Practical Course in Advanced 3D Microscopy - XI Microscopy Winter School 2017, University of Zurich

Publish Date: Jul 27, 2016

Deadline: Oct 31, 2016

Event Dates: from Jan 22, 2017 12:00 to Jan 27, 2017 11:00

About the XI Microscopy Winter School

This advanced microscopy course is intended for PhD students and post-graduates with prior experience in microscopy. The goal of the course is to teach and train fundamental knowledge and skills in a specific microscopic technique. Students will be able to apply this technique to their own present and future projects. Practical work consists of seven different modules covering a specific topic each (please see description below). Each practical module lasts throughout the whole course. Students will participate in one practical module only. For the practical training the students will use the most state-of-the-art instrumentation. Apart from practical modules, theoretical joined sessions will cover basic knowledge about all the different techniques for all students.

The trainings will take place on January 22 - 27, 2017.


  • Urs Ziegler, Andres Kaech - Center for Microscopy and Image Analysis, University of Zurich
  • Ohad Medalia, Matthias Eibauer - Department of Biochemistry, University of Zurich
  • Miriam Lucas, Nicolas Blanc - Scientific Center for Optical and Electron Microscopy, ETH Zurich


Module 1: Advanced Light Microscopy (12 students)
Heiko Gathje (Olympus), Urs Ziegler (ZMB, UZH), Dominik Haenni (ZMB, UZH), José María Mateos (ZMB, UZH), Jana Doehner (ZMB, UZH), Caroline Aemisseger (ZMB, UZH)

The first module will focus on general principles in advanced light microscopy for optimized imaging strategies. In depth lectures will cover optics, transmitted light and fluorescent microscopy. Practical training sessions with cells and tissue samples will focus on operating different types of fluorescent light microscopes (widefield, confocal laser scanning, multiphoton, superresolution and light sheet microscopes) with special focus upon how to achieve optimal data from different samples and research questions.

Module 2: Super-Resolution Light Microscopy (12 students)
Gabor Csucs (ScopeM, ETHZ)

The module will focus on three oft he most wide-spread super resolution techniques: SIM, STED and localization microscopy (PALM, dSTORM etc.). The participants will learn both the necessary sample preparation techniques but have extensive practical imaging session on the various instruments. The related image-processing challenges and the theoretical background of the various techniques will be also discusses. It is expected that the students have a solid practical and theoretical background in fluorescent microscopy (3D, confocal).

Module 3: Fine Structure Preparation for TEM (6 students)

Moritz Kirschmann, Andres Kaech (ZMB, UZH)

In this module you will learn how to prepare biological specimens for advanced electron microscopy techniques. Chemical and cryo fixation techniques (high-pressure freezing, freeze-substitution) will be used to preserve the fine structure of the tissue. Plastic embedded samples will be thin-sectioned by ultramicrotomy and imaged in the transmission electron microscope. You can bring your own samples.

Module 4: Immuno Electron Microscopy (6 students)
Heinz Schwarz (MPI Tübingen)

In this module you will learn how to perform immunolabeling experiments on plastic-embedded biological specimens. Ultrathin sectioning, handling and using antibodies, various strategies towards successful immunolabeling will be discussed and practically done on real samples. Validation of stainings by light and transmission electron microscopy is included. Samples will be provided.

Module 5: 3D Correlative Light and Electron Microscopy (12 students)
Miriam Lucas (ScopeM, ETHZ)

Correlative Light and Electron Microscopy (CLEM) combines large-scale volume imaging of cells or tissues in LM with a high-resolution description of their morphology using EM. The combination of 3D microscopy techniques such as confocal laser scanning microscopy (CLSM) and e.g. focused ion beam scanning electron microscopy (FIB-SEM) opens up exciting possibilities to expand morphological context description and analysis into to the third dimension – on the nm-scale! This module covers the basics of methodology and preparation techniques needed to perform light and electron microscopic investigations on identical sample areas by CLSM and FIB-SEM. You will learn to collect correlative data sets from one ROI in 2D and 3D, and get a better understanding of the different image characteristics. Further you will learn to correlate the different image types with software tools to finally align multimodal data in 3D and create 3D models. Samples will be provided.

Module 6: Volume Scanning Electron Microscopy (6 students)
Miriam Lucas (ScopeM, ETHZ)

The third dimension is of utmost importance for understanding the complex structural context of specimen, in biology as well as in material sciences. This module will SEM-based techniques for volume imaging: focused ion beam-SEM (FIB-SEM), serial-blockface SEM (aka 3View) and array tomography. In the former methods, a fresh blockface is created in situ in the SEM employing a focused ion beam, or a diamond knife respectively, and volume images are acquired by alternating cutting and imaging of the fresh blockface. Array tomography on the other hand images ribbons of sections (i.e. serial sections) prepared using conventional ultramicrotomy and loaded onto conductive supports for SEM. We will discuss the basics of methodology and preparation techniques needed for the described methods, followed by volume image acquisition. The module will be rounded up by image processing sessions covering the basics of post-processing of volume data, visualization and 3D modelling of structures of interest. Samples will be provided.

Module 7: Cryo-Electron Tomography (6 students)
Matthias Eibauer, Ohad Medalia (Department of Biochemistry, UZH)

Cryo-electron tomography is a versatile tool to obtain three-dimensional reconstructions of pleomorphic structures, such as cells, organelles and supramolecular assemblies, at a resolution of <5 nm. In the workshop, we will discuss and provide some training in all required steps of cryo-electron tomography: sample preparation by plunge freezing, data acquisition with the transmission electron microscope and finally the reconstruction of a tomogram.

Credit Points

The course accounts for 2-3 ECTS credit points, depending on your institution.

Course Fee

  • The course fee for attendants from academical institutions is CHF 400 (approx. 370 Euro).
  • The course fee of applicants from the MD-PHD program of the University of Zurich or students in the framework of the Kidney.CH NCCR is covered by these programs.
  • Applicants from industry should request information about industry course fee.

Application deadline

The deadline for submitting your application is October 31, 2016.

How to apply

The online application form will soon be in access.

For more information please click "Further official information" below.

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