[Neuroimaging] Job offer - Lead developer - Brain Image Analysis (Paris, France)

Olivier Colliot olivier.colliot at sorbonne-universite.fr
Wed Sep 9 06:09:16 EDT 2020


We are recruiting a lead developer for the open source neuroimaging 
software platform Clinica (www.clinica.run).
Could you please help us circulate the job offer?

Thanks in avance
Olivier Colliot
olivier.colliot at sorbonne-universite.fr



*Lead software developer*

*Brain image analysis*

*Keywords:*Python, neuroimaging, image analysis, medical imaging

*The topic: Clinica – Open Source software for brain image analysis*

The ARAMIS lab develops the Open Source software Clinica 
(www.clinica.run <http://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

*Your mission*

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, 

- 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).

*A vibrant scientific, technological, clinical and ethical environment*

You will work within the ARAMIS lab (www.aramislab.fr 
<http://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 also 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.

*Your profile*

-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 

*Salary: *depending on experience

*Type of contract: *fixed-term contract

*Ready to take up the challenge? *

Send your CV to olivier.colliot at sorbonne-universite.fr 
<mailto:olivier.colliot at sorbonne-universite.fr>and to 
ninon.burgos at icm-institute.org <mailto:ninon.burgos at icm-institute.org> .

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