|Lecturers:||Microscopy Imaging Center (MIC)|
|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
|Start:||September 22, 2017 (Fall Semester)|
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
|22.09.2017||2h, Introduction to Microscopy|
Basic knowledge in microscopy; Physics of light.
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|
|29.09.2017||2h Demonstration of Microscopes|
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.
|06.10.2017||2h Physics for microscopy|
Basic physical school knowledge.
Understanding what contrast, magnification and resolution means; understand the difference between rays and waves.
|Frenz M. (IAP)||PDF|
|13.10.2017||1h Fluorescence Microscopy|
Basic understanding of optics (Fluorescence and light path inside a fluorescence microscope will be discussed briefly during the lecture).
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)|
Basics in the physics of light; Basics in fluorescence microscopy.
Basics of TIRF theory; Typical TIRF applications; Quantitative aspects of TIRF.
|Belyaev Y. (TKI)||PDF|
|20.10.2017||1h Laser scanning microscopy|
Understanding the principles of fluorescence; Understanding the physical basics of light microscopy imaging.
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 of normal light microscopy and image property is required.
To introduce several application possibilities using confocal microscopy and image analysis softwares.
|Yousefi S. (PKI)||PDF|
|27.10.2017||1h Live cell imaging: Colorful cells and the time factor|
Principles of fluorescence, excitation and emission spectra of a fluorophore; Basics of cell biology.
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)|
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).
Principle of image generation in MP-IVM including technical parts; Applications and limitations of MP-IVM.
|Stein J. (TKI)|
|03.11.2017||1h Intravital microscopy (IVM)|
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|
Principles of fluorescence, excitation spectra and emission spectra; Basics of laser scanning confocal microscopy; Basics of chemical buffer systems (pH buffers, calcium buffers).
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)|
|10.11.2017||2h Super resolution imaging|
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.
"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)|
|17.11.2017||1h Mesoscopic imaging techniques: Optical projection tomography (OPT) and light sheet fluorescence microscopy (LSFM)|
Principle of fluorescent image generation. Principle of confocality (ie light detection of specific z-plane).
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 biology, physics and chemistry knowledge.
Understanding the working principle of AFM and learning about the possible applications of this microscope in biology.
|Fotiadis D. (IBMM)|
|24.11.2017||2h Transmission Electron Microscopy|
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
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)|
|01.12.2017||2h Scanning Electron Microscopy|
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.
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)|
|08.12.2017||MIC Symposium: Big Data in Light and Electron Microscopy||Info/Registration:||Link|
|15.12.2017||2h Cryo-Electron Microscopy (Cryo-EM) & Serial Block Face Scanning Electron Microscopy (SFB-SEM)|
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.
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)|
Basic knowledge in geometry and statistics.
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)|
|12.01.2018||2h 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)|