Postdoc: Single-cell Dynamics in Organoids using 3D imaging and AI Analysis

Date posted December 22, 2023
Type Postdoc positions

In this project you will develop next-generation cell tracking methods for organoids based on advanced AI approaches and novel biophysics concepts, in order to elucidate the remarkable self-renewal and differentiation capabilities of organoids. Over the past years, our two research groups (Tans and van Zon) have been at the forefront of developing AI methods to track cells in growing and developing organoids. These advances will allow you to push the boundaries of AI-enabled single-cell analysis, which are key both to fundamental science and screening applications. You will combine these methods with cutting-edge 3D confocal microscopy and fluorescent labelling, in collaboration with world leaders in organoid culturing technologies. 

Your methods will enable you to map the spatio-temporal dynamics of cells that remains invisible with other techniques. You will develop AI training and inference approaches using our unique multi-parameter data-sets and extensive Machine Learning expertise. These next generation tools will reveal the complex lineage relations between cells, as well as the internal structure of organoid cells. By applying these methods to organoids grown in our labs and that or our collaborators, you can elucidate long-standing issues such as this chicken and egg problem: how can individual stem cells receive spatial cues from the organoid architecture they reside in – yet autonomously generate that same architecture from scratch? Signaling cues must be pivotal to instructing cells when and how to differentiate. But when and where cells receive these cues, and how they respond to them, has remained poorly understood due to a lack of dynamic analysis methods. 

Organoids are revolutionizing the way to study tissue organization, disease, and drug effects, and limit reliance on animal testing. Organoids are transforming both fundamental and applied biology, as well as medical research. However, technical hurdles have limited direct study of the underlying cellular dynamics, which this project aims to overcome. Compared to others in the broad organoid scientific landscape, we focus on developing a unique physics-inspired approach, both in terms of the assays we develop and the questions we can answer. Within this environment, you will interact with several world-leading collaborators, and hence be trained in a wide spectrum of experimental techniques. 

You will operate in lively and close-knit research group of about 10 PhD students and postdocs, which work together in small teams on various projects in a highly supportive and social atmosphere. All the organoid research at AMOLF takes place jointly in two groups (the Tans and van Zon groups), which you will both be part of. This highly collaborative environment extends to the other biophysics research groups at the AMOLF institute, which is housed in a modern building in the east of Amsterdam.

About the group

Tans group:

Van Zon group:


We are looking for outstanding experimental physicists, chemists, or biologists with an interest in organoids, experience in AI, programming, and handling of complex data, who thrives in a diverse, collaborative, and supportive environment. Excellent verbal and written English skills are essential. You need to meet the requirements for a doctors-degree.

Terms of employment

The position is intended as full-time (40 hours / week, 12 months / year) appointment in the service of the Netherlands Foundation of Scientific Research Institutes (NWO-I) for the duration of 2+ years, with a salary in scale 10 (CAO-OI) which starts at 3170 Euro’s gross per month, and a range of employment benefits. AMOLF assists any new foreign Postdoc with housing and visa applications and compensates their transport costs and furnishing expenses.

Contact info

Prof. dr. ir. Sander Tans

Dr. Jeroen van Zon

Please feel free to send any informal enquiry about our group, this or other projects in our lab, or any other matter related to this ad.

You can respond to this vacancy online via the button below.
Please annex your: 
–  Full CV; 
–  Motivation on why you want to join the group (max. 1 page). 

It is important to us to know why you want to join our team. Hence, we will only consider your application if it entails your motivation letter.

Applications will be evaluated on a rolling basis and as soon as an excellent match is made, the position will be filled.

Online screening may be part of the selection.

AMOLF is highly committed to an inclusive and diverse work environment, and we greatly encourage candidates from any personal background and perspective to apply. AMOLF has won the NNV Diversity Award 2022, which is awarded every two years by the Netherlands Physical Society for demonstrating the most successful implementation of equality, diversity and inclusion (EDI).

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