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Contract : temporary Post doctoral position (18 months) starting April 1st, 2022
Employer : Aix-Marseille Université
Gross salary : depending on the professional background : the first year ranging from 2466 to 2891 €/month and the second year (last 6 months) between 2772 to 3197 €/month
RESEARCH FIELD(S)
Oceanography, Plankton, Time-series analysis, Image analysis, Ecology, Microscopy.
JOB LOCATION
Centre Européen de Recherche et d’Enseignement en Géosciences de l’Environnement, Europole de l’Arbois, Aix en Provence, France ; with frequent visits in Mediterreanean Insitute of Oceanography, Marseille, France
PI of the RapMed project
T. de Garidel, CEREGE, [garidel@cerege.fr]
JOB DESCRIPTION
The main tasks of the post-doc will be to study recent changes in microplankton size and community structure from the western Mediterranean Sea using an innovative workflow, based on automated images analyses of plankton.
This postdoc position is part of the RapMed project which aims at the study of dynamical changes in plankton communities under environmental perturbations. This project is funded by the Mediterranean Institute for the Environmental Transition (A*Midex), an interdisciplinary initiative aiming to tackle the challenges of the ongoing climate nexus.
The RapMed project aims to study the effects of recent environmental changes over the past two decades on planktonic communities in the sentinel region of the Gulf of Lions. The project will explore the dynamics of planktonic communities at highly resolved size-spectrum, based on the application and standardization of high throughput image processing methods. RapMed program is setting up an innovative processing chain based (named Particle Trieur) on machine learning approaches (convolutional neural networks). It delivers consistent patterns of planktonic size and taxonomic community structures in time series which should increase our understanding of the variability of planktonic communities and their resilience to environmental changes.
The post-doctoral research associate will focus on microscopic imaging techniques available at CEREGE and/or MIO (primarily automated microscopy, MiSo). The PDRA will investigate a sediment trap time series off Marseille (Planier’s trap) in collaboration with the CEFREM, and document past changes in biomineralizing taxa over the two last decades. The PDRA will assemble his/her own dataset, build and optimize a dedicated automatic recognition module for biomineralizing organisms in microscopy, this sediment trap time-series; and compare the ones gathered by the consortium, in order to reach a comprehensive view of recent changes in plankton communities.
The dynamical analysis of plankton communities and links with environmental variables will rely on the data analysis from long term time-series of national observational services (SNO SOMLIT, and MOOSE) off Marseille, discontinuous records such as SPECIMED and CALHIMED, and the shoreline CytoSense timeseries. The PDRA will conduct statistical analyses necessary to the interpretation of the datasets.
The recruited person will benefit from the expertise of the teams involved into the RapMed project including statistical skills for the dynamical analysis of plankton communities and link with environmental variables (MIO team), pattern mining and neural network classification (MIO, CEREGE and LAM teams, Queensland Univ. Technology) for the identification of plankton communities from image database or other measurement devices (non imaging flow cytometry, ocean color) and descriptors construction (MIO and CEREGE teams, size spectra, biovolume, …). Last, the post doc will interact with another post-doctoral research associate of the project, in charge of implementing the image analysis workflow derived from the existing tool (ParticleTrieur software / Miso GitHub)) which was originally designed for image recognition of fossil microplankton (Marchant et al, 2020).
QUALIFICATIONS/SKILLS/EDUCATION & RESEARCH REQUIREMENTS/DUTIES
- Fluent in English
- Knowledge in plankton and preferably of biomineralizing groups
- Knowledge in marine science or ecology
- Experience in microscopy
- Excellent communication skills
- Good programming skills in R or Python
- Notions about machine learning in general and more particular in neural networks
APPLICATION DEADLINE (If applicable)
January 21st, 2022
Start date by April 1st, 2022
REQUESTED DOCUMENTS OF APPLICATION
CV
Contact of 2 referees
Research statement (less than 2 pages)
CONTACT TO APPLY (EMAIL OR WEBSITE)
Website of the project : https://rapmed.osupytheas.fr
