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, 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 ]
[5]
V. Briane, C. Kervrann, M. Vimond.
Statistical analysis of particle trajectories in living cells, in: Physical Review E , June 2018, vol. 97, no 6, pp. 1-20. [ DOI : 10.1103/PhysRevE.97.062121 ]
https://hal.inria.fr/hal-01961971
[6]
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 ]
[7]
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
[8]
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
[9]
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
[10]
T. Pécot, C. Kervrann, J. Salamero, J. Boulanger.
Counting-based particle flux estimation for traffic analysis in live cell imaging, in: IEEE Journal of Selected Topics in Signal Processing, September 2015. [ DOI : 10.1109/JSTSP.2015.2482460 ]
https://hal.inria.fr/hal-01244946
Publications of the year

Doctoral Dissertations and Habilitation Theses

[11]
S. Manandhar.
3D Motion Estimation and Assessment in Fluorescence Microscopy Volume Sequences, Université de Rennes 1 [UR1], November 2019.
https://hal.archives-ouvertes.fr/tel-02418551
[12]
E. Moebel.
New strategies for the identification and enumeration of macromolecules in 3D images of cryo electron tomography, Université de Rennes 1, February 2019.
https://hal.inria.fr/tel-02153877

Articles in International Peer-Reviewed Journals

[13]
P. Bouthemy, B. M. Toledo Acosta, B. Delyon.
Robust model selection in 2D parametric motion estimation, in: Journal of Mathematical Imaging and Vision, September 2019, vol. 61, no 7, pp. 1022-1036. [ DOI : 10.1007/s10851-019-00883-2 ]
https://hal.archives-ouvertes.fr/hal-02315977
[14]
V. Briane, A. Salomon, M. Vimond, C. Kervrann.
A computational approach for detecting microdomains and confinement domains in cells: a simulation study, in: Physical Biology, December 2019, pp. 1-26, forthcoming. [ DOI : 10.1088/1478-3975/ab5e1d ]
https://hal.inria.fr/hal-02424860
[15]
V. Briane, M. Vimond, C. Kervrann.
An overview of diffusion models for intracellular dynamics analysis, in: Briefings in Bioinformatics, June 2019, pp. 1-15. [ DOI : 10.1093/bib/bbz052 ]
https://hal.inria.fr/hal-02424761
[16]
V. Briane, M. Vimond, C. A. Valadés-Cruz, A. Salomon, C. Wunder, C. Kervrann.
A sequential algorithm to detect diffusion switching along intracellular particle trajectories, in: Bioinformatics, June 2019, pp. 1-13. [ DOI : 10.1093/bioinformatics/btz489 ]
https://hal.inria.fr/hal-02424777
[17]
B. Combès, S. Prima.
An efficient EM-ICP algorithm for non-linear registration of large 3D point sets, in: Computer Vision and Image Understanding, November 2019, pp. 1-14. [ DOI : 10.1016/j.cviu.2019.102854 ]
https://hal.inria.fr/hal-02414127
[18]
F. Lavancier, A. Poinas, R. Waagepetersen.
Adaptive estimating function inference for non-stationary determinantal point processes, in: Scandinavian Journal of Statistics, 2019, pp. 1-35, forthcoming.
https://hal.archives-ouvertes.fr/hal-01816528
[19]
F. Lavancier, T. Pécot, L. Zengzhen, C. Kervrann.
Testing independence between two random sets for the analysis of colocalization in bioimaging, in: Biometrics, August 2019. [ DOI : 10.1111/biom.13115 ]
https://hal.archives-ouvertes.fr/hal-02369555
[20]
L. Maczyta, P. Bouthemy, O. Le Meur.
CNN-based temporal detection of motion saliency in videos, in: Pattern Recognition Letters, December 2019, vol. 128, pp. 298-305. [ DOI : 10.1016/j.patrec.2019.09.016 ]
https://hal.inria.fr/hal-02345209
[21]
S. Manandhar, P. Bouthemy, E. Welf, G. Danuser, P. Roudot, C. Kervrann.
3D Flow Field Estimation and Assessment for Live Cell Fluorescence Microscopy, in: Bioinformatics, October 2019, pp. 1-19, forthcoming. [ DOI : 10.1093/bioinformatics/btz780 ]
https://hal.archives-ouvertes.fr/hal-02308001
[22]
E. Moebel, C. Kervrann.
A Monte Carlo framework for missing wedge restoration and noise removal in cryo-electron tomography, in: Journal of Structural Biology: X, October 2019, pp. 1-18, Free Open Access. [ DOI : 10.1016/j.yjsbx.2019.100013 ]
https://hal.inria.fr/hal-02424804
[23]
A. Poinas, B. Delyon, F. Lavancier.
Mixing properties and central limit theorem for associated point processes, in: Bernoulli, 2019, vol. 25, no 3, pp. 1724-1754. [ DOI : 10.3150/18-BEJ1033 ]
https://hal.archives-ouvertes.fr/hal-01519096
[24]
G. Potier, R. Capoulade, J. Mérot, F. Lavancier, X. Heiligenstein, J. Salamero, P. Paul-Gilloteaux.
Automatic Registration of Correlative Microscopies with Error Assessment and Applications for the Optimization of Multimodal Acquisitions, in: Microscopy and Microanalysis, August 2019, vol. 25, no S2, pp. 1020-1021. [ DOI : 10.1017/S143192761900583X ]
https://hal.archives-ouvertes.fr/hal-02267554
[25]
S. Raman, S. Singh, T. Pécot, E. Caserta, K. Huang, J. Rittscher, G. Leone, R. Machiraju.
Capturing variations in nuclear phenotypes, in: Journal of computational science, September 2019, vol. 36, pp. 1-12. [ DOI : 10.1016/j.jocs.2019.07.001 ]
https://hal.inria.fr/hal-02424723

