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Portal > Offres > Offre UMR3664-ANTCOU-002 - Ingénieur-e (H/F) en analyse d'images (2 ans, renouvelable)

Engineer position in Image Analysis (2 years, extendable)

This offer is available in the following languages:
Français - Anglais

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General information

Reference : UMR3664-ANTCOU-002
Workplace : PARIS 05
Date of publication : Friday, July 05, 2019
Type of Contract : FTC Technical / Administrative
Contract Period : 24 months
Expected date of employment : 16 September 2019
Proportion of work : Full time
Remuneration : Gross monthly salary: 2140€-2664€ depending on qualifications and experience
Desired level of education : 5-year university degree
Experience required : Indifferent

Missions

Our team “Genome Functions in Space and Time” studies the 3D organization and dynamics of chromosomes in the cell nucleus and its role in regulating gene expression.

We use and develop a panel of single-molecule imaging techniques in both live and fixed cells to image DNA, RNAs and proteins inside the nucleus. Our interdisciplinary group also develops computational tools for data analysis and physical models of the genome and the nucleus.
More info: www.coulonlab.org

You will be the image analyst of the team and will have the chance to work on multiple projects.

Activities

Your responsibilities will be:
• To work with team members to analyze and help them analyze their own data
• To implement pipelines for automated high-throughput image analysis
• To develop new tools and expand current techniques in the following areas:
   - High-precision 3D reconstruction & quantification from sequential imaging techniques (Oligopaints, MERFISH) [1-3]
   - Spectral and kinetic demultiplexing, inspired from refs [4-6]
   - Multi-target tracking of particles in high-density and/or multi-channel images
   - Spatio-temporal correlative approaches for quantitative analysis of super-resolution and single particle tracking (SPT) data [6-8]
   - Automated microscope control
• To oversee software development (versioning, distribution) and data management practices (annotation, processing, storage) in the team.

Related literature:
[1] Bintu et al. (2018) Science, 362(6413) http://doi.org/10.1126/science.aau1783
[2] Mateo et al. (2019) Nature, 1–24. http://doi.org/10.1038/s41586-019-1035-4
[3] Jungmann et al. (2014) Nat Meth, 11(3), 313–318. http://doi.org/10.1038/nmeth.2835
[4] Ma et al. (2016) Nat Biotech, 34(5), 528–530. http://doi.org/10.1038/nbt.3526
[5] Eng et al. (2017) Nat Meth, 14(12), 1153–1155. http://doi.org/10.1038/nmeth.4500
[6] Jungmann et al. (2016) Nat Meth, 13(5), 439–442. http://doi.org/10.1038/nmeth.3804
[7] Sengupta et al. (2011) Nat Meth, 8(11), 969–975. http://doi.org/10.1038/nmeth.1704
[8] Schnitzbauer et al. (2018) PNAS, 115(13), 3219–3224. http://doi.org/10.1073/pnas.1711314115

Skills

[ *** : required     ** : recommended     * : appreciated ]

*** M.Sc., M.Eng. or Ph.D. degree in Computer Science, Physics or Mathematics

*** Python, SciPy, Matplotlib, scikit-image, Fiji/ImageJ
* Data visualization (PyViz, HoloViews, Bokeh)

*** High-density 3D spot detection/tracking, sub-pixel volumetric segmentation
** Super-resolution image reconstruction: PALM/STORM/PAINT, SOFI, SRRF
* Frequency-domain signal theory, mathematics of stochastic processes, model-based image analysis, optical flow

*** Scripting, software development, version control (Git, GitLab)
* Parallel/cluster computing (CentOS)
* Basic system admin (macOS, Windows, Linux)

** Micro-Manager: use and programming (BeanShell…)
* Optics development, microcontroller programming (Arduino)

*** Proficiency in English (written, spoken), which is the working language of the group
** Organization skills, autonomy, ability to communicate and present data / results

Work Context

The team is co-affiliated with a biology research unit (Nuclear Dynamics, UMR3664) and a physics research unit (Physical Chemistry, UMR168) at Institut Curie. You will be working in close contact with the experimentalists in the team.

Additional Information

Please apply through this website ('Portail Emploi' of the CNRS) with a cover letter, your CV and the contact details of 2-3 references.
Feel free to contact Antoine Coulon (recruitment@coulonlab.org) prior to application if you have any question about the position.

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