Offre en lien avec l’Action/le Réseau : – — –/– — –

Laboratoire/Entreprise : ARAMIS Lab (Institut du Cerveau / Inria)
Durée : CDD
Contact : ninon.burgos@icm-institute.org
Date limite de publication : 2020-12-31

Contexte :
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

Sujet :
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).

Profil du candidat :
Engineer with experience in medical image processing and Python development. An interest in neuroscience applications, as well as a curious and eager to learn personality will be highly appreciated.

Formation et compétences requises :
– PhD degree or Master+experience in the field of medical imaging
– 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

Adresse d’emploi :
Institut du Cerveau
Hôpital de la Pitié-Salpêtrière
47 boulevard de l’hôpital
75013 Paris

Document attaché : 202009111249_clinica_neuroimaging-v2.pdf