Student information

MSc thesis topic: Exploring novel quinoa variants: High-throughput phenotyping data analysis under drought stress

Image-based phenotyping platforms enable precise monitoring of plant behavior, providing insights into plant traits that enhance resilience to abiotic stresses. In the experiment that we conducted, we focus on assessing the response of novel quinoa variety to drought conditions. This thesis will explore diverse morphological and physiological adaptations of plants under drought stress by using advanced image analysis techniques as a research tool.

In a previous experiment, we have exposed novel quinoa varieties to drought stress. We used the high-throughput phenotyping system of NPEC - which allows us to track the plants development, physiology and photosynthesis response to drought over time. We offer an interesting thesis position where you’ll be able to work on the data that is obtained in this experiment. The goals are:

  • To predict biomass of the plant based on pixel count from side-view RGB pictures
  • To segment leaves, panicle and stem to understand the change in biomass allocation of the plant in response to drought over time
  • To convert 2D (top view) to 3D data of the plant

Relevance to research/projects at GRS or other groups

  • The research is conducted within the Plant breeding group, in collaboration with prof.dr.ir. L (Lammert) Kooistra from the GRS group.

Objectives and Research questions

  • How effectively can we predict plant biomass using pixel count data from side-view RGB images?
  • Is it possible to discern how biomass is allocated within the plant in response to drought stress by segmenting the leaves, panicle and stem in images?
  • Can we transform 2D data, such as top-view chlorophyll fluorescence measurements, into 3D representations to better understand the impact of drought on photosynthesis across the entire plant?

Requirements

  • Experience in R and Python
  • Basic knowledge on image analysis

Literature and information

  • High-Resolution Analysis of Growth and Transpiration of Quinoa Under Saline Conditions (Jaramillo Roman et al, 2021)

Theme(s): Sensing & measuring, Modelling & visualisation