Surface and volume assessment of Sabellaria alveolata (honeycombworms) reef habitats in the marine natural park of the Gironde Estuary and the Pertuis Sea.
Research fields: signal processing and image analysis ● machine/deep learning ● photogrammetry ● drone acquisitions
Location : IFREMER Centre de Bretagne – Brest, France
Lab / Team : DYNECO Laboratoire d’Ecologie Benthique Cotière (LEBCO)
Team leader and project PI : Dr. Stanislas Dubois
Type of contract : full-time job for 18 months
Employer: Ifremer, Centre de Bretagne
Deadline to send application: 30 November 2021
Expected to start: February or March 2022 (to be discussed)

Scientific framework of the project – Polychaetes of the family Sabellariidae are tubicolous and gregarious species, which construct biogenic formations in temperate coastal ecosystems. These bioconstructions are known to provide a number of important ecological roles and ecosystem services, such as coastline protection, or habitat provision for many species. In Europe, Sabellaria alveolata is a common intertidal species distributed from the coasts of Morocco to Scotland. Many of these reefs are threatened by anthropogenic pressures and it is now imperative to better understand the formation and evolution of these biogenic habitats in order to protect and manage them effectively. In particular, Sabellaria reefs are listed as key habitats under Annex 1 of the European Habitat Directive. Monitoring these reefs on a European scale is a critical challenge that needs to be addressed in order to provide relevant monitoring and indicators of the good health of S. alveolata bioconstructions.
Following the European REEHAB project (www.honeycombworms.com), the SISTER (Surface Imaging Solution for TEmperate Reefs) project aims to evaluate the surface area of the Sabellaria alveolata reef habitat on European coasts, using the foreshore of the Gironde Estuary and the Mer des Pertuis marine park as a demonstrator. This park – the largest in France – is home to the largest surface area of this remarkable habitat, where the reef formations present a great diversity of morphologies.

Specific objectives of this postdoctoral project.
We are looking for a motivated and dynamic young researcher to work with the team gathered for this project. The main missions will be:
1 – the development of a method for the surface and volume assessment of Sabellaria alveolata (honeycombworms) habitats using multispectral acquisitions made by airborne drones;
2 – the implementation of the processing chain and the elaboration of a standardized methodological guide including i – the field approach to be deployed to acquire the images (visible and near infrared) and ii – the automated processing chain to be used to obtain the surface and volume evaluation of the habitat, with classification and photogrammetry methods;
3 – participation in the creation of an educational tool based on virtual reality.

Specific tasks.
– Organize, set up, and participate in in situ data acquisition campaigns (drone overflights and field acquisitions);
– Exploit existing photogrammetry tools: software and scripts;
– Reconstruction of reefs in 3D;
– Develop classification and segmentation methods;
– Develop landscape indicators on the health status of reefs and their spatial and temporal evolution;
– Write a methodological guide and (at a minimum) one scientific article in a rank A journal.
Skills
– Good knowledge in signal processing and image analysis;
– Classification and segmentation methods and machine learning in general;
– Experience in Python programming highly appreciated;
– Mastery of photogrammetry software (Metashape and/or Pix4D) and scripts using an Structure from Motion type approach or equivalent;
– Proficiency in the use of GIS software such as ArcGIS or QGIS;
– Use of a supercomputer and parallelization (desired skill);
– Writing skills and good level of English (oral but especially written);
– Knowledges in the marine environment and motivation for marine ecology
– Dynamism and autonomy;
– Interest in teamwork, open-mindedness to dialogue with thematic experts from other disciplines.

Host team
The LEBCO team (ca. 15 researchers and engineers, 5 technicians) works on understanding the spatial patterns of biodiversity in coastal benthic habitats. With multidisciplinary approaches, the team seeks to understand the natural and anthropogenic processes that structure the populations and communities. Among the spatial approaches, the use of imagery (satellite or airborne) is a central axis in the team’s spatial ecology projects.
Within the team and besides Stan Dubois, the person recruited will work in close collaboration with Pierre-Olivier Liabot and Touria Bajjouk, specialists in imaging and multi- and hyper-spectral processing.
Scientific collaborations
The EPHE (École Pratique des Hautes Études) in Dinard (Antoine Collin and Dorothée James) is the main scientific partner of the SISTER project. A close link will be pursued with this team. The CERV (Centre Européen de Réalité Virtuelle) locatd in Brest will also be a privileged contact for the production of 3-dimensional data adapted to the representation in virtual reality.
Finally, LEBCO also relies on external collaborations with the main laboratories specializing in signal processing in Brittany (UBO/LGO, ENSSAT Lannion, CEVA, Télécom Bretagne, …) but also, at the national (ONERA, IGN, GIPSA-Lab, EPOC, Univ. Toulon, Univ. Nantes) and European levels.
How to apply?
Please send the following documents to Stanislas Dubois (Stanislas.Du[email protected])
(1) A CV and a letter of application showing your interests for the subject and how it fits in your scientific career;
(2) A synthetic and summarized list of your main works related to the subject (2 pages max.): scientific publications and/or reports
(3) Letters of recommendation (not mandatory but helpful);
(4) A copy of your engineering or doctoral degree.
If needed, do not hesitate to contact [email protected] for more information

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