Software Engineer for bio-image “on-the-fly” analysis and smart microscopy

The Rios’ group (also named Dream3DLab) is a multi-disciplinary team of imaging and organoid experts, bioengineers and computational scientists to develop 3D technology platforms to target the spatio-dynamic features of cancer and advance immunotherapy in a patient personalized manner. Through this 3D imaging, organoid and computational expertise, the Rios group can guide the Imagine PhD in performing innovate fundamental and translational cancer research, offering technology platforms with high potential to accelerate personalized medicine and improve treatment guidance.

The Princess Máxima (host institute of the Dream3DLab) is the largest childhood oncology center in Europe and facilitates a high-level interdisciplinary research environment strongly connected to clinical care. This forms an excellent environment for rapid clinical translation extended to adult oncology through connections with the University Medical Center Utrecht and Oncode (virtual host institute of the Dream3D Lab); independent Cancer Research Institute of the Netherlands, which provides key valorisation and legal support.

The Princess Máxima Center research department offers core facilities and shared resources essential to the project. This includes an Organoid Facility dedicated to providing quality-tested conditioned media and growth factors and, importantly, the Princess Máxima Imaging Center, founded and led by Dr. Rios. The Princess Máxima center stimulates an inspiring, welcoming and inclusive work environment and has an international committee in place to host events for and support international employees. In addition, a strong focus lies on mentoring and career support for early career scientists through round table discussions and open conversations with established scientist in diverse fields of interest.

The gravitational programme IMAGINE!

This position is one of many PhD positions available as part of the gravitational programme IMAGINE! (Innovative Microscopy And Guidance of cells In their Native Environment). IMAGINE! is an interdisciplinary programme combining cell, organoid, and tissue biology, as well as chemical and optical cell manipulation and analysis to study cell behaviour in development and cancer, and targeted drug delivery. Participating institutes are based throughout the Netherlands in Utrecht, Amsterdam, Delft, Rotterdam, Nijmegen, and Eindhoven. For more information on the individual positions, please visit our website

Job description

Until recently, processing and analysis of microscopy experiments has been limited to post hoc analysis. However, recent developments in microscopy systems now allow for interaction with microscopes during the process of imaging (see: ZEN)., allowing for “on-the-fly” analysis of data and event-driven adaptation of the imaging experiment based on this analysis (e.g. paper and paper). This opens the possibility for a whole new way of performing microscopy experiments. One such possibility is in the analysis of cell behaviour and subsequent event-driven adaptations in real-time.

We recently developed BEHAV3D (Nature Biotechnology 2022, DOI: 10.1038/s41587-022-01397-w See: Paper), a technology platform that provides a way to segment and track cells over time and analyse their behavioural patterns.

Currently, this analysis is performed post hoc, but for next-generation BEHAV3D you will develop “on-the-fly” deep-learning approaches capable of detecting and segmenting single cells and subsequent tracking to monitor cell dynamics and classify behavior in real-time. In collaboration with the Kapitein lab these robust computational methods will form the foundation for developing smart microscopy systems. Ultimately, such systems will allow for real-time analysis of complex dynamic scenarios and selection of single cells with specific dynamics and perturbations to perform light-driven alterations of the cellular state in collaboration with other members of the Imagine consortium including the Smith lab.


  • Master’s degree (or equivalent) in artificial intelligence, software engineering, physics, biology or similar;
  • background in some of these areas: computational science, software development, image analysis, artificial intelligence;
  • highly motivated and creative;
  • skill set: problem solving, analytical thinking, fluent in English;
  • interest to work in a highly collaborative and interdisciplinary environment.

If you feel that this role is the perfect match, but you do not yet meet all the qualifications, we also welcome you to apply.

Working at the Princess Máxima Center

A PhD position with a total duration of 4 years (full-time, 36 hours/week). You will initially be contracted for a period of one year, after which your performance will be evaluated and the contract may be extended for three more years. You will be working under daily supervision by an experienced senior scientist, in a very stimulating and cross-disciplinary research environment, combining cutting-edge research with state-of-the-art imaging methodology. The results of your studies will open new insights into pediatric cancer pathology and (potentially) treatment.

This position is for Your gross monthly salary will depend on experience and background, starting in scale 45 at € 2,541 and increasing to € 3,468 with 8,33% gross monthly salary holiday allowance and 8,33% end-of-year bonus. The Princess Máxima Center operates according to the collective labour agreement ‘cao algemene ziekenhuizen’.

Apply for this position?

If you are interested in this position or other positions of IMAGINE! we encourage you to apply for multiple positions (please indicate this by including the job title(s) and associated institute(s) in your application letter). Data Privacy note: Applications will be shared between participating institutes of IMAGINE! for the purpose and the duration of the recruitment process.

We like to receive your application before 3rd of February 2023. Please enclose:

  • your letter of motivation
  • your Curriculum vitae
  • reference letters are optional but appreciated

We highly encourage candidates from diverse backgrounds and nationalities to apply. We strive to create an open, diverse, and inclusive work environment for everyone. People of any gender identity, ethnicity or sexual orientation are welcome.

If this specific opportunity isn’t for you, but you know someone else who may be interested, please forward this vacancy to them.

Acquisitie naar aanleiding van deze vacature wordt niet op prijs gesteld.

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