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


Imagerie, FAIR data, Data management


Montpellier Ressources Imagerie (MRI, 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 ( 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 ( to manage image data according to the FAIR principles ( 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.


The student will be hosted at the Institute of Human Genetics (IGH,, 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 forum (


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.


Procédure : Envoyer mail a: Julio MATEOS LANGERAK: cc Frederic BANTIGNIES:

Date limite : 10 décembre 2021


Julio Mateos Langerak

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