Contract type : Fixed-term contract
Level of qualifications required : Graduate degree or equivalent
Other valued qualifications : PhD or Master+experience
Fonction : Temporary scientific engineer
A vibrant scientific, technological, clinical and ethical environment
You will work within the ARAMIS lab (www.aramislab.fr) at the Paris Brain Institute (http://www.icm-institute.org), one of the world top research institutes for neurosciences. The institute is ideally located at the heart of the Pitié-Salpêtrière hospital, downtown Paris.
The ARAMIS lab, which is part of Inria (the French National Institute for Research in Digital Science and Technology), is dedicated to the development of new computational approaches for the analysis of large neuroimaging and clinical data sets.
You will be strongly involved in scientific aspects of the work, such as discussion of methodological issues and interpretation of results. You will interact locally with the PhD students, postdoctoral fellows and engineers of the ARAMIS lab, as well as our medical collaborators. You will take part in the communications and publications resulting from the use of the software.
The topic: Clinica – Open Source software for brain image analysis
The ARAMIS lab develops the Open Source software Clinica (www.clinica.run), an end-to-end solution for brain image analysis. Clinica allows users to easily analyze large-scale clinical studies with advanced computational tools. To that purpose, it integrates tools for data management, image preprocessing for different modalities (anatomical MRI, diffusion MRI, PET), feature extraction, machine learning and statistics. Clinica is distributed freely to the scientific community and has 400+ users worldwide. It has been used to produce high impact medical publications which have advanced the understanding of neurodegenerative diseases such as Alzheimer’s disease, fronto-temporal dementia and amyotrophic lateral sclerosis. It is also widely used by researchers who apply machine learning to the diagnosis of brain diseases.
- Samper-González J, Burgos N, Bottani S, ..., Durrleman S, Evgeniou T, Colliot O, Reproducible evaluation of classification methods in Alzheimer’s disease: Framework and application to MRI and PET data. NeuroImage, 183:504–21,2018.
- Bertrand A, Wen J, Rinaldi D, Houot M, Sayah S, Camuzat A, Fournier C, Fontanella S, Routier A, Couratier P, Pasquier F, Habert M-O, Hannequin D, Martinaud O, Caroppo P, Levy R, Dubois B, Brice A, Durrleman S, Colliot O, and Le Ber I, Early cognitive, structural and microstructural changes in c9orf72 presymptomatic carriers before 40 years of age, JAMA Neurology, 75(2):236-245, 2018
- Wen J, Thibeau-Sutre E, Diaz-Melo M, …, Durrleman S, Burgos N, Colliot O, Convolutional Neural Networks for Classification of Alzheimer’s Disease: Overview and Reproducible Evaluation. Medical Image Analysis, 63: 101694, 2020
You will be the lead software developer of Clinica. As such, you will be in charge of:
- development of new features (image processing pipelines, traceability, visualization),
- validation of new analytic tools,
- project management (task follow-up, issue tracking, meeting organization),
- software maintenance,
- user support and animation of the community
- contribution to training and dissemination organized with the other engineers of the Inria center
In addition, you will be presenting the software at international scientific conferences and other events (organized for instance by Inria, ICM, CNRS…). Finally, you will contribute to ambitious medical studies, by deploying Clinica on large databases of patients, contributing to the interpretation of results and providing assistance to medical users (internal to the lab and external collaborators).
- Strong programming skills in Python
- Knowledge of digital image processing and medical imaging is mandatory
- Experience with neuroimaging data (and with neuroimage analysis software, e.g. Nipype, SPM, Freesurfer) would be a strong plus
- Good understanding of the software development process and tools (Git, continuous integration, tests)
- Excellent planning and organizational skills
- Good writing skills (documentation, website, scientific articles)
- Good relational and communication skills to interact with users and lab members
- 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
- Theme/Domain :
Computational Neuroscience and Medicine
Software engineering (BAP E)
- Town/city : Paris
- Inria Center : CRI de Paris
- Starting date : 2020-10-01
- Duration of contract : 3 years
- Deadline to apply : 2020-10-31
The keys to success
- PhD degree or Master+experience in the field of medical imaging
Inria is the French national research institute dedicated to digital science and technology. It employs 2,600 people. Its 200 agile project teams, generally run jointly with academic partners, include more than 3,500 scientists and engineers working to meet the challenges of digital technology, often at the interface with other disciplines. The Institute also employs numerous talents in over forty different professions. 900 research support staff contribute to the preparation and development of scientific and entrepreneurial projects that have a worldwide impact.
Instruction to apply
Defence Security :
This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.
Recruitment Policy :
As part of its diversity policy, all Inria positions are accessible to people with disabilities.
Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.