PhD positions

We currently have the following open position:

PhD student – Early Stage Researcher (ESR) (f/m)

INSPiRE-MED (Integrating Magnetic Resonance Spectroscopy and Multimodal Imaging for Research and Education in MEDicine)

Title: Maximize metabolic information in a multi-parametric study at ultra-high field, from pre-clinical to clinical validations

Project description

This position is one of the 15 ESR positions of the INSPiRE-MED European Training Network, which focuses on the development of Magnetic Resonance Spectroscopy (MRS) and MR Spectroscopic Imaging (MRSI) combined with Positron Emission Tomography (PET), enhanced by machine learning techniques.

The main objective of this study is to maximize the metabolic information in a multi-parametric approach at ultra-high field, from pre-clinical to clinical validations. We will first develop a multimodal MRS(I) approach for maximizing the metabolic content using optimized determination of diffusion proprieties of metabolites combined with optimized sequences for specific metabolites and macromolecules detection, with proton (1H) and hetero-nuclear MRS (31P) at high field. We will then evaluate the benefits of improved multimodal MRS in clinical and pre-clinical applications: extension of diagnostic evaluation from tissue structure characterization to changes in brain metabolites at macro- and micro-scale.

Research environment

This project is hosted by the Centre for Biomedical Research (CIBM). CIBM is involved in the INSPiRE project and is particularly known as a world leader in development and implementation of high field MRI/MRS of the brain. This center is the result of a major research and teaching initiative of the partners in the Science-Vie-Société (SVS) project, namely the Université de Genève (UniGE), the Université de Lausanne (UNIL) and the EPFL, as well as the corresponding University Hospitals, the Centre Hospitalier Universitaire Vaudois (CHUV) and les Hôpitaux Universitaires de Genève (HUG). The candidate will be part of a team composed of several PhD students and experienced researchers involved in developing new MR methodologies and doing exciting applications of MR spectroscopy and imaging on humans and rodents.

The selected candidate will be able to take advantage of the unique set-up of the INSPiRE-MED network, encompassing 12 academic and 9 industrial partners providing the young researchers with transferable and generic skills as well as a comprehensive, wide-ranging education on the basic principles of medical imaging and image analysis. This multi-disciplinary environment encompasses physics, mathematical and computer sciences, with applications in medicine and biological sciences.

Your profile

You should have a master’s degree in physics, biomedical physics, computer science, or a similar degree with an equivalent academic level. A genuine interest in magnetic resonance techniques, magnetic resonance spectroscopy data processing and research should motivate your application. Previous experience in MRI/MRS and programming skills (e.g. matlab) will be a plus. The candidate should be fluent in English and have strong social abilities allowing an active participation to the European network, fruitful exchanges with other students and researchers, and an excellent integration in the team of your research group. You should be ready and able to travel in Europe for the network meetings as well as for sharing the experience of your secondment team.

Eligibility and Mobility Rule

Early-Stage Researchers shall, at the time of recruitment by the host organization, be in the first four years (full-time equivalent research experience) of their research careers and have not been awarded a doctoral degree. At the time of recruitment by the host organization, researchers must not have resided or carried out their main activity (work, studies, etc.) in the country of their host organization for more than 12 months in the 3 years immediately prior to the reference date.

General

  • Location:CIBM/EPFL, Lausanne, Switzerland
  • Gross salary: (pre-employer/employee and income tax):  3270 €/month [110%, meaning 3597 €/month]
  • Mobility allowance: (pre-employer/employee and income tax): 600 €/month
  • Family allowance: (pre-employer/employee and income tax): 500 €/month (if applicable)
  • Start date: between January and October 2019
  • Duration: 36 Months

To apply: Please email your CV and motivation letter to Dr. Cristina Cudalbu: cristina [dot] cudalbu [at] epfl [dot] ch, please add in the email subject “INSPiRE-MED”

 

Advanced super-resolution reconstruction methods for quantitative magnetic resonance imaging of the developing fetal brain

Location: This project will take place in the Center for BioMedical Imaging (CIBM) and the Department of Radiology at the Lausanne University Hospital (CHUV) and the University of Lausanne (UNIL) in Switzerland.

