2021-04289 - Web developer for medical imaging platform

Contract type : Fixed-term contract

Renewable contract : Oui

Level of qualifications required : Graduate degree or equivalent

Fonction : Temporary scientific engineer

About the research centre or Inria department

The Inria Rennes - Bretagne Atlantique Centre is one of Inria's eight centres and has more than thirty research teams. The Inria Center is a major and recognized player in the field of digital sciences. It is at the heart of a rich R&D and innovation ecosystem: highly innovative PMEs, large industrial groups, competitiveness clusters, research and higher education players, laboratories of excellence, technological research institute, etc.

Context

Shanoir-NG (SHAring NeurOImaging Resources, Next Generation) is a platform that allows the sharing of in-vivo medical images, with their metadata, for clinical and preclinical research. The origin of the software is neuroimaging, but the platform is now perfectly usable for all kind of organs and pathologies. Shanoir allows the import of "raw" data from the various acquisition methods: DICOM (MR, CT, PT, NM), Bruker (preclinical), EEG (EDF + BrainVision) and "processed" data: NIfTI + Analyze. Shanoir-NG is a cloud-native state-of-the-art web application.

France Life Imaging (FLI) is a large-scale research infrastructure project aimed at establishing a coordinated and harmonized network of biomedical imaging in France. This project was selected by the call “investissements d’Avenir” as an “Infrastructure in Biology and Health”. Its objective is a) to coordinate nationwide research activities concerned with in vivo imaging and combine the skills to push the current technological barriers, and b) to provide scientists a convenient access to a complete range of imaging technologies (150 imaging systems) and integrated services. In addition, the infrastructure will be open to collaborations with industrial partners.

Within this infrastructure, the hub “Image Analysis and Management” (FLI-IAM) aims at building and operating an infrastructure to store, manage and process in vivo imaging data coming from human or pre-clinical studies. One of the main bricks of this infrastructure, allowing to store the data, is Shanoir-NG, developed and deployed at the Empenn laboratory.

Assignment

The goal of this position is to extend Shanoir-NG, to increase its interoperability on different levels
following the principles of open science and FAIR (find, access, interoperate, and reuse data):
- With academic portals, used by researchers world-wide to find medical data
- With biological or genetical databases, that are used by our partners
- With similar platforms or other infrastructures, e.g. in other countries
- With the processing platform VIP (https://www.creatis.insa-lyon.fr/vip/

Main activities

Objectives of the position:
In close cooperation with the technical manager, the main objectives of the position are:
- Gain a deep understanding of Shanoir-NG, its code structure and its data model
- Analyze standards, platforms or infrastructures of interest
--- Estimate the technical level and effort of interoperability
--- E.g. bioschema.org or France BioImaging (FBI, https://france-bioimaging.org/)
--- E.g. LabGuru or similar platforms
--- E.g. Canadian Open Neuroscience Platform (CONP)
- Implementation, testing and operate production deployment
--- Our production server is available on https://shanoir.irisa.fr
--- The goal is to deploy in production the developed extensions, to share data beyond FLI-IAM (see in “larger context”)

Skills

Scientific and technical qualifications:
- High level education in computer science (university or grande-école), specialized on software development
- 1-2 years of software development experience
- Good knowledge of Java Enterprise and Web Programming
- Good capability in technical and scientific English and oral practice
- Bonus
--- Knowledge in the field of medical imaging and image processing
--- Experience with GUI design, implementation and user experience
--- Experience with search engines and catalogs, type ElasticSearch or Apache Solr

Benefits package

  • Subsidized meals
  • Partial reimbursement of public transport costs

Remuneration

Monthly gross salary from 2562 euros according to diploma and experience