PhD course: Plant Imaging Techniques

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Title: Plant Imaging Techniques

Date: 14 – 18th May, 2018

Place: Lund (Medicon Village and Biology house)

Credits: 3 hp/ECTS

Responsible department: Department of Plant Breeding, SLU, Alnarp

Course responsible: Ramune Kuktaite,

With economic support from PlantLink.

This PhD Course: is aimed to give an overview on Plant Imaging Techniques a complex group of methods for acquiring, processing and visualization of structural or functional images of various plant objects or systems in plants, including extraction and processing of image-related information and using computer modeling. The course will allow PhD students to get familiar with the latest plant imaging and visualization methods including a number of microscopy and X-ray/neutron scattering techniques. During the course students will be introduced into areas of plant structural biology, computational biology and modern biology.

This course will be in the form of one week (3 credits), including seminars, lab practicals, computer exercises and literature reading (before the course). Course assignment “case study” will be given to the course participants. During literature reading (before the course) and during the course week, every student is suppose to evaluate and choose one/several imaging methods, and simulate a theoretical implementation of the chosen method into own PhD project. Summary of “case study” should be reported in a written form (max 2 A4 pages) during the last day of the course (and send via e-mail to An oral presentation of 5-10 min will be presented by each student during the last day of the course. The lectures, practicals (hands-on exercises) and literature will be held/given by experts in the fields of structural biology, plant biochemistry, computational biology and physics.


The aim of the course is to give a broad overview and critical assessment of morphology, structure characterization and quantification methods used in plants with a focus on its impact on functional properties of the plant components e.g. protein, starch, fibres etc. This will practically be achieved by creating images of various components of the plants and/or other similar systems down to the molecular level (micro and nano-) in order to visualize how structure and morphology effect the function of plant components. Image registration and processing methods, feature recognition and classification, as well as related data analysis and statistical tools will be discussed.


Introduction to plant imaging techniques by Confocal Laser Scanning Microscopy (CLSM), Fluorescence Microscopy, Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Light Microcopy (LM), X-ray computed tomography (CT) and digital imaging, Soft X-ray Scanning Transmission X-ray Microscopy (STXM), quantitative image analysis, neutron scattering. The lectures will give an overview on plant components biochemistry, structure and function, and the uses of advanced imaging techniques. Plant component characterization techniques will be discussed with emphasis on structural properties of various plant components i.e. proteins, cellular structures etc., that are essential for various functions in plants and other similar to plant systems (tissue).

Several examples with specific focus on plant structure will be introduced. Lab practicals will consist of introduction and guidance through technical parts of equipment and sample preparation in 4 groups for CLSM analysis e.g. protein histol-immunolabelling, hands-on on sample scanning and imaging, and quantitative image analysis.

Regarding SEM/TEM/LM techniques will be demonstrated and discussed in small groups, having various biological examples.

The use of CLSM in computational modeling will focus on data collection, analysis and design of a model using computational tools. Practical exercises for computational modeling will be included. Students will be introduced into several examples using structure-mechanistic modeling approach of biological material.

The X-ray CT which uses x-rays to create cross-sections of a plant object and later recreates a virtual model (3D model). This course will include several illustrative examples of plant origin. High resolution x-ray tomography and micro-computed tomography will be briefly introduced and discussed.

The Soft X-ray Scanning Transmission X-ray Microscopy (STXM) using analytical range in the soft X-ray region is a powerful analytical tool that be applied for studying fully hydrated biological materials and differentiation of biological molecules. Several biological examples will be illustrated in the course.

Expected Learning Outcomes

Upon completion of the course, participants are expected to:

  • Describe different plant imaging methods applicable to study structure of plant components including advantages and limitations of the studied methods.
  • Specify when the selected imaging method is an appropriate tool to address a specific objective.
  • Localize, relate and map major components of various plant materials at the molecular level.
  • Have a broad understanding on combination and use of various multi-microscopy and x-ray scattering correlative methods.
  • Have a broad understanding on the use of one or several plant imaging methods suited specifically to a certain research area.

Examination: The students are expected to take an active part in lectures, discussions and lab practices, which is required in order to accomplish the course. During the course week students choose to theoretically implement one or few plant imaging methods in relation to the own research (PhD) project. The individual “case study” should include reflections from the course literature, lectures, discussions and lab exercises. During the last day of the course the students present their “case study” in a written form (max 2 A4 pages), which should be sent on the 18st May, 2018, to the course responsible (e-mail: A summary of “case study” in a form of an oral 5 min presentation is also expected during the last day of the course.