesnel, L. Blanchoin, C. Kervrann, Z. Gueroui.
Confinement induces actin flow in a meiotic cytoplasm, in: Proceedings National Academy of Sciences USA, July 2012, vol. 109, no 29, pp. 11705–11710. [ DOI : 10.1073/pnas.1121583109 ]
http://hal.inria.fr/inserm-00717415