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Python Software Developer (2 positions) at European Molecular Biology Laboratory (EMBL)

Contract Duration: 3 years
Grading: 4, 5 or 6, depending on experience and qualifications

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations worldwide. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Barcelona (Spain), Grenoble (France), Hamburg (Germany), Hinxton near Cambridge (UK), Rome (Italy).

EMBL is seeking a highly motivated software developer to join the group of Dr. Anna Kreshuk. The research of the group is concerned with the development of machine learning tools for bioimage analysis. The successful applicant will join the team which develops the ilastik toolkit for interactive learning and segmentation.
Ilastik is a popular open source tool which allows users without image processing expertise to train classifiers interactively, segment images, extract and classify features and track dividing objects. We are looking for a developer for the following tasks:

  • Improve the integration of ilastik with other popular tools (ImageJ, Knime, CellProfiler, etc)
  • Simplify the development of new workflows and flatten the learning curve for outside contributors
  • Support and expand the user and developer community (together with rest of the team)
  • Further develop the core of ilastik to extend truly interactive processing to larger datasets and more complex workflows
  • Integrate new algorithms developed in the group into ilastik to make them accessible to life scientists

A couple of words about us: ilastik has been developed in the group of Fred Hamprecht at the University of Heidelberg and at the HHMI Janelia Research Campus. Anna Kreshuk has been leading the development in the recent years and, as she is establishing a new research group at EMBL, the ilastik team is moving with her. With the generous support of the DFG (the central research funding organization in Germany), we can now offer a new developer position. Our plans for the coming years include the overall improvement of the program UI, direct integration with other image processing tools and, from the methodological side, integration of deep learning tools in a form accessible to our users.

Qualifications and Experience
We are looking for an experienced Python developer with strong communication skills, preferably with experience in open source or scientific software development.
The requirements are as follows:

  • Degree in Computer Science or a related technical field or equivalent work experience
  • Excellent knowledge of Python, especially its numerical libraries
  • Working knowledge of C++, pybind11 or other tools for Python/C++ bridging
  • Experience with standard development tools: git, conda, cmake, continuous integration tools
  • Fluent English, oral and written

Optional, but desirable:

  • DevOps experience, including cross-platform builds and remote deployment
  • Java knowledge
  • Qt experience

Application Instructions
Please apply online through www.embl.org/jobs

To give us an impression of your code, please supply a link to an open source repository with your contributions. If you haven’t contributed to open source yet, please fix one of the small issues in the ilastik repo www.github.com/ilastik/ilastik and submit your fix as a pull request. The appropriate issues are tagged with “good first issue”.


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