Development of a web application to host image analysis tools and biology workflows

The Inria center at the University of Rennes is one of eight Inria centers 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 ecosystem of R&D and innovation, including highly innovative SMEs, large industrial groups, competitiveness clusters, research and higher education institutions, centers of excellence, and technological research institutes.

The aim of the internship is to develop a web application dedicated to hosting and sharing image analysis tools for biology.

Sairpico project team

The project will take place within the Sairpico team, which specializes in the development of innovative methods for the restoration and reconstruction of microscopy images, the analysis of motion and the calculation of molecule trajectories in the imaging of living cells, and the estimation of biophysical parameters.

Image analysis in biology

The community of biologists and microscopy image analysts uses numerous software components to extract and quantify the information required for their experiments (denoising, particle detection, segmentation, tracking, etc.). These highly diverse tools are developed in different programming languages, often require specific software environments, and are not easily accessible on a centralized platform. Without rigorous organization, image management and analysis in biology do not respect the FAIR (Findable, Accessible, Interoperable, Reproducible) principles, which establish that data must be easily found, accessible, interoperable and reproducible.

BioImageIT is an application that integrates data management with image analysis in a single solution. This workflow manager greatly simplifies the process of installing software components, managing dependencies and software environments, structuring metadata and running processing tools on computing clusters. Analysts can now create their own processing chains and run them to complete their experiments.

To promote the exchange and reproducibility of software components, the biology analyst community needs a web platform to host the tools required for their work. This includes software specific to each processing step, as well as entire workflows, whether in BioImageIT format or as a Jupyter notebook.

 

Responsibilities
With the help of research engineer Arthur Masson and, more broadly, the Sairpico team, the person recruited will develop a solution to facilitate the accessibility and sharing of image processing tools within the microscopy for biology analyst community.

Collaboration
The person recruited will be in contact with FBI Data, France-BioImaging's data management team.

Responsibilities
The person recruited will be responsible for the software development and deployment of the platform, and will take initiatives to design a tool adapted to the needs of the microscopy analyst community.

Main activities:

    Analyze the needs of the microscopy image analyst community, in particular with the France BioImaging FBI Data and FBIAS groups.
    Analyze existing sharing platforms (Knime Hub, nf-core, bioconda, etc.), then define platform specifications.
    Study web development solutions (Next.js, etc.) to make relevant technological choices.
    Implement unit and functional tests to meet specifications.
    Develop and deploy a web platform meeting the objectives set.

Additional activities :

    Write the platform documentation.
    (optional) Animate the user community.
    (optional) Present work progress to partners.

 

Technical skills and level required:

Fullstack web development with one or more web frameworks; proficiency in git; ability to write clear, documented and tested code.

 

Additional skills appreciated:

Ability to listen, to make proposals, to be autonomous, to plan and carry out projects.

• Subsidized meals
• Social, cultural and sports events and activities