Developer on a medical image processing platform using distributed (cloud) computing resources

Context:

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.

Within this infrastructure, the Node “Image Analysis and Management” (IAM) is coordinated by Inria. The objective of this node is to propose an infrastructure to store, manage and process in-vivo imaging data coming from human or pre-clinical procedures. We contribute to an archiving and management infrastructure of in-vivo images as well as provide solutions to process and manage the acquired data through dedicated software and hardware solutions. In addition, we have built a versatile image analysis and data management solution for in-vivo imaging that will allow the interoperability between distributed production sites and distributed users, heterogeneous and distributed storage solution implementing raw and meta-data indexing.

In this context and within the last years we have collected and maintained different kind of data, using the web-based image database, called Shanoir, and different kind of processing algorithms, using the Virtual Imaging Platform.

The Virtual Imaging Platform (VIP) is a web portal developed at CREATIS for the simulation and processing of massive data in medical imaging. One of the VIP main aims is to provide access to distributed computing resources in a transparent way for the end users. VIP has thus the capacity to manage large and complex workloads (generate, schedule and execute multiple jobs) automatically, while requiring no specific skills from its users. It is VIP developers and administrators that are in charge of making this possible. The VIP instance currently deployed at CREATIS uses mainly the storage and computing resources provided by the EGI e-infrastructure. A growing number of projects with various requirements (sometimes security driven) require access to computing and storage resources (e.g., local clusters, private/public clouds) that are not member of the EGI federation.

Objectives of the position

The main objectives of the position are

• Software development and testing
  • Adaptation of the current implementation of VIP and related dependencies for the targeted infrastructure
  • Implementation of the associated tests
  • Continuous integration (CI)
• Deployment and configuration
  • Automation on the deployment and configuration procedure on the targeted infrastructure with Ansible scripts
• Maintenance and support
  • Maintenance and support for the VIP instance deployed on the targeted infrastructure

Within this context, the recruited developer will work on deploying VIP on new computing and storage infrastructures, such as the ones provided by Eskemm Data. He/She will be under the supervision of the manager of the VIP platform and will interact with the other VIP engineers and the FLI-IAM engineering team. He/She will be hosted at the CREATIS lab (Villeurbanne).

This position offers:

• Rich communication and exchange with top level research teams in France dealing with medical imaging, image processing and medical image distributed data
• The chance to work in an interdisciplinary environment
• A working environment with innovative technological software solutions and highly motivating operational goals
• Enjoyable working environment: dynamic campus with sport activities and cultural facilities, soft mode transport

Scientific and technical qualifications:

• High level education in computer science (PhD or grande-école), specialized on computer science
• Software development experience (Java, Python, Bash)  
• Experience with IntelliJ or other IDEs, git, GitHub/Gitlab
• Experience with Linux operating systems
• Experience in the field of cluster and/or Cloud computing (Slurm, OpenStack, Kubernetes)
• Knowledge of Ansible
• Rigor, autonomy, technical curiosity, passion for new technologies
• Good capability in technical and scientific English

• Subsidized meals
• Partial reimbursement of public transport costs
• Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
• Possibility of teleworking (after 6 months of employment) and flexible organization of working hours
• Professional equipment available (videoconferencing, loan of computer equipment, etc.)
• Social, cultural and sports events and activities
• Access to vocational training
• Social security coverage