Scientific Internship: Shedding light on fungal carbon transport from image data

Date posted August 12, 2022
Type Scientific Internships

Mycorrhizal Fungi are ubiquitous symbiotic soil organisms that are critical to the majority of terrestrial ecosystems. They form underground networks that account for 25-50 percentage of soil biomass worldwide and support plant growth by forming underground trade networks that impact global carbon fluxes. Yet, the mechanisms underlying the fungal transport processes that support this underground carbon economy remain largely unknown.

In this project, you will develop data analysis tools to extract transport statsitics from flow videos acquired in a newly built multi-scale fungal imaging setup at AMOLF (see here for an example movie!), with the aim of creating a first-of-its-kind dynamic map of carbon traffic across an entire mycorrhizal colony.

The project will be embedded within an HFSP-funded consortium to pioneer the biophysics of fungi in symbiotic contexts. The team includes biologists, physicists and engineers from the labs of

You will be guided by a PhD student (Corentin Bisot), and will collaborate with members of all participating labs through regular consortium-wide Zoom meetings. Your work on this project can have direct impact on real-world ecology/conservation efforts through SPUN (Society for the Protection of Underground Networks), a non-profit organization recently launched by a member of our team (Prof. Kiers) see here for a recent feature in Science.

About the group

The Systems Biology group (Group Leader: Tom Shimizu) focuses on developing a physical understanding of biological behavior. We develop in vivo experiments to measure dynamics at multiple spatial and organizational scales, as well as theoretical modeling and data analysis frameworks to connect phenomena across those scales. Primary model systems are the bacterium E. coli, the nematode C. elegans, and symbiotic microbial communities.


We are seeking highly motivated students with strong quantitative and computational skills.
We are looking for someone comfortable in code development, using git and coding in Python. Formal requirements: You have a Bachelors degree in physics, mathematics, computer science, or quantitative biology, and are enrolled in a Masters program in one of these areas.
The internship must be a mandatory part of your curriculum. You have a nationality of an EU-member state and/or you are a student at a Netherlands University. Please note: As of January 2021 the UK is no longer an EU member state. The intended duration of the internship is 6-10 months. Starting date is flexible, but the position will be filled as soon as we identify a good match.

Terms of employment

At the start of the traineeship your trainee plan will be set out, in consultation with your AMOLF supervisor.

Contact info

Prof.dr. Tom Shimizu
Group leader Systems Biology
For informal inquiries, please reach out to cc-ing .

You can respond to this vacancy online via the button below.
Please annex your:
–  Resume;
–  List of followed courses plus grades;
–  A brief 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. Hence, we greatly encourage candidates from any personal background and perspective to apply.

Commercial activities in response to this ad are not appreciated.