Start date: January 2019 (roughly)

Project description: Today, there is an increasing awareness that early brain development has an influence on health later in life. However, the study of brain maturation in vivo is challenging as it involves several complex intertwined processes. Quantitative MR imaging (qMRI) has gained a lot of attention in recent years and was shown to provide sensitive information on subtle changes in brain tissue after birth. Combining this sensitivity with super-resolution techniques adapted to prenatal imaging would allow high-resolution 3D quantitative MR imaging of the fetal brain, presenting a great opportunity to learn and understand more about the processes governing early brain maturation in utero.

The main goal of this project is to develop advanced quantitative imaging techniques for studying the maturation of the human brain in its early stages of development, when it undergoes the most significant changes. To this end, we will conceive and implement new SR reconstruction methods in conjunction with novel segmentation and MR image acquisition schemes. Specifically we will develop (i) an integrated reconstruction and segmentation framework for T2w fetal imaging, (ii) a SR framework for the reconstruction of diffusion MR images (dMRI), and (iii) new qMRI sequences for T1 and T2 mapping of the fetal brain. This project is funded by the Swiss National Science Foundation (SNSF 205321_182602), total duration of 48 months, three research positions are currently available: 2 PhD students and 1 post-doc.

Research environment: This project is hosted at Medical Image Analysis Laboratory (MIAL), lead by Dr M. Bach Cuadra, of the Radiology Department and Center for Biomedical Imaging (CIBM) of the Lausanne University and University Hospital (CHUV/UNIL). MIAL is a group of ~10 engineers with the aim at develop novel image processing methods to allow a more effective use of emerging medical images, balanced between fundamental research aspects of image processing and application-oriented projects. We have access to several state-of-the-art clinical MRI scanners, and we have active collaborations with the CHUV departments of Radiology, Neurology, Neurosurgery, and Cardiology as well as with the ACIT Siemens and EPFL.

This project will be held in collaboration with the Radiology Department at CHUV (lead by Prof. R. Meuli), the MR CHUV CIBM unit (lead by Prof. M. Stuber), Universitäts-Kinderspital Zürich (KISPI), Center for MR-Research (Dr A. Jakab) and ACIT group at Siemens Healthineers Switzerland (lead by Dr. T. Kober).

 

2 PhD student researchers for

« Quantitative MR imaging of the in-vivo fetal brain »

Position:We are looking for two motivated students for a PhD candidacy positions (4 years funding with annual renewal of contract) at the Medical Image Analysis Laboratory of the Radiology Department and Center for Biomedical Imaging, Lausanne University.

Description : We look for two PhD student candidates that will work jointly with a post-doctoral researcher expert in MR physics and under the direction of Dr. Meritxell Bach Cuadra. The two PhD thesis projects are:

  1. The development machine learning segmentation methods for the fetal brain analysis and their integration to a joint segmentation-super-resolution reconstruction of T2-weighted and T2 quantitative images of the fetal brain.
  2. The development of an image processing pipeline for the super-resolution reconstruction of diffusion fetal brain MRI, including the exploration of new acquisition schemes on phantom data.

Profile:

  • You should have a master’s (MSc) degree in physics, computer science, or electrical engineering, or similar degree with an equivalent academic level.
  • A genuine interest in signal and image processing and machine learning techniques is a must.
  • Strong mathematical background.
  • Good programing skills in C++, ITK and Python (knowledge of MevisLab is a plus).
  • Prior exposure to medical imaging and or neuroimaging is a plus.
  • Good skills in English (oral and written).
  • Rigorous work habits, a curious and critical mind, and a good sense of initiative.
  • A high-level perseverance and a strong personal commitment are expected.

We offer :

  • A multidisciplinary project between cutting-edge brain imaging and advanced image processing, MR physics, and clinical context.
  • An extremely stimulating field of research within a highly specialized and qualified scientific environment.
  • Access to state-of-the-art clinical MRI scanners.

Gross salary (pre-employer/employee tax): In compliance with Swiss National Science Foundation and UNIL.

