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Advanced Course – 3D Plant Microscopy and Image Processing

Resolving the subcellular localization of a fluorescent compound in intact plant tissues or whole organs is a challenging task. Specific problems are posed by the high refractive nature of fresh tissues, sample thickness and stress-induced autofluorescence in dissected tissues. Together with classical problems of photobleaching and phototoxicity, these plants-specific issues make high-resolution and time-lapse imaging of fluorescent reporter proteins (or counterstaining) dye very challenging.

The aim of this course is to obtain both an overview and a specific practice. First, this course will give an overview of available microscopy imaging solutions depending on applications. We will specifically practice confocal laser scanning microscopy imaging of Arabidopsis tissues using different mounting and clearing agents; the aim is to learn customizing the acquisition parameters towards maximum possible resolution within specific constraints of speed, viability, bleaching and signal diffraction levels in fresh vs. fixed tissues. The course also offers a brief introduction to high-resolution two-photon microscopy for deep tissue imaging.

Secondly, we will learn to exploite the benefits of 3D imaging at the qualitative and quantitative level. We will practice 3D volume rendering, preparation of attractive image material for publication, image segmentation and extraction of quantitative information for statistical analyses.

Individual Performance and Assessment: In order to complete the course and to receive the credit point, students will be required to attend the whole course and to actively participate.

Prior knowledge: The course is designed for students with a prior experience in CSLM imaging and whose research involves (or will involve) 3D imaging in plant tissues. Applicants are welcome to bring their own samples and should contact the coordinator beforehand.


1 ECTS (30 learning hours)
Every two years (next 2022)

Lecturer: Célia Baroux (UZH, Coordinator) and Alexis Maizel (Guest speaker), Center for Organism Science, University of Heidelberg

Alpine Plant Ecology – International Summer School

It’s a comprehensive graduate course on alpine plant life in the Swiss central Alps, jointly organized by the University of Basel and the Zurich-Basel Plant Science Center (PSC) for graduate students with basic training in plant science. The course covers microclimatology, vegetation ecology, reproduction biology, aspects of biodiversity, soil science, ecophysiology and ecosystem ecology. Morning and evening lectures, field excursions and team-work on small projects will make this week, in a truly alpine environment, a life time experience. The ALPFOR research station is surrounded by a great variety of typical alpine vegetation, including glacier forfields.

Individual performance and assessment: Credits will be given on a pass/fail basis (active participation, design and presentation of a mini-poster).


3 ECTS (90 learning hours)
Annually (Spring semester)
Lecturer: Dr. Erika Hiltbrunner, Prof. Christian Körner, University of Basel, et al.

Chlorophyll Fluorescence - Principles and Analysis

Chlorophyll fluorescence analysis is one of the most powerful and widely used techniques by plant physiologists and ecophysiologists. Chlorophyll fluorescence is used for rapid non-​invasive measurement of photosystem II activity. PSII activity is very sensitive to range of biotic and abiotic factors and therefore chlorophyll fluorescence technique is used as rapid indicator of photosynthetic performance of plants in different developmental stages and/or in response to changing environment. The course will consist of lectures related to the theoretical background of this technique and practicals where different measuring protocols will be used to illustrate the types of information that fluorescence can provide. We will use both imaging and non-​imaging tools for analysis of chlorophyll fluorescence kinetics. The analysed samples will be plants from Arabidopsis thaliana, including mutants affected in photosynthetic acclimation mechanisms as a case study.

Individual Performance and Assessment: At the end of the course the students will be asked to prepare a short report and present how they can use Chl fluorescence in their research. They will briefly present the background, problem, design and the experiments that could be performed.

1 ECTS (30 learning hours)
Biannually (last 2022, next 2024)
Lecturer: Dr Diana Santelia, ETHZ; Klára Panzarová, Photon Systems Instruments (PSI); Tracy Lawson, University of Essex (UK), Fiamma Longoni, University of Neuchâtel.

Concepts in Evolutionary Biology (BIO 395)

In collaboration with URPP

Concepts in evolutionary biology are often used ambiguously, partly because the same terms may have different usage in other fields in biology. The course is designed for graduate students with interdisciplinary projects encompassing evolutionary biology and other disciplines. It provides lectures and simple calculation exercises in population and quantitative genetics.

1 ECTS (30 learning hours)

Annually (autumn semester)
Lecturer: Prof. Barbara König, Prof. Lukas Keller, Prof. Michael Krützen, Prof. Marcelo Sanchez, Prof. Kentaro Shimizu, Prof. Anne Roulin, Dr. Anna K. Lindholm Krützen, University of Zurich


Crop Phenotyping


Crops are exposed to different abiotic stress factors during their development. Adaptation of crops to extreme environmental conditions during the course of the growing season (e.g. cold and heat stress; water-​saturated or dry soils) has been achieved by plant breeding in the last century. However, there is enormous potential for optimization by means of modern crop phenotyping.

