A National Research Infrastructure for Biological Imaging

PhD position (Computer Sciences) in Image Analysis – arivis AG, Rostock-Germany

Organization: arivis AG (based in Germany)

Position Information:

PhD position in Image Analysis – “Deciphering PI3K biology in health and disease (Phd)”


Arivis AG (based in Germany) is looking for a talented and driven person to join their team in their Business Unit Imaging Science as a

PhD (Computer Sciences) in Image Analysis

Starting date: April – September 2016
Duration: 36 months with excellent chance for a permanent deployment

An Early Stage Researcher (Ph.D. student) position is available at the arivis AG in Rostock, Germany as part of the Marie Sklodowska-Curie Innovative Training Network “Deciphering PI3K biology in health and disease (Phd)”.

arivis develops and provides IT solutions focused on the Life Sciences industry. Our product portfolio ranges from solutions in imaging science, regulatory, raw data archiving and production to quality management for medical and pharmaceutical products. arivis solutions help customers to meet the world wide ever increasing regulatory, quality and compliance requirements in research, clinical trials, approval and maintenance of medical devices and medicinal products. arivis products are used by small and medium sized biotech companies as well as by the world’s leading medical device and pharmaceutical companies and by international renowned research associations, organizations and universities. Headquartered in Munich, arivis is an international fast growing company with subsidiaries in Rostock, Berlin (Headquarter BioMedion GmbH), Phoenix, AZ (Headquarter arivis Inc.) and Washington (D.C.).

Our revolutionary, award winning software enables users to visualize, analyze, distribute and to manage even multi-terabyte multi-dimensional (2D, 3D, 4D, 5D) image datasets that are e.g. created by microscopes or scanners, very fast, efficient – and on ordinary PCs and laptops! Our main product arivis Vision4D is used widely in microscopy-based applications. The arivis .sis format is powered by the arivis ImageCore technology and ensures constant RAM-independent access to large images during navigation and zoom as well as powerful image analysis.

Responsibilities and Project Topics:

arivis’ contribution to the EU funded project will be software tools for quantification of biological sample data, including

  • Development of new software to quantify immunofluorescence images.
  • Algorithms for automated and semi automated tracing of tree-like 2D and 3D structures such as blood vessels or neurons.
  • UI and interaction concepts for interactive tracing.
  • Application of algorithms to large images, development of tiling and multiscale approaches as well as parallelization concepts and implementations.
  • Integration of algorithms into a scalable software environment.

The focus will be on development of software algorithms for manual, semi automatic and automatic vessel tracing.

The Consortium:

The consortium includes ten project partners from the UK, France, Germany, Switzerland, Italy and Spain, and will train 15 Early Stage Researchers in in vitro and in vivo approaches to the analysis of physiological processes to pathological situations. For more details please refer to

Recruited researchers will benefit from interactions with other members of the consortium through joint research training, scientific collaborations and participation in project meetings.

Required Qualifications:

We are looking for highly motivated individuals with evidence of high academic achievements. Candidates should bring:

  • Masters degree in computer sciences, mathematics or a similar field.
  • Strong background in image analysis, algorithm development and implementation.
  • Languages: English required, German optional.
  • Development in C++/C#/Python/MATLAB


The MSC ITN programme offers a highly competitive and attractive salary. The successful candidates will receive a salary in accordance with the regulations for MSC Fellows/early stage researchers (ESRs) for 3 years. Exact salary will be confirmed upon appointment but will involve a generous Living Allowance and monthly mobility allowance depending on the successful candidate’s family situation. In addition to their individual scientific projects, all fellows will benefit from further continuing education, which includes internships and secondments, a variety of training modules as well as transferable skills courses and active participation in workshops and conferences.
More information is at

Application Details:

We seek candidates with a Masters degree in computer sciences, mathematics or a similar field with a strong background in image analysis, algorithm development and implementation. Candidates will travel and work in collaborators laboratories in Europe.

We can only consider candidates from within the EU. Furthermore, candidates with German nationality or who have lived in Germany for longer than 12 months during the past 3 years are excluded from applying for this specific position, but are strongly encouraged to apply for remaining positions with partners of the consortium outside Germany. Details of the other available Phd projects can be found on the consortium website

The candidate must take up the ESR position before 1st September 2016.

Please send your application to Applications should consist of an up-to-date CV and cover letter including the applicant’s motives to apply. Please provide supporting documents, personal statement, degree transcripts and certificates and references.