Successful applications are subject to academic approval from the UNIL and Doctoral School; the selected candidate will be enrolled in Life Science Doctoral School at UNIL.

To apply: If you recognize yourself in this profile and want to take up a new challenge, address your complete application (CV, list of publications and 2 references) before December 9th 2018 to: Meritxell [dot] BachCuadra [at] unil [dot] ch, with “SNF – Fetal” in the mail subject.

 

PhD student in MR Physics

The laboratory of functional and metabolic MRI of the University of Geneva is offering a PhD scholarship in physics. The laboratory is closely linked to the Center for Biomedical Imaging (CIBM) of the University of Geneva with the mission to advance bioimaging techniques (MRI) addressing biomedical and clinical questions. Specifically, the laboratory aims at developing new acquisition and reconstruction techniques for metabolic imaging.

The laboratory is housed in the radiology department of university hospital of Geneva.

The position is related to a 4-years project funded by the Swiss National Science Foundation (SNF) on Kidney Preservation with Hydrogen Sulfide and Pre-Transplant Assessment by MRI. The goal is to develop MRI and 31P metabolic imaging techniques of the kidney to assess its viability before transplantation.

We are looking for an enthusiastic PhD student willing to work in a multidisciplinary team.

The appointee will work primarily on a 3T MRI clinical system (Prisma, Siemens) located in the radiology department in Geneva. The post-holder will benefit from a very rich research environment provided by the CIBM (signal processing, experimental MRI, ultra high field MRI cores).

Duties and Responsibilities

  • Carry through and independent research project under supervision
  • Complete PhD courses
  • Conduct necessary MRI experiments and analysis, communicate the results
  • Participate actively in the research project including participation to meetings and stay at other
    research groups
  • Disseminate results through scientific publication and conference presentation
  • Completing a PhD thesis on original research

 

Qualifications

  • Master degree, preferably in physics, Biomedical imaging/engineering or related field
  • Strong interest in medical imaging application
  • Good programming abilities with Matlab, python, C or C++
  • Excellent communication skills
  • Experience in modeling or signal/image processing
  • Good language skills in English and French

Application
Applicants should send by email a CV and letter to Prof. Francois Lazeyras (francois [dot] lazeyras [at] unige [dot] ch)

Starting date: January 1st 2019

 

PhD student – Developing quantitative MRI of the neck for the assessment of stroke risk

Background
Atherosclerosis results in the formation of plaque in the carotid arteries, which can lead to lethal stroke when it ruptures. While surgery and therapy can be used to prevent such rupture, current medical imaging is not specific enough to predict which plaques will rupture. MRI can be used to quantify several rupture risk factors, but not the inflammation severity of the plaque, which is thought to be the most critical risk factor. The goal of this project is therefore to develop a new combined fluorine-19 (19F) MRI and parameter (T1 and T2) mapping technique for the quantification of plaque rupture risk factors: 19F MRI will be used for inflammation mapping, while the parameter mapping will be used for tissue characterization. The project is funded by the Swiss National Science Foundation (SNSF).

Project description
You will have two parallel multidisciplinary projects that focus on MRI of the neck. In the first you will develop and validate a new 3D motion-resolved parameter mapping technique, while in the second project you will optimize the performance of 19F MRI in the clinical setting. These projects will involve programming MRI pulse sequences in Matlab and C++, mathematical optimization and image reconstruction, as well as scanning phantoms and healthy volunteers. Once both techniques have been optimized, they will be validated in a clinical trial with patients that will undergo plaque removal surgery (endarterectomy) to avoid stroke.

Time
The position is available immediately; a PhD program will normally take 4 years to complete.

Location
This PhD project will take place in the Center for BioMedical Imaging (CIBM) and the Department of Radiology at the Lausanne University Hospital (CHUV) and the University of Lausanne (UNIL) in Switzerland. You will be part of a group of ~15 engineers and physicists that is embedded in the hospital. The group has access to 4 state-of-the-art clinical MRI scanners, and has active collaborations with the Departments of Neurology and Cardiology as well as the research department of Siemens.

