Lecture Series on Advanced Microscopy

Lecturers: Microscopy Imaging Center (MIC)
Responsible: Ruth Lyck
Type: Lecture, 2h per week, 3 ECTS
Target audience: Graduate School for Cellular and Biomedical Sciences
Master of Biomedical Science
Master of Molecular Life Sciences
Master of Biomedical Engineering and others
Time: Friday, 8:15-10:00
Start: September 22, 2017 (Fall Semester)
KSL: 9256
ERW Auditorium A225, Inst of Anatomy, Bühlstrasse 26, Plan
EXAM: 8:30 - 11:00 Lecture Room G. Wokerstrasse 5 Nr 3 on Plan , Plan
"Lesesaal",1st floor, entrance Anatomy, Bühlstr. 26, Plan



22.09.20172h, Introduction to Microscopy
Basic knowledge:
Basic knowledge in microscopy; Physics of light.
Learning objectives:
Microscopy techniques and range of magnification; History of microscopy; Light microscopy – a short introduction: Visible light, different techniques; Electron microscopy – a short introduction: Electron beam, different techniques; Basics of microscopy preparation techniques; Pitfalls of microscopy.
Tschanz S. (Anatomy)PDF
Administrative Introduction
29.09.20172h Demonstration of Microscopes
Learning objectives:
Bright field vs Fluorescence; Blurry images from thick samples; Light sources; Pinhole, 3D reconstruction; Equipment for live cell imaging; Scanning electron microscope versus Transmission electron microscope.
Various teachers
06.10.20172h Physics for microscopy
Basic knowledge:
Basic physical school knowledge.
Learning objectives:
Understanding what contrast, magnification and resolution means; understand the difference between rays and waves.
Frenz M. (IAP)PDF
13.10.20171h Fluorescence Microscopy
Basic knowledge:
Basic understanding of optics (Fluorescence and light path inside a fluorescence microscope will be discussed briefly during the lecture).
Learning objectives:
Overview of fluorescence microscopy from sample preparation to acquisition to image analysis. This lecture aims to serve as a basis for the following lectures focusing on laser scanning microscopy and image processing.
Blank F. (DBMR, MU50)PDF
 1h Total internal reflection fluorescence microscopy (TIRF)
Basic knowledge:
Basics in the physics of light; Basics in fluorescence microscopy.
Learning objectives:
Basics of TIRF theory; Typical TIRF applications; Quantitative aspects of TIRF.
Belyaev Y. (TKI)PDF
20.10.20171h Laser scanning microscopy
Basic knowledge:
Understanding the principles of fluorescence; Understanding the physical basics of light microscopy imaging.
Learning objectives:
Basic principles and technical requirements for laser scanning microscopy; Data acquisition and data visualization; Understanding the difference to conventional fluorescence microscopy.
Rothen-Rutishauser B. (AMI)PDF
 1h Laser scanning microscopy: Specific applications (FRET, FRAP, Spectral unmixing) & digital image restoration
Basic knowledge:
Basic knowledge of normal light microscopy and image property is required.
Learning objectives:
To introduce several application possibilities using confocal microscopy and image analysis softwares.
Yousefi S. (PKI)PDF
27.10.20171h Live cell imaging: Colorful cells and the time factor
Basic knowledge:
Principles of fluorescence, excitation and emission spectra of a fluorophore; Basics of cell biology.
Learning objectives:
Time intervals for image acquisition; time acceleration in fast motion movies; Origin and variants of green and red fluorescent proteins; Fluorescent proteins in life science research.
Lyck R. (TKI)
 1h Multiphoton intravital microscopy (MP-IVM)
Basic knowledge:
Principle of fluorescent image generation; Wide field versus point scanning systems; Light path, dichroid versus bandpass filters; Detection systems: CCD for wide field and PMT for point-scanning; Principle of confocality (ie light detection of specific z-plane).
Learning objectives:
Principle of image generation in MP-IVM including technical parts; Applications and limitations of MP-IVM.
Stein J. (TKI)
03.11.20171h Intravital microscopy (IVM)
Learning objectives:
Definition of "epifluorescence intravital microscopy"; Differentiation between IVM and 2P-IVM; Concept of IVM microscopic observation of leukocyte endothelial interactions in the live, anesthetized animal; Outcome measure and interpretation of IVM; Limits and restrictions of IVM approach.
Enzmann G. (TKI)
 1h Calcium-imaging with confocal microscopy
Basic knowledge:
Principles of fluorescence, excitation spectra and emission spectra; Basics of laser scanning confocal microscopy; Basics of chemical buffer systems (pH buffers, calcium buffers).
Learning objectives:
Understand properties of fluorescent calcium indicators (intensometric and ratiometric, chemical and genetic); Know techniques for intra-cellular loading of calcium indicators; Ability to select appropriate calcium indicator based on wavelength and calcium affinity; Know advantages and disadvantages of the various calcium indicators; Understand limitations of time-resolved confocal microscopy (sensitivity, temporal and spatial resolution, bleaching, signal-to-noise-ratio).
