13/01/2021

Researcher - Development of neural networks for Bio-imaging 3D segmentation


  • ORGANISATION/COMPANY
    CEA
  • RESEARCH FIELD
    Biological sciencesOther
    Computer scienceProgramming
    TechnologyComputer technology
  • RESEARCHER PROFILE
    First Stage Researcher (R1)
  • APPLICATION DEADLINE
    13/02/2021 22:00 - Europe/Athens
  • LOCATION
    France › Grenoble
  • TYPE OF CONTRACT
    Temporary
  • JOB STATUS
    Full-time
  • HOURS PER WEEK
    39
  • OFFER STARTING DATE
    01/01/2021
  • EU RESEARCH FRAMEWORK PROGRAMME
    H2020

OFFER DESCRIPTION

The Laboratory LSIV at CEA-Leti Grenoble has an opening for setting up neural networks dedicated to the 3D analysis of organoids refractive index distributions obtained by means of 3D phase microscopy.

We are currently developing a novel 3D phase microscope dedicated to the monitoring of organoids directly into the incubator. The sample’s 3D refractive index distribution will be recovered in a quantitative manner thanks to a physical neural network able to implement the multi-slice beam propagation method[1] and or the wave propagation method[2],[3].

To further develop this 3D imaging platform, the recruited person will be responsible for developing and assessing neural networks computing 3D image processing tasks. The objective is to obtain from the 3D refractive index distribution a comprehensive 3D description of the geometry of the organoids. To this aim, the recruited person will conduct three distinctive tasks. The first task will be the definition of an annotated reference 3D dataset. The second task will deal with the development of dedicated neural networks, namely 3D cell detection, 3D cell segmentation and 3D object description. The last task will be the exhaustive assessment of the neural networks on different organoids and experimental conditions.

 

Location: Laboratory LSIV at CEA-LETI Grenoble.

Requirements:

  • PhD degree in computer science or engineering with a strong interest in 3D bio-imaging.
  • Solid background in deep learning for image processing.
  • Solid background in 3D segmentation.
  • Successful experience working in a bio-imaging group is asset.
  • Fluent in French, and/or English (oral and written), clear and effective communication skills.

Offer:

  • Access to top class research facilities.
  • Work within an interdisciplinary European project
  • Work in a team of motivated researchers with diverse backgrounds.
  • 24 Months full time contract, starting March 2021.
  • Salary: 30 000 - 35 000 euros/year depending on candidate qualifications.
  • Grenoble is located close to a large number of outdoor activities.

Contact

Interested candidates should contact Dr. Cédric ALLIER.

Cedric.Allier@cea.fr

 

[1] Chowdhury, S., Chen, M., Eckert, R., Ren, D., Wu, F., Repina, N., & Waller, L. (2019). High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images. Optica, 6(9), 1211-1219.

[2] Lim, J., Ayoub, A. B., Antoine, E. E., & Psaltis, D. (2019). High-fidelity optical diffraction tomography of multiple scattering samples. Light: Science & Applications, 8(1), 1-12.,

[3] Brenner, K. H., & Singer, W. (1993). Light propagation through microlenses: a new simulation method. Applied optics, 32(26), 4984-4988.

More Information

Map Information

Job Work Location Personal Assistance locations
Work location(s)
1 position(s) available at
CEA
France
Grenoble
38054
17 avenue des Martyrs

EURAXESS offer ID: 594514

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