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Note: Half day practical sessions start at 14:30 unless stated otherwise (Please check travel information in advance as for some sessions you have to skip the afternoon lecture)
1. Serial block-face SEM
Potential dates: 07./12./14. September 2023
Maximal number of participants: 4
The third dimension is of utmost importance for understanding the complex structural context of specimen. This demo covers a specific scanning electron microscopy (SEM)-based technique for volume imaging, so-called 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. This technique is highly efficient for acquisition and reconstruction of the 3D ultrastructure of tissue and cell-culture samples. You will explore this imaging technology and see how 3D datasets can be reconstructed and used to produce 3D models.
Meeting point: HPT C 10, ETH Hönggerberg Campus
2. FIB-SEM tomography
Potential dates: 05./11./12. September 2023
Maximal number of participants: 3
In this demo, the workflow for 3D data acquisition in a focused ion beam - scanning electron microscope (FIB-SEM) will be shown. Sample preparation strategies for live science specimens for electron microscopy will be discussed. Options for correlative microscopy will be presented. Within a biological, sample we will find a region of interest and perform serial cross sectioning and imaging. Images will be analyzed and possible views of a tomogram will be displayed.
Meeting point: HPT C 10, ETH Hönggerberg Campus
3. Array tomography (volume EM)
Potential dates: 06./07. September 2023
Maximal number of participants: 3
The third dimension is of utmost importance for understanding the complex structural context of specimen. This demo covers a specific scanning electron microscopy (SEM)-based technique for volume imaging using serial sections of resin-embedded samples, so-called array tomography. These are prepared using conventional ultramicrotomy and mounted onto a conductive support for SEM. Basics of methodology, image characteristics and sample preparation techniques will be demonstrated. You will learn how the investigation of biological ultrastructure can be made more efficient and expressive
Meeting point: HPM C 57.2, ETH Hönggerberg Campus
4. Structures of fibrillar proteins in health & disease by electron microscopy
Potential dates: 05./06. September 2023
Maximal number of participants: 8
Electron microscopy, at room or cryo temperatures, is a powerful imaging technique to determine structures of biological macromolecules. Single particle analysis (SPA) is a well-established routine technique to determine structures of globular proteins. Whilst a relative technique, termed helical reconstruction, is applied to solve structures of fibrillar proteins.
Since contrast of biological specimens is usually poor, most projects are initiated by applying a contrast enhancing fast and easy method called negative staining. Biological sample is deposited onto an EM carbon coated grid and surrounded by heavy atom stain to enhance contrast for screening sample quality. For obtaining structure in near-native state, the specimen is vitrified for imaging under low-dose cryo conditions.
The session will cover sample preparation and imaging under TEM. Basic principles and methodology of sample preparation and imaging will be discussed and demonstrated. Besides Cryo-EM workflow, you will also get an insight to cryo-EM applications in structure determination of disease-relevant fibrillar proteins.
Meeting point: HPM C 55.2, ETH Hönggerberg Campus
5. Fluorescence microscopy
Potential dates: 05./11. September 2023
Maximal number of participants: 8
Introducing and demonstrating a fluorescent light microscope (wide-field and confocal imaging mode).
Meeting point: HPM E14, ETH Hönggerberg Campus
6. Super resolution microscopy
Potential dates: 12./14. September 2023
Maximal number of participants: 8
This practical part will comprise the principles and the demonstration of two super resolution techniques, two fluorescence microscopy methods overcoming the optical diffraction limit:
During these afternoon sessions, you will also gain some hands-on experience on both systems and learn how to process the raw SIM data.
Meeting point: ZMB - Y42 Floor H, UZH Irchel
7. Functional and diffusion MRI of the brain
Potential dates: 05./07. September 2023
Maximal number of participants: 10
To familiarize with practical in-vivo MR imaging of human organ function and its architecture.
Meeting point: ETZ F 91
8. Positron emission tomography
Potential dates: 06./11. September 2023
Maximal number of participants: 6
You will get guided tours in our "B-lab" where we synthesize our PET tracers and in the small-animal PET lab where we evaluate our PET tracers in mice and rats. We will show you the details of PET experiments with mice and rats in videos taken during our research.
