[PDF] 18 months Post-doctoral position in France Aix Marseille University

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Institut ITEM

- Aix Marseille Université Item -contact@univ-amu.fr - Site web ITEM

18 months Post

-doctoral position in France

Aix Marseille University

o

JOB TITLE

Post doc opening on dynamical detection of changes in plankton community structures and link with environmental variables : an image recognition approach. o

JOB PROFILE/TYPE :

Contract

: temporary Post doctoral position (18 months) starting on March 2021 the 1st

Employer : Aix-Marseille Université

Gross salary depending on your professional background : the first year ranging from

2466 to 2891 €/month and the second year (last 6 months) between 2744 to 3169

€/month o

KEYWORDS

Discriminative pattern mining, neural networks, image recognition, time-series analysis, tipping points. Oceanography o

JOB LOCATION

Aix Marseille University (France): MIO (Campus Luminy - Marseille) with frequent visits in CEREGE, Aix en Provence and LAM, Marseille. o

ADVISORS

D. Nerini (MIO) [david.nerini@univ-amu.fr] & P. Duarte Neto (UFRPE, Brasil) [pjduarteneto@gmail.com o

PI of the RapMed project

T. de Garidel, CEREGE,

[garidel@cerege.fr] o

JOB DESCRIPTION

This 18-months' post-doctoral fellow is funded by the new

Mediterranean Institute for

Environmental Transition (A*Midex), an interdisciplinary initiative aiming to tackle the challenges of the ongoing climate nexus, and will begin on March 2021.

The post-doctoral position is part of the RapMed

project which aims at the study of dynamical changes in plankton communities under environmental perturbations.

The RapMed project aims to study

the effects of rece nt environmental changes over the past two decades on planktonic communities in the sentinel region of the Gulf of Lion s. A recent transition of planktonic communities, with a decrease in plankton size, is

Institut ITEM

- Aix Marseille Université Item -contact@univ-amu.fr - Site web ITEM synchronous with a drastic decrease in fisheries catch. To understand the processes involved at the lower trophic levels, the project will explore the dynamics of planktonic communities at all size scales at high resolution, based on the application and standardization of high throughput image processing methods. RapMed will set up an innovative processing chain based on machine learning approaches (convolutional neural networks). The results of RapMed will provide a better understanding of the variability of planktonic communities and their resilience to environmental changes. The dynamical analysis of phytoplankton communities and links with environmental variables will rely on the data analysis from (1) time-series of national observational stations where the OSU Pytheas is involved (SNO SOMLIT, and MOOSE), (2) the use of images from oceanographic cruises (N/O Antédon , ....) and from flow cytometry image acquisition. The main objective of this post-doc will be to set up an optimized image processing chain, focused on plankton but applicable to any other biological or inorganic particle. This task will be built on MiSo libraries (Python, TensorFlow) developed within the ANR project FIRST at CEREGE (GitHub ), which operates routinely for fossil microplankton using neural networks for classification and species recognition. As the final ambition of the project is to be able to routinely process a great number of images, Important work will focus on workflow optimization and code paralleliza tion in order to be able to process massive data from the consortium.

Description of the position:

The candidate will set up an optimized image processing chain, focused on plankton images but applicable to any other biological or inorganic particle. The starting project will be built on an existing tool (ParticleTrieur software / Miso GitHub )) for image recognition of fossil microplankton developed at the CEREGE (Marchant et al, 2020). The main tasks of the post-doc applicant will relate to (i) the management of the images collected by the different sampling devices of the consortium (cytometry, ...), the long-term data management plan and compliance with FAIR standards for their subsequent integration into international databases; (ii) the test and application of automatic classification techniques for images with a high level of noise (using CNNs); (iii) the integration of covariates as classification criteria (Random Forest, e.g. Ellen, et al, 2019 and possible prediction of dynamics of communities; and (iv) the integration of geometric models for each target ta xon to extract some relevant descriptors of communities (biovolume, size spectra, ...) (e.g.

Moberg & Sosik, 2012).

Some of the challenging tasks are the

detection of new morphological classes that may ari se in the time series (as invasive species) and that are not part of the pre-trained images, and the optimization of the computation for massive data sets produced by the instruments. 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

Institut ITEM

- Aix Marseille Université Item -contact@univ-amu.fr - Site web ITEM devices (cytometry , ...) and descriptors construction (MIO and CEREGE teams, size spectra, biovolume, ...). o QUALIFICATIONS/SKILLS/EDUCATION & RESEARCH REQUIREMENTS/DUTIES The post-doc will be hired for 18 months with the following preferred skills: • Knowledgeable about clustering of large data set • Knowledgeable about image processing and analysis • Knowledgeable about machine learning in general and more particular in neural networks • Good programming skills in Python and in R (for further statistical analysis of links between environmental variables and change in plankton community) • Basic knowledge in parallel programming • Fluent in English (understanding and writing) • Knowledge in marine science or ecology The post-doc will be hired in an international group and is expected to be a team-player in a collaborative project. o

APPLICATION DEADLINE (If applicable)

November 18yh, 2020

o REQUESTED DOCUMENTS OF APPLICATION AND CONTACT TO APPLY To apply, candidates should send a CV, names and contact of at least 2 referees and a statement letter to David Nerini [david.nerini@univ-amu.fr] and Paulo Duarte Neto [pjduarteneto@gmail.com], and carbon copy to the PI of the project T. de Garidel [garidel@cerege.fr].

The selected candidates will be interviewed

(remotely) at the end of november/early december for an expected start in March 2021.quotesdbs_dbs48.pdfusesText_48

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