In this course, the most important mechanisms of plant adjustment towards stress will be explained, as well as critical stages identified in which stress affects yield most severely. We will dissect growth and development into three main trait categories which can be related to ideotype concepts:

(i) Timing of key stages;

(ii) Quantities at defined time points or periods and

(iii) Dose-​response curves.

The lecture will put a strong focus on hands-​on experience for both the handling of plants and sensors as well as coding in R and Python. You will learn how to use passive imaging sensors, like thermal, hyperspectral or RGB cameras but also active sensors like laser scanners and chlorophyll fluorometers. You will set up your own R and Python environment and work on different aspects of the whole crop phenotyping workflow in small expert-​teams. Each team will contribute a piece of information to the common phenotyping experiment which will be presented jointly at the final field day in June. At this day, different experts from ETH, Agroscope and Syngenta will provide hands-​on experience in the field. See abstract for more details..

Individual Performance and Assessment: PhD students will take part in the MSc course 751-​4106-00 G Crop Phenotyping. A reduced workload will allow to acquire 2 ECTS points: Participants enrolled in the PSC are required to i) give a presentation, ii) participate in the group work carried out during the season, and iii) submit one of 5 exercises.


2 ECTS (60 learning hours)
annually (last spring 2021)
Lecturer: Dr. Andreas Hund, Lukas Roth, Jonas Anderegg, Prof. Achim Walter, Jörg Leipner (ETHZ)

Current Challenges in Plant Breeding (ETH VVZ 751-3603-00L)

Given current discussions and efforts towards more sustainable agricultural production systems, we will investigate what plant breeding can contribute i) to reduce the input of plant protection products, ii) to make our crops genetically ready for future climatic conditions and iii) to evaluate what traits might become important in alternative production systems.

The educational objectives cover both thematic competences and soft skills:

Thematic competences:

  1. Deepening of scientific knowledge in plant breeding
  2. Critical evaluation of current challenges and new concepts in plant breeding
  3. Promotion of collaboration and Master thesis projects with practical plant breeders

Soft skills:

  1. Independent literature research to get familiar with the selected topic
  2. Critical evaluation and consolidation of the acquired knowledge in an interdisciplinary team 
  3. Establishment of a scientific presentation in an interdisciplinary team
  4. Presentation and discussion of the teamwork outcome
  5. Establishing contacts and strengthening the network to national and international plant breeders and scientist

Individual Performance and Assessment: On November 6, 2020, from 2 to 5pm, the enrolled students will be introduced to the concept, topic and the lecturers/tutors involved in 'Current challenges in plant breeding'. After an input talk by the lecturers, four to six specific aspects/questions for the above-mentioned topics will be identified and phrased. The tutors and the enrolled students will be assigned to four to six different groups, to critically evaluate one aspect/question. The students, guided by tutors, will prepare a presentation of 15 minutes (plus 5 minutes discussion) covering their specific question/aspect. Participation in this introductory lecture mandatory.

On January 26, 2021, a one-day seminar on the selected topic will be organized. The presentations of the students will be complemented with keynote talks from national and international experts. The seminar will be public and serve as annual meeting of the 'Working Group Plant Breeding' from the Swiss Society of Agronomy, bringing together the experts in plant breeding.

2 ECTS (60h learning hours)
Annually (Fall semester)
Lecturer: Prof. Bruno Studer and Dr. Andreas Hund, ETH Zurich

Genetic Diversity: Analysis (ETH VVZ 701-1425-00L)

The course will provide hands-on training for advanced students (e.g. master, doctoral or post-doctoral level) in genomic data analysis. The focus is on high-throughput sequencing applications and data analysis with a strong emphasis on reproducibility and report writing. We cover the fundamentals of bio-computing. Exercises will help to better understand the theory. It is, however, not a copy-paste course, but a more applied data analysis with discussion.

The course extends over two weeks so that the participants have enough time to digest and apply what they have learned at their own pace. It is our goal that the course participants understand the applications and have time to question them. Have a look at our previous course website and current course website for more details.

Individual Performance and Assessment: You have the chance to work on a project of your choice with you own data. Students interested in the credit points have to hand in a project report.

2 ECTS (60 learning hours)
Annually (Spring semester)
Lecturer: Dr. Jean-Claude Walser & Dr. Niklaus Zemp, Genetic Diversity Center, ETH Zurich

Genetic Diversity: Techniques (ETH VVZ 701-1425-01L)

This course provides training for advanced students (master, doctoral or post-doctoral level) in how to measure and collect genetic diversity data from populations, experiments, field and laboratory. Different DNA/RNA extraction, genotyping and gene expression techniques will be addressed. After an introduction (one afternoon), students will have 3 weeks to work in groups of two through different protocols according to their timetable. At the end, the whole group meets for another afternoon to present the techniques/results and to discuss the advantages and disadvantages of the different techniques. Examples are: RNA/DNA extraction, SNP genotyping, pyrosequencing, real-time qPCR.

