PhD Position - Deep learning for reconstructing the fibre architecture of the human brain from microscopic images

Jülich Research Centre (FZJ)

Jülich, Germany

Work group:

INM-1 – Strukturelle und funktionelle Organisation des Gehirns



Area of research:

PHD Thesis



Job description:

To address human brain organization at its various spatial and temporal scales, the Institute of Neuroscience and Medicine – Structural and Functional Organization of the Brain (INM-1) develops a high-resolution 3D brain model, which takes into account cytoarchitecture, connectivity, molecular organization, as well as genetic and functional measurements. In this challenging scientific setting, the "Big Data Analytics" group develops machine learning algorithms to analyze extremely large amounts of image data on High Performance Computing systems, and develops software solutions for interacting with large datasets through cloud-based infrastructures. We are part of the Helmholtz Artificial Intelligence Cooperation Unit (HAICU), which aims to reach an international leadership position in applied AI by combining AI-based analytics with Helmholtz’ unique research questions and data sets – bringing together scientists from all Helmholtz centers and fostering transdisciplinary research.


Your Job:



  • You develop advanced Deep Learning algorithms for image analysis, with the goal of extracting the structure of nerve fibres from fascinating digital scans of the human brain at microscopic resolution

  • You cooperate closely with our neuroscientists and physicists, to build up a solid understanding of the imaging process and scientific context and incorporate it in your algorithm design

  • You work with experts at the Jülich Supercomputing Center (JSC), to run your algorithms on large distributed computer systems

  • You generate internationally visible scientific results, by authoring high-quality research papers and presenting your work at international conferences

  • You connect with researchers in other Helmholtz centers to discuss scientific applications of AI methods, and become a part of the AI expert network of different HAICU units in Germany

  • You do occasional national and international travels to strengthen scientific cooperations

Your Profile:

  • Excellent university degree in computer science, mathematics or a comparable field of study
  • Very good knowledge in image processing, computer vision, and machine learning
  • Practical experience with deep learning algorithms and software libraries
  • Distinct analytical and numerical skills
  • Solid programming skills, preferably in Python and C/C++, ideally with first experience in parallel/distributed programming
  • An interest in neuroscience
  • Very high motivation and frustration tolerance for solving methodological problem
  • An interest to work in interdisciplinary, international teams
  • Very good English skills

Our Offer:

  • A challenging and varied activity in an interdisciplinary, international research environment, with close contact to national and international experts in AI and neuroscience
  • The opportunity to work with world class technical equipment and infrastructure, innovative software technologies, and fascinating neuroscience data
  • An exciting working environment on an attractive research campus, located between the cities of Cologne, Düsseldorf, and Aachen
  • Outstanding scientific and technical infrastructure – ideal conditions for successfully completing a doctoral degree
  • Chance of participating in (international) conferences and project meetings
  • Continuous scientific mentoring by your scientific advisor
  • Further development of your personal strengths, e.g. via a comprehensive further training programme
  • Participation in overarching seminars including certificate
  • Salary and social benefits in conformity with the provisions of the Collective Agreement for the Civil Service (TVöD)
  • Recruitment at the next possible date
  • Information on employment as a PhD student at Forschungszentrum Jülich can be found here www.fz-juelich.de/gp/Careers_Docs

Forschungszentrum Jülich promotes equal opportunities and diversity in its employment relations.We also welcome applications from disabled persons.


Please apply via recruiter’s website.

Quote Reference: 2019D-232

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