Your profile
We are looking for highly motivated candidates with a Master’s degree in engineering, physics, life science or a similar degree, preferably at ease with programming and applied mathematics.

Supervision and contact
For further information or to apply (including a CV and two references), please contact Dr. Ruud van Heeswijk, PhD (ruud [dot] van-heeswijk [at] chuv [dot] ch), or visit CardioVascular Magnetic Resonance research center.

PhD student at CHUV MR

  • Do you have an Masters degree in Physics, Engineering or SV?
  • Would you like to use your engineering skills to help improve modern diagnostic technology, to make it more time efficient, easier to use, and more affordable?
  • Would you like to be part of a team that changes the way magnetic resonance imaging (MRI) of the heart is done?

Should the answer to the above questions be “yes”, then please apply for a PhD position at CIBM-CHUV-MR that consists of 17 engineers and physicists and that is working in a direct interdisciplinary and translational collaboration with industry and medical professionals at the CHUV.

Please contact Prof. Matthias Stuber (matthias [dot] stuber [at] chuv [dot] ch) or PD Dr. Ruud van Heeswijk (Ruud [dot] Van-Heeswijk [at] chuv [dot] ch), should you be interested.

PhD student – Functional Renal Magnetic Resonance Imaging

The Faculties of Medicine and Science of the Geneva University Hospital are seeking to fill a full-time (100%) vacancy in the Department of Radiology and Medical Informatics in the context of the EU COST action CA16103 and the Swiss National Science Foundation SNSF-COST project 177140 for a

PhD student in the field of functional renal magnetic resonance imaging in
chronic kidney diseases.

About the EU COST action CA16103 « PARENCHIMA » and the SNSF-COST project 177140 (COST action CA16103) The overall aim of EU cost action PARENCHIMA is to eliminate the main barriers to the broader study, commercial exploitation and clinical use of renal MRI biomarkers. PARENCHIMA will coordinate the research of leading European groups in this area to:

  1. improve the reproducibility and standardisation of renal MRI biomarkers;
  2. increase their availability by developing an open-access toolbox with software and data; and
  3. demonstrate biological validity and clinical utility in a prospective multicentre clinical study.

To support this networking COST action, the Swiss National Science Foundation (SNSF) has funded a multicentric study on renal MRI in chronic kidney disease patients. This study includes the funding for the present PhD student position.

About the functional cardiac and renal imaging group
We are a clinical research group in the radiology department of Geneva University Hospital with a strong focus on cardiac and renal imaging. Our group is composed of radiologists and MR specialists with a strong collaborative network inside the CIBM.

Job description – your research tasks
Specifically, you will be responsible for the acquisition and analysis of renal MRI exams in chronic kidney patients scheduled before their renal biopsy in the 2 centers (Geneva and Lausanne) in collaboration with Dr Menno Pruijm and Pr H. Thoeny. You will develop MR pulse sequences and reconstruction algorithms as well as work on the optimisation of a multiparametric renal MR acquisition protocol. Using the expertise available in the EU COST network, advanced analysis tools in this patient cohort will also be developed. You will work closely with radiologists and nephrologists to interpret the data. You will be located in Geneva but you will travel once a week to Lausanne and Fribourg according to the patient recruitment.

Profile and requirements

  • Master or equivalent, preferably in MR Physics, Biomedical
  • Imaging/Engineering or related field
  • Programming abilities with Matlab, C and C++, as well as R
  • Good communication skills
  • Experience in signal/image processing is an advantage
  • Good level of written and spoken English

General

  • Full time position, starting in September 2018
  • Standard SNSF salary for PhD student (CHF 47’040/year)
  • Four year PhD program
  • The call will be closed on July 15th 2018 and an answer will be given to candidates at the end of July 2018.
  • For questions about the profile and the description of duties, please contact:

Prof. Dr. Jean-Paul Vallée or Dr. Lindsey Crowe

Applications
Applications should be sent by email including a CV, motivation statement, master final marks, list of publications if any and at least 2 reference letters to:Prof. Dr. Jean-Paul Vallée