Meeting point: 14:30 ETH Hönggerberg, bus station (ETH link, Shuttlebus): departs from ETH main building (below Polyterrasse/cafeteria)
Location of lab: ETH Hönggerberg, HCI building, D floor, room D418
9. 3D structural analysis by cryo-electron microscopy
Potential dates: 12. September 2023
Maximal number of participants: 6
In this course, students will experience cryo-EM data acquisition and image analysis to reconstruct 3D structure of biological macromolecules.
Meeting point: PSI EAST reception (in front of the bus stop), Paul Scherrer Institute
Note: Long travel distance! For this session you will have to leave early and skip the afternoon lecture, but of course you can enjoy the slides afterwards. If there is time, we will make a lab tour to see SLS (synchrotron). All participants must wear long trousers to be allowed to enter labs at PSI.
10. Near-infrared spectroscopy
Potential dates: 07. September 2023
Maximal number of participants: 10
Near-infrared spectroscopy is a diagnostic tool to investigate tissue oxygenation with near-infrared light. The practical session will consist of an introduction, how the method works including technology, examples of applications and outlook. The major part will be practical measurements with NIRS equipment.
Meeting point: CAB G57
11. SPECT/CT imaging
Potential dates: 06./07./14. September 2023
Maximal number of participants: 6
The practical will show the procedure to image living animals with SPECT/CT. The technical aspects of the SPECT/CT will be explained.
Meeting point: Entrance PSI East, Paul Scherrer Institute; Meeting time: 13:50 hr.
Note: Long travel distance! For this session you will have to leave early and skip the afternoon lecture, but of course you can enjoy the slides afterwards. All participants must wear long trousers to be allowed to enter labs at PSI.
12. Synchrotron X-ray tomography
Potential dates: 05. September 2023
Maximal number of participants: 8
This practical session foresees the visit of the Swiss Light Source at the Paul Scherrer Institute in Villigen, a third-generation synchrotron source, and in particular of the TOMCAT beamline, dedicated to X-ray tomographic microscopy experiments. In addition to the hardware for the different tomographic techniques (phase contrast, nano-tomography, dynamic and in-situ experiments), a palette of different samples and acquired datasets will be presented and discussed. If beam availability permits, a tomographic scan of a few test samples will be acquired and the data reconstructed.
Meeting point: Entrance PSI West, Paul Scherrer Institute
Note: Long travel distance! For this session you will have to leave early and skip the afternoon lecture, but of course you can enjoy the slides afterwards. All participants must wear long trousers to be allowed to enter labs at PSI.
13. MRI biomarker qualification on the fertilized chicken egg: a 3R experimental model
Potential dates: 07./14. September 2023
Maximal number of participants: 4
The session explains how the 3R principle (Reduce, Refine, Replace) is applied in research using animal models. We present the CAM Model as one example and show how it contributes to MRI biomarker qualification and discuss practical issues for its use. This is followed by an overview of studies conducted in our and other labs in this model, as well as a practical demonstration.
Meeting point: University Hospital Zurich, outside entrance HOER (entrance close to Dick & Davy Cafeteria)
14. Practical insight in ultrasound imaging, Doppler application and advanced ultrasound signal processing
Potential dates: 05. September 2023
Maximal number of participants: 8
In this practical session students will receive an insight into the transmission and reception methods of ultrasound imaging and the related signal processing to receive an echo image and a Doppler flow spectrogram. The session will be composed of three parts:
Meeting point: ETF, Room C109
15. In vivo two-photon imaging in the mouse brain
Potential dates: 05./06./12. September 2023
Maximal number of participants: 4
Students will learn the principles of two-photon microscopy, the main components of a two-photon microscope and its application for imaging of various physiological processes such as capillary blood flow, dynamics of brain energy metabolites and astrocytic calcium activity in the mouse brain. They will have the opportunity to follow a real measurement, identify important aspects for in vivo two-photon imaging and participate in preliminary data analysis.
Meeting point: Building 17, Faculty axis on H floor, Institute of Pharmacology and Toxicology, UZH Irchel Campus, Winterthurerstrasse 190, 8057 Zurich
16. Advanced processing and visualization of MRI data for research and clinical needs
Potential dates: 05./06./11. September 2023
Maximal number of participants: 10
This practical session will provide students with an introduction to the DICOM image format and skills to perform image manipulation and analysis including filtering, registration and segmentation. An introduction and tutorial of open source image analysis software and libraries will be included along with some basic programming. Datasets used for processing and visualization will include MR bone imaging, 4D-flow cardiac MRI and T1 and diffusion weighted brain MRI.
