Ifremer - French Research Institute for Exploitation of the Sea

PhD : Untangle nested scales of spatial organization in Cold Water Coral communities: advances in 3D-modelling and computer vision (M/F)

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Reference: PV-2023-1287/1


Duration of contract:3 ans

Start date:

Deadline for applications:23/04/2023

The Institute and the recruiting department

A pioneer in ocean science, IFREMER’s cutting-edge research is grounded in sustainable development and open science. Our vision is to advance science, expertise and innovation to:

- Protect and restore the ocean

- Sustainably use marine resources to benefit society

- Create and share ocean data, information & knowledge.

With more than 1,500 personnel spread along the French coastline in more than 20 sites, the Institute explores the 3 great oceans: the Indian, Atlantic and Pacific oceans. A leader in ocean science, IFREMER is managing the French Oceanographic Fleet and its dedicated scientists create ground-breaking technology to push the boundaries of ocean exploration and knowledge, from the abyss to the atmosphere-ocean interface.

Well-established in the international scientific community, our scientists, engineers and technicians are committed to advance knowledge about our planet’s last unexplored frontiers. They provide the science we need for informed decision-making and public policy and they transfer this knowledge and technology to businesses to fulfill public and private needs. Core to our mission is also to strengthen public awareness about the importance of understanding the ocean and its resources, and empowering future generations of leaders through education and outreach national campaigns.

Founded in 1984, IFREMER is a French public organization and its budget approximates 240 million euros. It is operating under the joint authority of the French Ministry for Higher Education, Research and Innovation, the french Ministry of the Sea, the French Ministry for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.

General areas of responsibility

The UMR BEEP (Biology and Ecology of marine Ecosystems of the deeP) aims to study the biology and ecology of deep-sea ecosystems through a multidisciplinary and holistic approach, from microorganisms to megafauna, and from the molecule to the community. Research focuses on the description and dynamics of biological diversity, biotic and environmental interactions, as well as the adaptation and response of biological systems under natural and anthropogenic constraints. These issues are addressed at different spatial and temporal scales depending on the ecosystems studied: chemosynthetic ecosystems, cold-water corals, seamounts or abyssal plains.


Submarine canyons are among the largest and most complex geoforms in the deep sea, hosting a wide diversity of habitats, including cold-water corals (CWC), and supporting numerous ecosystem services.

However, one of the main challenges in the study of these complex environments is to integrate nested scales of spatial structuration. Each scale has its own ecological processes, acquisition techniques (multi-beam echo sounder, photogrammetry, faunal annotation) and modelling algorithms.

The objective of the thesis will be to carry out a multi-year and multi-scale mapping of the Lampaul canyon habitats in order to assess and monitor the health of the CWC. Beyond environmental monitoring, this multi-scale mapping will also be used to better understand the processes and factors that control coral distribution and dynamics. The influence of the engineering role of coral (reef-builders or not) on ecosystem functions will be investigated.

To this end, a workflow integrating multiple spatial scales will be developed to operationalize, accelerate, and automate the use of imagery data to map coral habitats.

Key words

Submarine canyon, cold-water corals, high resolution mapping, structure from motion, deep learning, species distribution modeling

Required Knowledge, skills, and characteristics

  • Master in Science and/or engineering degree in ecology, oceanography, biostatistics or equivalent
  • Interest and good knowledge in marine ecology and spatial biostatistics
  • Good practical knowledge in programming for image processing (Python, C++, ...) and biostatistics (R)
  • Skills and/or knowledge in computer vision (machine learning, photogrammetry) and 3D data processing appreciated
  • Fluent English

Specific working conditions

  • The Ph.D. position is at located at Centre Ifremer de Bretagne, in Plouzané
  • Travels are expected in France and abroad, including a stay of a few weeks in a laboratory abroad
  • The PhD position requires work at sea

PhD is a real opportunity to work on Ifremer's scientific and technological priority themes. It entitles the holder to a gross monthly salary of 2300 euros gross for a period of 3 years, which cannot be combined with other scholarships. 

How to apply for this position ?

Your application file must include :

  • a curriculum vitae
  • a covering letter
  • a reference letter
  • an academic transcript (Bachelor + Master 1 and first semester Master 2)

Your application must be compiled into 2 PDF files, up to 3 MB for each file:

In case of any problem in attaching your documents, please upload your CV on this page (this step is mandatory for your application to be considered) and send all the documents to the thesis supervisor : lenaick.menot@ifremer.fr

The deadline for applications is April 23rd, 2023. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject co-supervisor (lenaick.menot@ifremer.fr).

In paralell, please submit your application to the doctoral school : Ecole Doctorale des Sciences de Mer et du Littoral (https://theses.doctorat-bretagneloire.fr/sml/campagne-2023)

Doctoral students' contracts will start as of October 2nd, 2023, subject to the submission of administrative documents authorizing Ifremer to recruit the doctoral student (certificate of completion of the Master 2 or engineering degree + visa for foreign doctoral students outside the EU).

How to apply for this position

Deadline for applications: 23/04/2023

All applications are processed exclusively via our website. Interested candidates can apply by clicking the “Apply” button. 

Job details

PhD : Untangle nested scales of spatial organization in Cold Water Coral communities: advances in 3D-modelling and computer vision (M/F)
1625 Route de Sainte-Anne Plouzané, France
Application deadline
2023-04-23 23:59:59
Job type
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Ifremer conceives and operates tools for observation, experimentation and monitoring, and manage the oceanographic databases.

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