Individual Performance and Assessment: Students have to attend on the two afternoons (8 hours) and do the individual work in between (around 52 hours). At the end they have to present a technique and their results in a talk.

1 ECTS (30 learning hours)
Annually (Fall semester)
Lecturer: Dr. Aria M. Minder, ETH Zurich

Introduction to Light Microscopy and Image Processing

Light microscopy is a frequently used tool in plant sciences. Still, many are not aware of all the factors that are necessary for good quality, reproducible microscopy images. The aim of the course is to give the participants a practice-oriented introduction to the basics of light microscopy, including a short introduction to image processing. This 3-day course offers a basic introduction into light microscopy. During the mornings lectures will summarize the necessary theory and the afternoon session will concentrate on practical, hands-on exercises. The following subjects will be dealt with transmission microscopy (phase contrast, DIC), fluorescence microscopy (including confocal imaging), basics of image processing.

Individual Performance and Assessment: Active participation during the course and in the hands-on training is necessary.

1 ECTS (30 learning hours)
Every two years (autumn 2023)
Lecturer: Dr. Gábor Csúc and Nicolas Blanc, ETH Zurich,

Microbiomics I: The Microbiome of the Plant-Soil System

The plant-soil microbiome is an essential component of agroecosystems, regulating crop growth, nutrient use efficiency, stress resilience, and disease resistance. In this course, students will develop a fundamental understanding of (i) how microorganisms shape the functioning of the plant-soil system, (ii) how ecosystem management and global changes are influencing diversity and functioning of these microbial systems, and (iii) how the microbiome might be managed to improve sustainable agricultural production. A strong focus will be placed on getting to know the methodological toolbox to study microbes in the environment including different next-generation DNA sequencing applications such as metabarcoding and metagenomics. Theoretical input lectures will be combined with presentations of current research projects. Flipped classroom assignments will be used to critically discuss research findings of specific publications or to evaluate the strength and limitation of the specific methods. 

Individual Performance and Assessment: In order to obtain the ECTS points, participants are required to actively participate in the lectures and flipped classroom assignments.

2 ECTS (56 learning hours)
Annually (Spring semester)
Lecturer: Hartmann Martin, Institute of Agricultural Sciences, ETH Zurich

Sustainable Plant Systems (ETH VVZ 551-0209-00)


Future demand in agricultural output is supposed to match the needs of 9-billion people with less input of resources. We will discuss current plant science research in the context of sustainability on the production side. A special focus will be on research on agro-ecological systems and farming system research. Can we transform our agricultural practices and move behind existing paradigms to develop innovative and sustainable agriculture production systems? Where does current research indicate on directions for transformation of current practice and how can we assess and analyze them though research? The seminar is set up as a blended-learning seminar, i.e. a combination of face-to-face meetings and self-organized learning with provided online learning material. The seminar comprises two workshop afternoons and an intensive, well-structured self-study/ group work phase in between the workshops. Students can earn 2 ECTS for successful completion of the seminar.

Key objectives for the seminar are

(1) participants will be able to discuss issues of sustainability in the context of current plant science research topics

(2) participants will be able to phrase their own visions for sustainability in plant sciences, their group work topic and their own MSc or PhD project.

Individual Performance and Assessment: ungraded semester performance. Students will actively participate during the two afternoons with presentations on the second afternoon (8 hours). In between the will independently work in the online course with assignments to be handed in and they will in groups prepare a presentation and essay on a sustainability topic (52 hours).


2 ECTS (60 learning hours)
Annually (Fall semester)
Lecturer: Dr. G. Singh Bhullar, FIBL; Dr. Franz Bender, Agroscope; Dr. Frank Liebisch and Dr. Melanie Paschke, ETH Zurich

► This course addresses PhD and Master's students

Transdisciplinary Seminar on Research for Sustainable Development (ETH VVZ 701-0015-00L)

The participants understand the specific challenges of inter- and transdisciplinary research in general and in the context of sustainable development in particular. They know methods and concepts to address these challenges and apply them to their research projects. The seminar covers the following topics: Theories and concepts of inter- and transdisciplinary research, The specific challenges of inter- and transdisciplinary research, Involving stakeholders, Collaborating disciplines, Exploration of tools and methods, Analysing participants' projects to improve inter- and transdisciplinary elements.

Individual Performance and Assessment: Ungraded semester performance. Active participation during the course days: 24 hours and preparation work for paper presentation in between (36 hours).

2 ECTS (60 learning hours)
Annually (Fall semester)
M. Stauffacher, C. E. Pohl and B. Vienni Baptista, ETH.


for PhD students at ETH: register via MyStudies.

for PhD students at Uni Basel: you have to register as Special student "University of Basel (UBa)" at ETHZ first.

for PhD students at UZH: you have to register as Special student "University of Zurich (UZH)" at ETHZ first.

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