Meeting point: ETZ D61-1
17. Functional renal MRI
Potential dates: 07./11. September 2023
Maximal number of participants: 8
An overview on MRI techniques for assessment of kidney function is provided. The students will learn the basis of different functional MRI techniques such as diffusion weighted imaging (DWI), intravoxel incoherent motion (IVIM), diffusion tensor imaging (DTI), and blood oxygenation level dependent (BOLD) imaging. Moreover, respective MRI data sets will be acquired in healthy volunteers, and post-processing will be done using suitable software tools.
Meeting point: MR centre, University Hospital Zurich, V floor, Raemistrasse 100, 8091 Zurich
18. Macromolecular crystallography (MX)
Potential dates: 14. September 2023
Maximal number of participants: 6
The session will include a short introduction to the Swiss light source. In the practical part you will handle protein crystals and freeze them in liquid nitrogen. Furthermore, you will collect data on these crystals at the bending magnet beamline X06DA and use these data to solve the atomic structure of the protein.
Meeting point: Entrance PSI West, Paul Scherrer Institute
Note: Long travel distance! For this session you will have to leave early and skip the afternoon lecture, but of course you can enjoy the slides afterwards. All participants must wear long trousers to be allowed to enter labs at PSI.
19. Ultrasound imaging of the human heart
Potential dates: 06. September 2023
Maximal number of participants: 10
This afternoon hands-on session provides an overview of ultrasound of the heart (echocardiography) and its clinical applications. The students are introduced to the principles of ultrasound imaging and will learn basics of the anatomy and function of the heart. Participants will get the opportunity to receive hands-on experience in conducting an echocardiographic examination.
Maximum number of students: 10
Meeting point: USZ Main Entrance, Rämistrasse 100
20. Three-dimensional laser scanning confocal microscopy of optically cleared hematopoietic tissues
Potential dates: 05./12. September 2023
Maximal number of participants: 6
In this practical session students will receive a theoretical and practical introduction to the use of advanced confocal microscopy to generate 3D reconstructions of large tissue volumes. The session will include an overview of the currently available protocols for optical clearing of tissues enabling deep tissue imaging, as well as a hands on session comprising image acquisition and analysis of pre-processed hematopoietic organs, including bone marrow, liver and spleen.
Meeting point: Main entrance Häldeliweg 4, UZH Central Campus
21. Next generation of sequencing and high-end mass spectrometry
Potential dates: 11. September 2023
Maximal number of participants: 12
Molecular profiling of complex biological systems at the level of genes, transcripts, proteins and metabolites at omics scales. Introductory presentation and lab tours in groups to illustrate latest methods and technologies in the areas of next generation sequencing and high-end mass spectrometry.
Meeting point: Campus Irchel Y59 G30
22. X-ray imaging techniques and 3D image analysis
Potential dates: 14. September 2023
Maximal number of participants: 10
Empa's center for X-ray analytics develops X-ray methodologies in the fields of X-ray diffraction (XRD), scattering (SAXS) and imaging (XCT) for understanding materials structure in life- and material science. State-of-the art XCT lab equipment combined with image reconstruction and processing, using in-house and commercial tools provide qualitative and quantitative non-destructive analysis for a wide range of materials and tissues with spatial resolutions down to 300nm. Basic and applied developments in the domains of soft materials characterization, wood and cellulose analysis, tumor and thrombus analysis, biofilm and cartilage imaging, and many others are part of the activities. For the workshop participants, the course offers a great opportunity to get a hands-on experience on the XCT instrument(s) with real experiments on selected samples. In addition, a guided tour is given highlighting the main activities of Empa's Center for X-ray analytics.
Meeting point: Reception Empa Dübendorf
23. Imaging visualization techniques for anatomy teaching including mixed reality
Potential dates: 11./14. September 2023
Maximal number of participants: 6
A novel open-source mixed reality applications for Hololens glasses to visualize organ structure and function will be demonstrated.
Meeting point: ETZ E 81
