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Wednesday, 29 August 2018 11:25

[EXPIRED] Industrial Ph.D. Vacancy in 3D Image Analysis of the Obese Brain

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Job description:

We are looking for a talented student with a MSc or equivalent to work on a combined PhD project between DTU compute, Danish Research Centre for Magnetic Resonance (DRCMR) and Gubra. If you have an interest in bio-medical imaging and want to be part of discovering the mechanisms of obesity and how it affects the brain, this is the project for you.

A global obesity epidemic is roaming the world today and constitutes a major concern in public health. Although obesity affects many organs in the body, it is widely accepted that the key regulator of appetite and energy control is the brain. Recently, the development of a new imaging technology, light sheet fluorescence microscopy (LSFM), has made it possible to visualize the whole brain of an adult mouse in 3D with single cell resolution, hereby enabling a deeper understanding of how the brain responds to changes in body weight gain or loss in unprecedented detail (link).

The aim of this PhD project is to expand the use of light sheet microscopy by creating an automated 3D registration model of the mouse brain to encompass in vivo imaging modalities, such a MRI. Furthermore, computational modelling of diseased and healthy brains will aid the analyses and scientific understanding of brain activity related to appetite regulation and drug induced changes in body weight and support the development of new and better therapies in the fight against obesity.

Desired Skills and Experience:

For this PhD project we are looking for a talented and dedicated student. The focus of the project is on developing and implementing image registration of image data sets obtained using light sheet microscopy or MRI from various pre-clinical animal models of obesity. We are looking for a competent person with a strong computational background and a keen interest in quantitative image analysis and 3D reconstruction; a student who can navigate and collaborate in an energetic environment and help drive the project forward. The student will be employed at Gubra and enrolled at DTU Compute (located 10 kilometers from each other) and although your tasks are varied, they will include:

  • Development of algorithms and protocols for quantitative image analysis
  • Registration and segmentation of 3D volumes
  • Working with various imaging modalities (LFSM, MRI, light microscopy, etc.)
  • Following relevant PhD courses (at DTU, international PhD-schools and others)

Professional qualifications:

  • Strong computational skills and experience with quantitative image analysis
  • Experience with image registration is an advantage
  • Experiences in programming for data analysis using e.g. Matlab, Python, C or other language

Personal qualifications:

  • You are ambitious and innovative
  • You are not afraid to take responsibility and initiative
  • You can communicate in English (oral and written)

Please apply no later than September 15th, 2018 by uploading your motivated cover letter and resume here: 


If you have questions for the position, please call Group Leader Jacob Hecksher-Sørensen at +45 2986 9407 or Anders Bjorholm Dahl at +45 5189 6913.

About Gubra:

Gubra is a biotech company and contract research organization focusing exclusively on obesity, diabetes and related metabolic disorders. Gubra has a dual strategy: to become a preferred service partner for big pharma and biotech companies with obesity and diabetes programs, and secondly to develop innovative in-house target and drug discovery programs – alone or with 3rd party - targeting obesity and diabetes. The company currently employs 140+ people. It is privately owned and funded by revenue generated in the contract research organization. Gubra delivers preclinical pharmacology, assay, histology and molecular biology services to a broad palette (>50 customers) of biotech and pharmaceutical industry within its core areas. Due its contract research activities, Gubra finances its own research and discovery activities within the same core areas, mainly focusing on target discovery in gut, liver and brain as well as peptide drug discovery within diabetes and obesity. Over the past year, Gubra has invested in new imaging equipment that will enable 3D imaging of metabolic diseases. Gubra employs several experts in the field of obesity and imaging. Gubra has conducted 100+ client studies on obesity.

About DTU compute:

The Department of Applied Mathematics and Computer Science (DTU Compute) is one of the 20 departments at DU and employs approximately 400 people in total. The study will take place in the Section for Image Analysis and Computer Graphics, one of the 11 research sections at DTU Compute. The section for Image Analysis and Computer Graphics employs 12 permanent faculty members and around 45 including PhDs and postdocs. Research in the section concerns image analysis and computer graphics applied to different areas including medicine, materials, and production. Medical image analysis has been a core focus area for the group with many teaching activities and research collaborations with both hospitals and medical industry typically involving PhDs and postdocs that spend time both in the group and at the clinical partner. Several of these collaborations has specifically involved histopathology focusing on methods to quantify features in stained tissue and using these for revealing disease patterns. 

About DRCMR:

The Danish Research Centre for Magnetic Resonance (DRCMR) is one of the leading research centres for biomedical MRI in Europe (www.drcmr.dk). Our mission is to triangulate MR physics and basic physiology from preclinical to clinical research. Approximately 75 researchers from a diverse range of disciplines are currently pursuing basic and clinically applied MR research and its validation with a focus on structural, functional, and metabolic MRI of the human brain and its disorders. The DRCMR is embedded in the Centre for Functional and Diagnostic Imaging and Research, a large diagnostic imaging department including all biomedical imaging modalities at Copenhagen University Hospital Hvidovre. DRCMR has a state-of-the-art MR-research infrastructure enabling translational research, which includes a pre-clinical 7T MR scanner, six whole-body MR scanners (one 7T, three 3T and two 1.5T scanners) and a High-Performance Computer cluster for neuroimaging. The DRCMR have pre-clinical labs, a neuropsychology laboratory, an EEG laboratory, and two laboratories for non-invasive brain stimulation.