Offre d'emploi Imaging Data Engineer for Medical Radiology Department

Description

Contexte

The Lausanne University Hospital (CHUV) is one of five Swiss university hospitals. Through its collaboration with the Faculty of Biology and Medicine of the University of Lausanne and the EPFL, CHUV plays a leading role in the areas of medical care, medical research and training.

The Radiology Department has a strong research focus, with several groups dedicated to advancing magnetic resonance imaging (MRI) acquisition, improving image processing and machine learning for radiology, as well as radiologists that are very active in clinical research.

Part of the CIBM constellation, the CIBM Data Science CHUV-HUG Imaging for Precision Medicine Section focuses on developing machine learning methods to integrate imaging with other types of data, in particular -omics data. The ambition is to leverage this combination to improve diagnostic, prognostic, subtyping, and treatment planning for individual patients. In support of this aim, the section develops data science tools and infrastructure integrating with hospital IT systems at every stage of fundamental research—from pre-study planning to post-study analysis—while also creating reusable methods for various areas of biomedical imaging.

The Lundin Family Brain Tumour Research Centre at CHUV is a trailblazing institution committed to driving progress in the field of brain tumour research, with a mission to promote clinical innovation aimed at enhancing the survival and quality of life for patients with this illness. Efforts concentrate on transformative brain tumor research, clinician and researcher training, and building a large open-access brain and spinal cord tumour database.

Mission

PROJECT DESCRIPTION

The overarching goal is to develop the data science infrastructure necessary for large-scale, automated medical image storage, sharing, and processing, according to best national and international standards. This infrastructure is developed jointly by CIBM and the Lundin Center for Brain Tumor Research under two projects with overlapping aims:

- The Multi-institution computable biomedical imaging platform project, supported by the CIBM and Swiss Data Science Center, aim at building an open research imaging data infrastructure linking the two University Hospitals of Lausanne and Geneva, the Universities of Lausanne and Geneva, and the EPFL. The core platform we use and contribute to is the open source, INRIA-led Shanoir project.

- The CHUV-Lundin Brain Tumor Database project, funded by the Lundin Family Center for Brain Tumor Research, aims at building the most complete brain tumor database in the world, comprising clinical data, imaging data, and omics data. With a target size of several thousand patients, and a commitment to open science from the beginning, this ambitious project aims at supporting data-driven research in brain cancer.

Tasks for the imaging data engineer position include

• Develop image selection and depersonalization tools and pipelines based on metadata
• Develop and integrate ETL workflows and ensure correct data formats
• Integrate and develop tools for semantic data annotation and metadata management
• Interface with the storage and computing environment in each institution
• Develop, integrate and automate image analysis tools and services, including interfaces with existing platforms in institutions.
• Integrate and develop image segmentation tools and pipelines
• Prepare deployment of tools in the form of containers
• Optimize data processing, including performance, scaling, traceability, reproducibility.
• Use good development practices, including version control, unit tests, integration tests, CI/CD
• Develop and maintain documentation for pipelines and tools, including data dictionaries and standard procedures

The imaging data engineer will be affiliated to both the CIBM Data Science CHUV-HUG Imaging for Precision Medicine Section and the Lundin Family Brain Cancer Research Center at CHUV, under supervision of Dr Jonas Richiardi, Section Head at CIBM and Imaging Workgroup coordinator at the Lundin Family center. Most of the role's responsibilities will be carried out on-site at the Translational Machine Learning Laboratory (TML), part of the Department of Medical Radiology. To enhance cross-department collaboration, the imaging data engineer will be regularly embedded into the CHUV IT department’s data science team (DSI) or the HUG IT department imaging team (DSI), dedicating between half a day and a full day each week to improve collaborative efforts.

Profil

• MSc or PhD in computer science, data science, or related fields such as electrical engineering, biomedical engineering, applied mathematics, or statistics
• Demonstrated previous experience in DataOps, data processing, and big data pipelines
• Very good knowledge of Python 3.10+, including relevant data science libraries such as pandas/polars, SQLalchemy
• Demonstrated previous experience in software development, including object-oriented programming, architecture design, documentation, testing, and deployment.
• Experience in medical imaging, including international standards such as DICOM, and community standards such as BIDS, is a strong advantage
• English knowledge (B1+) mandatory, French knowledge (B1+) is a strong advantage
• Knowledge of ML libraries such as scikit-learn and Pytorch is an asset

As part of the CIBM Data Science CHUV-HUG section, the Lundin Center, and the Translational Machine Learning Laboratory, you will be part of a great team of scientists and engineers with various technical backgrounds, and interactions with medical professionals will be very frequent. Thus, the work environment and the project require strong communication ability and professionalism. Excellent inter-personal skills are as important as technical skills.

Our team has a gender equity focus and we strongly encourage women to apply to this position.

Nous offrons

To become an employee of the world-famous University Hospital Center from the Canton of Vaud is an assurance of:

• First-rate social benefits such as a Paternity Leave of 20 days and a Maternity Leave of 4 months (there is also the possibility to obtain a complementary breastfeeding leave of 1 month)
• Regular salary progression adapted to your responsibilities
• A 13th salary and 25 days of vacations per year
• A right to at least three days of training per year, by accessing a wide offer of courses not only from the CHUV Training Center but also from external providers
• Possibility to access one of the 500 furnished apartments offered in the surrounding neighborhoods in case of relocation in Switzerland
• Discounts proposed on social and cultural events, goodies and other services, thanks to the “H-Oxygène” association
• Signing up to our Mobility Plan and benefit from different advantages (discounts on public transportation, promotion of “Mobility” car fleet and discounts on electric bikes)
• Being able to enjoy our high-quality corporate restaurants, located in every hospital building, with employees’ discount

Contact et envoi de candidature

Contact person in case of questions about this role : Dr Jonas Richiardi - Research Manager -  (Please do not send your application by email)

All of our applications are processed electronically. For this reason, we kindly ask you to apply exclusively by clicking on the APPLY button at the bottom of the advertisement.

Should you experience any problems with your application, you can consult our document "". In case of technical issues, you can contact our Recruitment team who will help you ( / +41 21 314 85 70) 

The CHUV applies the highest quality requirements as part of its recruitment process. In addition, mindful to promote workplace diversity and inclusion we strive to ensure equal treatment and avoid any discrimination. We are looking forward to receiving your application.

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