Who are we?

The Jan IngenHousz Institute (JII) is a philanthropically funded, open science institution dedicated to improving photosynthesis to enhance crop production and resilience. JII is located on the campus of Wageningen University & Research (WUR), and partners with WUR and other institutions worldwide.

Our goal is to contribute to global food security in the face of climate change, biodiversity challenges, and population growth. Our ambition is to unravel the secrets of photosynthesis in the real world by developing and deploying an open science platform of sensors, data, methods and fundamental knowledge that will reveal the factors that control photosynthesis under real-world conditions and deploy these tools globally to enable multiple crop improvement pipelines.

The background of the project

This three-year project is a collaboration between JII and the Netherlands Plant Eco-phenotyping Centre (NPEC). NPEC is a high-tech facility that provides plant phenotyping to the research community and continuously works to stay state of the art. Since 2018, its experiments have produced more than 250 terabytes of data, including chlorophyll fluorescence imaging data. JII develops novel phenotyping technologies, such as leaf sensors that provide time-series fluorescence data. In this project, you will develop methods and pipelines that validate these new technologies from leaf to canopy and from closed environments to the field. These methods and pipelines will then be integrated into NPEC's facilities by professional software engineers, giving the researchers who use NPEC new research possibilities.

You will be connected to both JII and NPEC. At JII, you will be part of a strongly dedicated and highly integrated team of engineers, data scientists, modelers, biochemists, biophysicists, geneticists, and plant breeders, working collaboratively at national and international levels. At NPEC, you will work closely with the software engineers and the staff who run the phenotyping infrastructure.

What will you do?

This is first and foremost a research position. You will develop new methods and pipelines to bridge the gap between point measurements of chlorophyll fluorescence and whole-canopy imaging, and you will keep in mind that these methods will feed into NPEC's facilities. Your work will include:

• Develop an image analysis pipeline for 2D chlorophyll fluorescence imaging, including plant segmentation and leaf tracking within a canopy;

• Determine the optimal placement of spot CF measurements (on which leaves and which parts of leaves) so they best represent the canopy;

• Validate image-based predictions against actual spot measurements, and quantify the impact of the sensor itself on the measurement spot;

• Scale up the approach in the NPEC facility to test representativeness across genotypes and throughout the growing season, using Arabidopsis and barley as model systems;

• Develop 3D imaging methods that combine chlorophyll fluorescence with 3D point clouds, using sub-canopy LED illumination and ray tracing to model fluorescence on leaves not directly visible to the camera;

• Translate these results into practical guidelines for what needs to be imaged in the field and how to link it to spot measurements, and into pipelines that strengthen NPEC's phenotyping services;

• Explore follow-up imaging strategies based on your findings, such as deploying a new chlorophyll fluorescence camera on the NPEC conveyor belt;

• Publish your findings in peer-reviewed journals and present them at international conferences and to JII and NPEC partners.

  
  

Who are you?

• You have a PhD in plant biology, genetics, breeding, physiology, agronomy or another relevant plant science field.

• You have proven experience in programming for image and data analysis (e.g., segmentation, 3D point clouds, visualization); this is essential for the role.

• You have experience with, or a strong interest in, sensor development.

• You are comfortable working in iterative design processes and are able to experiment and self-test.

• You thrive in highly collaborative environments, where you contribute to both your own and your colleagues' research.

• You are a proactive and independent researcher who works in a solution-oriented way, is motivated to keep learning, and is passionate about contributing to the institute's mission.

• You have a good track record in written and oral scientific communication.

• You have good English language skills, as you will work in an international team where English is the primary language.

  
  

What do we offer?

• A position of 38 hours in scale 10 of the NU collective labour agreement (€3706 to €5760,‑). Although we are not covered by a collective agreement, we follow the salary scales of the NU agreement. You will be located at the Jan IngenHousz Institute in Wageningen, NL.

• You will receive 8% holiday pay and an 8.3% year-end bonus.

• We start with a 1-year contract, and if both parties wish to continue collaborating, an extended contract will follow.

• You will work in an intellectually stimulating and challenging environment with opportunities to increase your knowledge and skill levels, leading to job advancement.

• You will contribute to building an institute with significant societal relevance.

  
  

Response

If you have questions about this position, you can contact Tom Theeuwen, JII Research Fellow and Program lead, tom.theeuwen@jii.org. Send your CV and a short summary of motivations and experience in an email containing the header “Research Associate (Postdoc) – Chlorophyll fluorescence imaging from leaf to canopy.” to hrm@jii.org . We will start reviewing the application by November 1^st but the vacancy will stay open until the position is filled.