Call for Expression of Interest - Marie S. Curie Postdoctoral Fellowship:Quantifying 3D benthic fauna spatial interactions using X-rays CT-Scan

This job offer has expired

    Computer science
    Established Researcher (R3)
    Recognised Researcher (R2)
    07/05/2021 23:00 - Europe/Athens
    France › Plouzane


  •  Call for expression of interest description

The Marie S. Curie Postdoctoral Fellowship (MSCA-PF) programme is a highly renowned EU-funded scheme. It offers talented scientists the unique chance to set up 2-year research projects on their own with the support of a supervising team. Besides providing an attractive grant, it represents a major opportunity to boost the career of promising researchers.

The Laboratory of Environmental Marine Sciences (LEMAR) is thus looking for excellent postdoctoral researchers with an international profile to write a persuasive proposal to apply for a Marie S. Curie Postdoctoral Fellowship grant in 2021 (deadline of the EU call set on September 15th, 2021). The topic and research team presented below have been identified in this regard.

  •  Key words

Image processing - CT-Scan - 2D-3D image processing - computering - bioturbation - sediments

  • Research project description


Bioturbation, which represents all the activities induced by all animal and plant organisms living in sediments and soils, are key processes in the coastal ecosystems functioning (Aller and Cochran 2019). They are associated with the construction and maintenance of root networks, galleries or burrows, with feeding, movement and irrigation modes, continually rework the sediments, which modifies their physical structure and their chemical and microbiological composition (Kristensen et al., 2012). The effects of bioturbation, however, depend on the variability of environmental conditions, which act directly on the structure, and composition of the biodiversity of the organisms present in the environment, and on their behavior. Understanding the impact of these activities on ecosystem functioning requires precise quantification of bioturbation at the sediment-water interface. This can be done by quantifying the space occupied by organisms in the sediment, which requires advanced medical technologies as the Computed Axial Tomography allowing detailed information on the structural volume of biogenic structures (Michaud et al., 2003; Capowiez et al., 2021).

However, the different natures of sediments coupled to the variable animals’ behavior and size make sensitive the description and quantification of the burrows architecture and their connectivity within sediments. Heterogeneity of the primary structure of natural sediments over depth make more complex the tomographic densities signal and their distinction from various irrigated and/or, abandoned burrows with more or less branched. This postdoctoral research project aims at characterizing the structural architecture of the bioturbation structures from various species and/or individuals and from various environments, in order to identify and quantify the spatial interactions within benthic communities.

The fellow will:

- set up an experiment for a few months to extract the 4D space-time analysis of the biogenic structures with single and mixed communities;

- work on the development of image processing algorithms

- extract the burrows structure characteristics to describe the respective roles of studied invertebrates, isolated and in combination;

- valorize the results through international peer-reviewed publications and conferences

The post-doctoral fellow will combine engineering approaches with ecological works in the field and in the laboratory.

She/he will start working from a database of Dicom pictures (still unexploited) issued from previous experiments and field observations in Sub-Arctic, tropical (i.e., mangroves) and temperate areas.

Additional samples of pictures could be obtained through setting up of new experiments and field works.

  • Supervisor

Emma Michaud is an expert on Biodiversity-Ecosystem Functioning (BEF) Relationships through the bioturbation processes studies that she has further developed through her PhD (2006) and post-doctoral (2007-2010) in Canada and USA. She has been a permanent researcher in France for the past ten years, at the French National Centre for Scientific (CNRS) within the Laboratory of Environmental Marine Sciences (LEMAR) located at the European Institute for Marine Studies (IUEM). She is interested in the functional ecology in coastal ecosystems and wetlands storing large amounts of sedimentary carbon (i.e., Mangroves, Estuaries, Arctic fjords). Her research topics focus on i) organism-sediment interactions, ii) bioturbation activities and biogeochemical cycles, iii) development, improvement and applications of 2D and 3D benthic imaging techniques.

E. Michaud was strongly involved as the Principal Investigator in National projects from which she has obtained over 700k€ of financial support for field campaigns, scientific equipment, post-doctoral and doctoral positions. Being also an active participant in national and international projects (NSF, USA; CRSNG, Canada; NRC, Norway; NSC, Poland), she is in close collaboration with the specific international networks on bioturbation processes and sustainability of the Mangroves's and Artic's ecosystems.

Three relevant references with the current call for expression of interest:

1- E. Michaud, G. Desrosiers, B. Long, L. de Montety, J.F. Crémer, E. Pelletier, J. Locat, F. Gilbert, G. Stora. 2003. Use of axial tomography to follow temporal changes of benthic communities in an unstable sedimentary environment (Ha!Ha! Bay, Saguenay Fjord). J. Exp. Mar. Biol. Ecol.Vol. 285-286, 265-282.

2- E. Michaud, R.C. Aller, G. Stora. 2010. Sedimentary organic matter distributions and burrowing activity: natural patterns and experimental artifacts. Estuar., Coast. Shelf Sci.. 90, 21-34.