Invited Conferences

[26]
P. Bouthemy.
Intensity-based methods for fully automated registration in 2D and 3D CLEM, in: CMI 2019 - Correlated Multimodal Imaging Conference, Vienne, Austria, November 2019.
https://hal.inria.fr/hal-02419522
[27]
C. Kervrann.
A fast statistical colocalization method for 3D live cell imaging and super-resolutionmicroscopy, in: "Statistical modeling for Shapes and Imaging” workshop, Paris, France, March 2019.
https://hal.inria.fr/hal-02424596
[28]
C. Kervrann.
Computational methods for intracellular dynamics in live cell imaging, in: “Random Walks and Intracellular Transport” workshop, Manchester, United Kingdom, April 2019.
https://hal.inria.fr/hal-02424594
[29]
C. Kervrann.
Statistical methods for intracellular dynamics classification in live cell imaging, in: “Bioimage Processing” workshop, Cambridge, United Kingdom, June 2019.
https://hal.inria.fr/hal-02424593

International Conferences with Proceedings

[30]
I. Gubins, G. Van Der Schot, R. Veltkamp, F. Forster, X. Du, X. Zeng, Z. Zhu, L. Chang, M. Xu, E. Moebel, A. Martinez-Sanchez, C. Kervrann, T. M. Lai, X. Han, G. Terashi, D. Kihara, B. A. Himes, J. Zhang, S. Gao, Y. Hao, Z. Lv, X. Wan, Z. Yang, Z. Ding, X. Cui, F. Zhang.
Classification in cryo-electron tomograms, in: Eurographics Workshop on 3D Object Retrieval, Genova, Italy, May 2019. [ DOI : 10.2312/3dor.20191061 ]
https://hal.inria.fr/hal-02424712
[31]
L. Maczyta, P. Bouthemy, O. Le Meur.
Unsupervised motion saliency map estimation based on optical flow inpainting, in: ICIP 2019 - IEEE International Conference on Image Processing, Taipei, Taiwan, IEEE, September 2019, pp. 4469-4473. [ DOI : 10.1109/ICIP.2019.8803542 ]
https://hal.inria.fr/hal-02065112

