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Scientist in Microscopy Automation and Image Analysis

European Molecular Biology Laboratory (EMBL) - Ellenberg Group

Location: Heidelberg - Germany
Salary: Commensurate with experience and qualifications
Hours: Full Time
Contract Type: Fixed-Term/Contract
Placed On: 10th July 2019
Closes: 31st August 2019
Job Ref: HD01560

About the team/job

We are seeking for a highly motivated and excellent scientist to join our team. The Ellenberg group is part of the Cell Biology & Biophysics Unit and a multidisciplinary team consisting of biologists, chemists, physicists and computer scientists. Our overall goal is to systematically elucidate the mechanisms underlying cell division (mitosis & meiosis) and nuclear organisation (chromosomes & nuclear pores) with cutting-edge imaging technology. For that purpose, we are developing a broad range of advanced light and electron microscopy technologies to assay the functions of the involved molecular machinery non-invasively, automate the imaging process itself to address as many molecular components as possible, and computationally process image data to extract biochemical and biophysical parameters.

Your role

The successful candidate will have technology development and research as well as scientific collaboration tasks. S/he will develop software tools for intelligent microscope automation based on machine learning of image data. This automation enables to execute complex (e.g. multiplexed and/or multiposition) and quantitative multidimensional imaging experiments fully automatically to achieve high throughput and reproducibility. Microscopy technologies include super-resolution, confocal, fluorescence correlation spectroscopy and light-sheet microscopy or their combinations. The position requires to newly develop and adapt existing instrument automation softwares in different programming environments (e.g. MatLab, Fiji, CellProfiler). In addition to microscope automation, the candidate will also develop or adapt tools for real-time image data analysis and/or data modelling.

In addition to these research and technology development tasks, the candidate will also collaborate with scientists in the Ellenberg group for systems biology projects, as well as with other EMBL scientists and international visitors that aim to carry out such high-throughput microscopy experiments at EMBL. To this end s/he will work in close collaboration with the members of the Ellenberg Group and EMBL’s Microscopy Facilities.

The successful candidate should be able to work creatively and independently, be well organised, rigorous, and enjoy working in an international team within a highly collaborative atmosphere.

You have

  • Master/Diploma or PhD in physics, computer science, engineering or equivalent.
  • Excellent programming skills.
  • Experience in software control of scientific instrumentation.
  • Excellent communication skills and fluency in English.

You might also have

  • Good knowledge of relevant programming languages including C++, Python, LabView, MatLab and Visual Basics for Applications (VBA).
  • Experience with fluorescence microscopy automation or equivalent
  • Computational image analysis and modelling of the derived data.

In your online application, you will be asked to include a cover letter and a detailed CV.  In addition, you will be asked to list the contact details of 3 referees.

Further information about the position can be obtained from the Research Manager of the Ellenberg Lab ( 

Interviews are planned for the week of 23-27 September 2019.

The initial contract is for a period of 3 years with the possibility of a fixed-term extension.

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* Salary has been converted at the prevailing rate on the date placed
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