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Portail > Offres > Offre UMR7093-JEAIRI-003 - Ingénieur d'étude pour la gestion de données issues d'images de plancton (H/F)

Engineer (M/F) in data management for plankton images

This offer is available in the following languages:
Français - Anglais

Date Limite Candidature : lundi 15 mars 2021

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General information

Reference : UMR7093-JEAIRI-003
Workplace : VILLEFRANCHE SUR MER
Date of publication : Monday, February 22, 2021
Type of Contract : FTC Technical / Administrative
Contract Period : 8 months
Expected date of employment : 1 June 2021
Proportion of work : Full time
Remuneration : Between 2100 and 2500€ per months before taxes depending on experience.
Desired level of education : 3-year university degree
Experience required : Indifferent

Missions

Manage the quantitative imaging data collected by the team and its partners through various ongoing projects.
Members of COMPLEx are involved in several ongoing projects: pan-oceanic cruises with the Tara shooner, TRIATLAS and AtlanECO for plankton ecology in the offshore Atlantic, JERICO-S3 for coastal observations, BlueCloud for data integration at European level, MarTERA and TechOceanS for instrument development, etc. In all projects, one of their goals is to collect plankton images and extract data from them. A major hindrance to the quick extraction of knowledge from the data is the amount of data handling needed between its acquisition and its use, for which the team has no dedicated expertise and therefore developed only sub-optimal approaches. This position is destined to fulfil this pivotal role in the team's activity.

Activities

● ensure the data collected fits in the existing data stores and databases of the team
● develop quality control routines and dashboards before database ingestion, that are usable by other operators with no programming background
● develop custom database extractions routines/packages using the APIs of the databases
● provide overview tables and plots of the extracted data
● specify requirements for the development of the quality control routines, the APIs etc. to distribute to subcontractors
● possibly help rewrite some data processing routines involving computer vision algorithms

It may be relevant for the candidate to go at sea to participate in and understand the full process from data acquisition to data storage.

Skills

General skills:
● Database and APIs usage
● Data handling in various formats: geospatial, flat tables, etc.
● Unit testing of code and data properties
● Interactive dashboards building
● Some knowledge of image processing/computer vision would be a plus
Technical skills :
● Proficiency in scripting languages such as R and Python (or MATLAB).
● Knowledge of SQL.
● Applicants should be comfortable handling datasets with millions of records and interacting with the databases that host them, all in a Unix environment.
● Experience will image processing software such as scikit-image or ImageJ would be a plus
Transdisciplinary skills:
● Ability to interact with environmental scientists, who may have limited knowledge of the technical domain of expertise of the position
● Write synthetic reports and tutorials for other team members
● Scientific and technical English (B2 level for written and oral). French would be a plus, but it is not mandatory.
● An interest towards ecology, marine in particular would be welcome to keep the applicant motivated.
Human skills:
● Strong ability for teamwork, since the position is at a central place in the team
● Autonomy to suggest and implement technical solutions

Work Context

The Laboratory of Oceanography of Villefranche-sur-mer (LOV; http://lov.obs-vlfr.fr/) is located close to Nice, on the French Riviera. It belongs to one of the three marine stations of Sorbonne Université. With about 90 permanent staff, the LOV generates and analyses a large quantity of marine data, including imaging, genomic, and satellite data to study the ocean.
The COMPLEx (COMPutational PLankton Ecology) team gathers ~30 members studying marine plankton by collecting data with quantitative imaging instruments and high throughput genomics, then feeding into numerical analysis methods (modeling, statistics, machine learning). Plankton encompasses all organisms roaming with marine currents. Those organisms are responsible for producing some of the oxygen we breathe, storing the carbon we emit, feeding the fish we eat; plankton is therefore a major building block of Earth's ecosystem. COMPLEx strongly interacts with the Quantitative Imaging Platform of Villefranche (PIQv; https://sites.google.com/view/piqv), which oversees the operation of tools that the team develops. Those tools include imaging sensors, such as the Underwater Vision Profiler or the ZooScan, and software packages, such as ZooProcess or the EcoTaxa web application (https://ecotaxa.obs-vlfr.fr/) that uses machine learning to assist taxonomists into sorting plankton images. We also have a long experience in interacting with computer scientists, in academia (e.g. LS2N in Nantes, I3S in Nice, ENSTA in Paris, MIP in Kiel) but also in the private sector (e.g. Google Brain lab in Paris).

Constraints and risks

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Additional Information

For more information, please contact irisson@obs-vlfr.fr.

The initial contract is for 8 months but a second contrat on the same theme is already planned for 11 more months, on a different financial source.

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