Conferences without Proceedings

[32]
H. Bouvrais, D. Fairbrass, L. Chesneau, N. Soler, Y. Le Cunff, T. Pécot, C. Kervrann, J. Pécréaux.
Two dynamic behaviours of the microtubules at the cell cortex reveal the pulling and pushing forces that position the mitotic spondle in C. elegans embryos, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.
https://hal.inria.fr/hal-02424688
[33]
A. Caranfil, C. Kervrann, Y. Le Cunff, J. Pecreaux.
Studying oscillatory behavior in asymmetric division of Caenorhabditis elegans embryo with fluorescence microscopy, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.
https://hal.inria.fr/hal-02424686
[34]
A. Caranfil, Y. Le Le Cunff, C. Kervrann, J. Pécréaux.
Modelling oscillatory behavior in asymmetric division of C. elegans embryo, in: BioHazard – Stochastic Models for Biology – Conference, Rennes, France, August 2019.
https://hal.inria.fr/hal-02424703
[35]
Y. Lu, C. Billaudeau, R. Carballlido-Lopez, C. Kervrann, A. Trubuil.
3D stochastic process simulation for better interpretation of molecular dynamics related to cell wall biogenesis observed with TIRF microscopy, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.
https://hal.inria.fr/hal-02424699
[36]
Y. Lu, P. Hodara, C. Kervrann, A. Trubuil.
Probabilistic overall reconstruction of membrane-associated molecular dynamics from partial observations in rod-shaped bacteria, in: "Seeing is Believing" Conference, Heidelberg, Germany, October 2019.
https://hal.inria.fr/hal-02424598
[37]
S. Manandhar, P. Bouthemy, P. Roudot, C. Kervrann.
3D motion estimation in 3D light microscopy image sequences: application to cell migration, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.
https://hal.inria.fr/hal-02424694
[38]
E. Moebel, C. Kervrann.
3D ConvNets improve macromolecule localization in 3D cellular cryo-electron tomograms, in: Quantitative BioImaging (QBI) Conference, Rennes, France, January 2019, vol. 2.
https://hal.inria.fr/hal-02424696
[39]
A. Salomon, V. Briane, M. Vimond, C. A. Valadés-Cruz, C. Kervrann.
Analysing and quantifying intracellular particles movements in 3D LLSM data, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.
https://hal.inria.fr/hal-02424609
[40]
C. A. Valadés-Cruz, A. Forrester, C. Wunder, C. Kervrann, J. Salamero, L. Johannes.
3D tracking of endocytic events using lattice light sheet microscopy, in: QBI 2019 - Quantitative BioImaging Conference, Rennes, France, January 2019.
https://hal.inria.fr/hal-02424697

Other Publications

[41]
H. Bouvrais, L. Chesneau, D. Fairbrass, Y. Le Cunff, N. Soler, T. Pécot, C. Kervrann, J. Pecreaux.
Two dynamical behaviours of the microtubules at cell cortex reveal pulling and pushing forces that position the spindle in C. elegans embryo, May 2019, working paper or preprint.
https://hal.inria.fr/hal-02424717
[42]
X. Le Goff, J. Comelles, C. Kervrann, D. Riveline.
Ends and middle: global force balance determines septum location in fission yeast, December 2019, working paper or preprint. [ DOI : 10.1101/520007 ]
https://hal.archives-ouvertes.fr/hal-02398985
[43]
Y. Lu, P. Hodara, C. Kervrann, A. Trubuil.
An inverse problem approach to the probabilistic reconstruction of particle tracks on a censored and closed surface, October 2019, working paper or preprint.
https://hal.inria.fr/hal-02323939
References in notes
[44]
F. Amat, E. Myers, P. Keller.
Fast and robust optical flow for time-lapse microscopy using super-voxel, in: Bioinformatics, 2012, vol. 29, no 3, pp. 373–380.
[45]
D. Axelrod.
Total Internal Reflection Fluorescent Microscopy in cell biology, in: Traffic, 2004, vol. 2, pp. 4658–4668.
[46]
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.
[47]
B. Chen et al.
Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution, in: Science, 2014, vol. 346, no 6208, 1257998 p.
[48]
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.
[49]
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.
[50]
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.
[51]
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.
[52]
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