Niggli E. (Physio)
10.11.20172h Super resolution imaging
Basic knowledge:
Point spread function (PSF); Theoretical background on the resolution of a microscope; Image formation; Optical imaging of a lens as a Fourier Transformation; Optical transfer function; Laser scanning microscopy; Fluorescence.
Learning objectives:
"breaking the resolution limit" - from the point spread function of a conventional microscope to the engineering of the PSF; Stimulated emission depletion microscopy (STED): Physical principle, experimental setup; Structured illumination microscopy: Physical principle of resolution enhancement, experimental setup and procedure, contrast to z-sectioning with structured illumination microscopy (SIM); STORM/PALM: Principle of localization microscopy.
Nevian T. (Physio)
17.11.20171h Mesoscopic imaging techniques: Optical projection tomography (OPT) and light sheet fluorescence microscopy (LSFM)
Basic knowledge:
Principle of fluorescent image generation. Principle of confocality (ie light detection of specific z-plane).
Learning objectives:
Principle of image generation in OPT and LFSM; Applications and limitations of OPT and LFSM.
Stein J. (TKI)
 1h Atomic Force Microscopy (AFM) in Biology
Basic knowledge:
Basic biology, physics and chemistry knowledge.
Learning objectives:
Understanding the working principle of AFM and learning about the possible applications of this microscope in biology.
Fotiadis D. (IBMM)
24.11.20172h Transmission Electron Microscopy
Basic knowledge:
Basic properties of electromagnetic waves (wavelength, interference, diffraction, resolution limit); Basic building blocks of an electron microscope and lens aberration; Electron-material scattering; Contrast formation; Elastic interactions; Inelastic interactions
Learning objectives:
Understand how an electron interacts with a very thin layer of matter; Understand in a non-mathematical way: elastic scattering, inelastic scattering, principles of electron dispersive X-ray; Understand amplitude contrast, have a notion of phase contrast; Understand the (aberration) limits of electromagnetic lenses.
Vanhecke D. (AMI)
01.12.20172h Scanning Electron Microscopy
Basic knowledge:
Elementary knowledge about physical optics (wavelength, focal length, numerical aperture, depth of field); Elementary knowledge about atomic nuclei and electron shells as well as atomic mass; Knowledge about different types of electron guns; A grasp of the essence of a histogram.
Learning objectives:
Different illumination modes in microscopy; Probe formation and electron sample interactions; Contrast formation (topographical contrast, material contrast); Signal generation, collection and handling; Sample preparation; Common artifacts.
Stoffel M. (Vet. Anatomy)
08.12.2017MIC Symposium: Big Data in Light and Electron MicroscopyInfo/Registration:Link
15.12.20172h Cryo-Electron Microscopy (Cryo-EM) & Serial Block Face Scanning Electron Microscopy (SFB-SEM)
Basic knowledge:
What is an electron? Notions of biology; Geometrical optics; Basic knowledge of diffraction; Principles of transmission electron microscope (TEM) function; Principles of scanning electron microscope (SEM) function; Principles of biological specimen preparation for conventional TEM; Principles of biological specimen preparation for conventional SEM.
Learning objectives:
Artefacts commonly happening during conventional TEM preparation; Physico-chemical origin of these artefacts; Rationale for applying cryo-EM; Meaning of vitrification and ways of achieving it; Principles of single particle cryo-EM; Pros and Cons vs X-ray crystallography; Principles of cryo-electron tomography; Rationale for applying SBF-SEM; Principle of SBF-SEM procedure; Pros and Cons vs TEM serial sections; Segmentations: pitfalls and arising methods.
Zuber B. (Anatomy)
22.12.20172h Stereology
Basic knowledge:
Basic knowledge in geometry and statistics.
Learning objectives:
Reasons for quantification in microscopy; Problems of quantification in microscopy; Examples of "bad" quantification; Sources of bias in microscopic quantification (=Stereology); Steps of a stereologic approach; Sampling; Measurement; Reference Volume; Useful parameters (volume, area, length, number); Application and design of a stereologic study: Sampling steps (hierarchical, SUR/IUR), measurement steps (point-/Intersection count, test grid); Issues of number estimation: 3D sample, dissector; Precision versus Unbiasedness; Efficiency of stereology; Limitations of stereology.
Tschanz S. (Anatomy)
12.01.20182h Written exam. Entrance at 8.15 am. Written exam from 8.30 - 10.30 in the Lecture Hall of building G. Woker Strasse 5.Lyck R. (TKI)

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