Winter School 2016

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10th Microscopy Winter School 2016

Practical Course in Advanced 3D Microscopy in Zurich, 17.- 22. January 2016

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 eight (8) 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.



Venue: ETH Zurich and University of Zurich



  • Urs Ziegler, Andres Kaech, Center for Microscopy and Image Analysis, University of Zürich
  • Martin Pilhofer, Institute of Molecular Biology and Biophysics, ETH Zurich
  • Gabor Csucs, Roger Wepf, Scientific Center for Optical and Electron Microscopy, ETH Zurich


Registration, Course Fees and Credit Points


Registration Deadline: October 31, 2015 /Application for Registration

Course fee for attendants from academical institutions: 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, please request information about industry course fee.

Credit Points

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

Informations: Information, timetables and module descriptions will be updated continuously.


Flyer Winter School 2016 (PDF, 216 KB)

Schedule Winter School 2016 (PDF, 21 KB)


Modules 2016


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 Microscopy (CLSM/FIB-SEM) (12 students)

Miriam Lucas, Philippe Gasser, Maja Günthert, Anne Greet Bittermann, Joakim Reuteler (ScopeM, ETHZ)

From 3D LM structure to 3D EM structure. This module will teach the basics of methodology and preparation techniques needed to perform light and electron microscopic investigations on identical / same sample areas by confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB/SEM). You will learn to collect correlative data sets from one ROI in 2D and 3D using the described imaging techniques, 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: Array Tomography - 2D Correlative Microscopy (6 students)

Falk Lucas, Roger Wepf (ScopeM, ETHZ)

From 2/3D (in-vivo) structure to 3D SEM structure (FLM, CLSM, array tomography SEM) with the Shuttle and Find tool. This module will teach the basics of methodology and preparation techniques needed to perform light and electron microscopic investigations on identical / same sample areas. You will learn to collect 2D and 3D data by fluorescence light microscopy FLM, (CLSM) and SEM and get a better understanding of the different image characteristics and learn that SEM conquer TEM ultrastructure application nowadays. Further you will see that array tomography can be combined with immuno-cytochemistry to localize antigens on serial sections for FLM and SEM. Finally you learn to correlate the different image types with software tools to finally align multimodal data and antigen maps in 3D. Samples will be provided.


Module 7: Serial Block-Face Scanning Electron Microscopy (3View) (3 students)

Miriam Lucas, Anne-Greet Bittermann, Roger Wepf (ScopeM, ETHZ)

This module will focus on acquisition and reconstruction of 3Dtissue ultrastructure, using serial block-face SEM (SBF-SEM). A microtome built into an SEM enables serial sectioning, and automated imaging of the resulting consecutive block-faces yields the 3D dataset. By applying SBF-SEM to various animal and plant tissues, you will explore the possibility of this 3D imaging technology and learn how 3D datasets can be reconstructed and used to produce 3D models. Samples will be provided.


Module 8: Cryo-Electron Tomography (3 students)

Martin Pilhofer (Institute of Molecular Biology and Biophysics, ETHZ)

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.

Application for Registration (Deadline: October 31, 2015) Application for Registration


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