3- Brunier, G., Michaud, E., Fleury, J., Anthony, E.J., Morvan, S., Gardel, A. 2020. Assessing the relationships between macro-faunal burrowing activity and mudflat geomorphology from UAV-based Structure-from-Motion photogrammetry. Remote Sensing of Environment. Doi: 10.1016/j.rse.2020.111717

For further information, please visit E. Michaud's page on LEMAR website and E. Michaud's Researchgate profile

  • Department/Research

The Laboratory of Environmental Marine Sciences (LEMAR) is a strongly interdisciplinary laboratory that brings together ecologists, biologists, biogeochemists, chemists, physicists and marine environment lawyers. Its objectives are (1) to conduct research on topics of fundamental research or societal importance; (2) to contribute to the achievement of sustainable development objectives in both North and South countries; (3) to bring innovations in relation to the economic world and results that support public policies; (4) to engage in interdisciplinary training in the field of marine and coastal science. The fellow will be included within the DISCOVERY team of the LEMAR which is specialized on the diversity, structure and dynamics of populations and communities. Also, transversal research axes within the laboratory, based on regions of interests (South/North) or on methodologies, allow to keep active collaborative work between the scientists of the different research teams of the laboratory.

LEMAR research unit is part of the European University Institute for Marine Studies (IUEM). IUEM is a multidisciplinary institute in the field of marine and coastal sciences, dedicated to three missions: research, training and observation. Besides the LEMAR research unit, IUEM gathers scientists from a vast array of research backgrounds in 6 other research units, ranging from geography, geology, biotechnologies, physics up to maritime law and economics. IUEM belongs to the University of Western Brittany (Université de Bretagne Occidentale - UBO). In the ARWU World University Rankings 2019 (the "Shanghai" ranking), IUEM occupies the 12th place worldwide research organizations in oceanography, making UBO the third university in the EU and the first French university in this field.

IUEM is part of EUR Isblue (Interdisciplinary School for the Blue Planet) which gathers most of the forces in marine science and technology in West and South Brittany (France), belonging to universities (UBO, UBS), national research organisms (CNRS, Ifremer, IRD), engineering schools (IMT-Atlantique, ENSTA Bretagne, ENIB) and the French naval academy.

Locally, the fellow will be integrated in a very good and active working environment for research and formation, and full of synergies with foreign partners. She/he will have access to experimental rooms, experimental reservoirs for studying benthic infauna, marine instrumentation and computing facilities for algorithm development and calculations. She/he will be involved in the international thematic school of bioturbation expected in Brest at the end of 2022 gathering the terrestrial and aquatic ecologists, and engineers and modellers around the bioturbation processes studies.

  • Suggestion for interdisciplinary / intersectoral secondments

Outside of LEMAR, the fellow could develop collaborative work with the local engineering schools (IMT-Atlantique, ENSTA Bretagne, ENIB) for computing sciences expertise through the EUR Isblue consortium. Strong collaborations with our national and international partners around CT-Scan platforms are also expected. 3-6 months secondment spent with one of these platforms, specifically with P. Francus from INRS Canada (http://ctscan.ete.inrs.ca/en/) could be planned in order to develop the 4D experiments through our partnership with IFQM (http://www.ifqm.info/fr/).

  • Skills requirements

Primary Specific Skill Requirements: Image processing (2D and 3D), tomography-Xrays data analysis, computer algorithms, rendering techniques, geostatistics

Secondary Specific Skill Requirements: Ecology of sediments or soils, Sedimentology

Software knowledge requirements: Python, R or Matlab (other specific programms for dicom pictures processing can be proposed)

Required Languages: English or French

Publications: good level of publications in international peer-reviewed journals (for instance at least 1 per year since the PhD in 1st author)

More Information

Eligibility criteria

Academic qualification: By the MSCA-PF call deadline (September 15th, 2021), applicants must be in possession of a doctoral degree, defined as a successfully defended doctoral thesis, even if the doctoral degree has yet to be awarded.



Research experienceApplicants must have a maximum of 8 years full-time equivalent experience in research, measured from the date applicants were in possession of a doctoral degree. Years of experience outside research and career breaks (e.g. due to parental leave), will not be taken into account.


Nationality & Mobility rulesApplicants can be of any nationality but must not have resided more than 12 months in France in the 36 months immediately prior to the MSCA-PF call deadline (September 15th, 2021).

Selection process

We encourage all motivated researchers to apply through the EU Survey application forme (link here) before May 7th, 2021. Your application has to include:

  • a CV including : (i) the exact date of your stay in each position and/or country and (ii) a list of publications;
  • a research outline (up to 2 pages) identifying the research synergies with the faculty members and pre-identified topics described above

Estimated Timetable

  • Deadline to apply to the present call for expression of interest: 7th May 2021
  • Selection of the most promising application(s): May-June 2021
  • Writing the MSCA-PF proposal with the support of the above-mentioned supervisor(s): June-September 2021
  • Expected MSCA-PF 2021 call deadline: 15th September 2021
  • Publication of the evaluation results: February 2022
  • Start of the research project (if funded): May 2022 (at the earliest)

Offer Requirements


  •  Primary Specific Skill Requirements: Image processing (2D and 3D), tomography-Xrays data analysis, computer algorithms, rendering techniques, geostatistics


  • Secondary Specific Skill Requirements: Ecology of sediments or soils, Sedimentology


  • Software knowledge requirements: Python, R or Matlab (other specific programms for dicom pictures processing can be proposed)


  • Required Languages: English or French


  • Publications: good level of publications in international peer-reviewed journals (for instance at least 1 per year since the PhD in 1st author)


Work location(s)
1 position(s) available at
Rue Dumont d Urville

EURAXESS offer ID: 622526


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