[3dem] Post-doctoral position (Urgent !)

Denis Chrétien denis.chretien at univ-rennes1.fr
Wed Sep 28 06:43:29 PDT 2011


Image Denoising, Segmentation and 3D Reconstruction in Cryo-Electron Microscopy

Position type: Post-doctoral Fellow Functional

Location: Rennes, France

INRIA research theme: Computation sciences for biology, medicine and the environnement

Project: SERPICO

Surpervisors: Charles Kervrann (INRIA) and Denis Chrétien (CNRS)

Contact: charles.kervrann at inria.fr, denis.chretien at univ-rennes1.fr

The work will be conducted in collaboration between the SERPICO (Space TimE RePresentation, Imaging and cellular dynamics of molecular Complexes / INRIA Rennes) team and the TIPs (Tubulin and Interacting Proteins / UMR 6026, CNRS University of Rennes 1) team. The main objective is to develop image processing methods and algorithms to facilitate the understanding of biological polymers (microtubules involved in cell division and vesicle trafficking) from cryo-EM microscopy images. The candidate will participate in an interdisciplinary project involving cell biologists, computer scientists, and applied mathematicians. He/She is expected to play a central role in creating and applying computational techniques to analyze cryo-EM imaging data, in close collaboration with experimentalists and modelers. We refer the candidate to the following websites for more information:

http://serpico.rennes.inria.fr/doku.php

http://www.umr6026.univ-rennes1.fr/english/home/research/tips/

Mission

Cryo-electron tomography allows 3D observation of biological specimens in their hydrated state. Generally, cryo-tomograms have very low signal-to-noise ratios, and conventional image processing methods yield poor results. In previous works, we have proposed several contributions: 1/ Conditional Random Fields (CRF) Framework for image segmentation; 2/ patch-based methods and machine learning techniques for image denoising; 3/ algorithms to automatically straighten images of curved microtubules and improve 3D reconstructions of microtubules using back-projection methods. We need to pursue our efforts to combine these approaches and to improve the promising results.  

Description

SERPICO and TIPs teams are interested in longitudinal projections of microtubules (i.e. perpendicular to the microtubule axis). Microtubules are composed of identical subunits that arrange together to form a helical lattice. Because of their symmetry, most of their information can be retrieved from their Fourier spectrum. However, due to their flexibility, microtubules are generally curved and their Fourier transform can no longer be used for symmetry analysis. To that end, we have proposed a method to automatically determine the local orientations and centers of short segments of microtubules in cryo-electron microscope images. The proposed algorithm (TubuleJ/ http://www.umr6026.univ-rennes1.fr/english/home/research/tips/Software/) exploits the helical symmetry of microtubules and the corresponding properties in the Fourier domain, so it can be easily extended to process other helical objects. The objective of the post-doc position is to extend to 3D this approach, which takes into account the redundancy of information embedded in cryo-EM 3D images. We will focus on non-helicoidal 3D microtubules decorated by molecular motors. Matching techniques and segmentation algorithms for tracking polymer units will be studied. Moreover, new statistical denoising algorithms will be investigated for visualization and reconstruction.

Skills and profile

This position requires background in applied mathematics, numerical analysis, and statistics as well as in image processing. A good practice in computer science, especially in JAVA or in object oriented programming (C++), and an experience in biological imaging will be appreciated.

Candidates should have a strong background in image processing and reconstruction methods, applied mathematics, computer science or related fields. Solid programming experience is required, especially in JAVA or in object-oriented programming (C/C++). Excellent collaborative skills will be appreciated. Previous experience with biology, biological imaging  and/or microscopy is preferred but not required.

Benefits

Duration : 16 months

Salary: approx. EUR 2,138 and includes social security

Possibility of French courses

Social Insurance

Help for housing

Participation for transportation and restauration costs

Scientific Resident card and help for husband/wife visa

Additional information

We stongly recommend the applicants to submit before October 7 2011.

Coquelle, F., Blestel, S., Heichette, C., Arnal, I., Kervrann, C., and D. Chrétien. Cryo-electron tomography of microtubules assembled in vitro from purified components. Methods in Molecular Biology, 2011, 777:193-208.

P.M. Carlton, J. Boulanger, Ch. Kervrann, J.-B. Sibarita, J. Salamero, S. Gordon-Messer, J.E. Haber, S. Haase, L. Shao, L. Winoto, A. Matsuda,, P. Kner, S. Usawa, Y. Strukov, M. Gustafsson, Z. Kam, D. Agard, J. Sedat. Fast live simultaneous multi-wavelength 4-dimensional optical microscopy. Proc Natl Acad Sci USA, 107(37): 16016-16022, 2010

J. Boulanger, Ch. Kervrann, P. Bouthemy, P. Elbau, J.-B. Sibarita, J. Salamero. Patch-based non-local functional for denoising fluorescence microscopy image sequences. IEEE Trans on Medical Imaging, 29(2): 442-454, 2010

S. Blestel, Ch. Kervrann, D. Chrétien  Fourier-based method for detecting curved microtubule centers:  application to straightening of cryo-electron microscope images Proc. IEEE Int Symp Biomedical Imaging: From Nano to Macro (ISBI’09), pp. 298-301, 2009
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Université de Rennes 1
UMR 6026, équipe TIPs
Campus de Beaulieu, Bât. 13
35042 Rennes Cedex
France

Tel. +33 (0)2 23 23 67 64
http://www.umr6026.univ-rennes1.fr/
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