Image Data annotation

 Stage · Stage M2  · 6 mois    Bac+5 / Master   CNRS. Biocampus Montpellier et Institute de Genetiqeu Humaine · Montpellier (France)

 Date de prise de poste : 17 janvier 2022

Mots-Clés

Imagerie, FAIR data, Data management

Description

Montpellier Ressources Imagerie (MRI, https://www.mri.cnrs.fr/) is a large core facility providing access to state of the art microscopy resources and expertise to the research community, mainly in Montpellier, but also across France (https://www.mri.cnrs.fr/). As a key aspect of its activity, MRI wants to promote good data annotation practices among researchers. We have put in place an OMERO server (https://www.openmicroscopy.org/omero/) to manage image data according to the FAIR principles (https://www.go-fair.org/). Correct and thorough data and metadata annotation is fundamental for scientific research. It allows for a proper review process, grants reproducibility and casts information as a resource, empowering reuse of knowledge, recognition of the researchers work and saving valuable resources.

In this rotation project of 6 months, we aim to research and understand the requirements of the FAIR principles and provide practical guidelines for the researchers to annotate their data. We also want to apply those practices through a recently developed annotation web tool.

The role of the student will be to:

  • Test this tool and validate their compatibility with the FAIR principles.
  • Train an already selected group of scientists to the usage of this tool.
  • Supervise the scientist’s usage of the tool on a regular base and provide feedback to the developer to improve the tool.
  • Interact with the broader community providing tools for microscopy image data management.
  • Develop clear guidelines for the homogenization, standardization, and completeness of data annotation according to the FAIR principles and in a way that is ready for publication.

ENVIRONMENT

The student will be hosted at the Institute of Human Genetics (IGH, https://www.igh.cnrs.fr/), where the three research teams fulfill their research activity and one of MRI’s core facility sites is hosted. The IGH is a joint research institute dedicated to excellence in fundamental research and study of pathologies.

The work will be supervised by:

  • Julio Mateos-Langerak: Ingénieur de Recherche CNRS. Data management responsible at MRI.
  • Guillaume Gay: Ingénieur de Recherche Université de Montpellier. Developer of annotation tools.
  • Frédéric Bantignies: Directeur de Recherche CNRS.

The student will have to closely interact with a number of different actors of the research community such as researchers, technical staff and developers. In particular, the student will have to interact with a very active network constructed around the data management of microscopy, mainly through the image.sc forum (https://forum.image.sc/).

DIDACTIC CONTENT

The student will acquire a good understanding of the state-of-the-art scientific data management: what it is, what are the motivations and what are the FAIR principles. He/She will learn how it is implemented in practice, in this case, in a concrete data modality in biologic research, that is microscopy data.

The student will learn what is the research data work flow and life cycle: how microscopy data is collected, analyzed, managed and published along the research process.

Importantly, the student will develop his interactivity skills through working in a multidisciplinary environment where understanding the needs of the user community will have to be ‘translated’ into concrete implementations in a software tool.

Candidature

Procédure : Envoyer mail a: Julio MATEOS LANGERAK: julio.mateos-langerak@igh.cnrs.fr cc Frederic BANTIGNIES: frederic.bantignies@igh.cnrs.fr

Date limite : 10 décembre 2021

Contacts

Julio Mateos Langerak

 juNOSPAMlio.mateos-langerak@igh.cnrs.fr

Offre publiée le 17 novembre 2021, affichage jusqu'au 17 décembre 2021