MR Spectroscopy: pre-processing et Graphical User Interface
Recrutement en cours/passé: 
Recrutement en cours

Keywords MR spectroscopy, signal processing, Graphical User Interface

Contexte The cQuest software (Custom - QUantitation based on semi-parametric QUantum ESTimation )realizes the quantification of magnetic resonance spectroscopy signals: it extracts physical parameters from thesignal, including the contribution (directly related to the concentration) of resonant molecules. The user can designits quantification strategy and can control the constraints applied at the time of adjustment. The main advantageof the software is its modularity: the user can, via a parameter file constraints feed with knowledge a priori andadjust the model that will be used to analyze the spectroscopy data. So he has the potential to adapt to any typeof acquisition (all types of nuclei, organs, or NMR spectroscopy techniques). In addition, it is a command-linesoftware that can be launched on a computing cluster to quantify many signals in series. 

Objectifs The objective of this internship is to make the use of this soft easier by the development of a graphical interface that will allow the user to:

  1. do pre-processing in interactive mode to prepare the signal for the quantification stage
  2. easily create the parameter file and the \textit{a priori} knowledge used by the quantification software
  3. view and manipulate the quantification results

It is proposed to develop this interface in Python, starting in particular from the open-source nmrglue ( module.This library offers read routines for several file formats and 1D and 2D spectral viewing routines.We will evaluate during the internship the possibility of doing a second version in javascript that can be used via a web interface.

Application For the internship, the candidate will be asked serious and autonomy as well as:

  • good programming skills
  • knowledge in python
  • knowledge in javascript
  • notions of signal processing

Interested candidates will send any relevant documents (cover letter, CV, letters of reference, transcripts, ...) to: michael.sdika[at] and helene.ratiney[at]

Location, Duration, Indemnities

  • Laboratoire CREATIS3 , Lyon, France
  • Applications for internships of 3 or 6 months will be considered
  • about 500 euros / mois.


Region Auvergne Rhone Alpes

As part of the 2015-2020 State-Region Plan Contracts, the région Auvergne-Rhône-Alpes is financing a Magnetic Resonance Imaging and Spectroscopy system at high magnetic field of 11.7T to contribute to the research and innovation. This equipment is co-financed by the Délégation Régionale à la Recherche et à la Technologie and the Centre National de la Recherche Scientifique. This equipment will be acquired by INSA Lyon and operated by the PILoT platform of the CREATIS laboratory located on the LyonTech-La Doua campus to increase the imaging capacity in basic and preclinical research at the University of Lyon and the région Auvergne-Rhône-Alpes.