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
except for November 30: 10.00 am - 4.00 pm
Start: September 21, 2018 (Fall Semester)
KSL: 9256
ERW Auditorium A224, 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
Langhans Auditorium, Plan


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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. (ANA)Downloads
Demonstration of Microscopes
Learning objectives:
Bright field vs Fluorescence; Light sources; Blurry images from thick samples; Pinhole; 3D reconstruction; Equipment for live cell imaging; Scanning electron microscope versus Transmission electron microscope.
Various teachersDownloads
Contrast, Magnification and Resolution - Laws of Physics for Microscopists
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)Downloads
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)Downloads
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.
Blank F. (DBMR, MU50)Downloads
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)Downloads
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)Downloads
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. (MIC)Downloads
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.
Nevian T. (PYL)Downloads
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)Downloads
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. (PYL)Downloads
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. (PYL)Downloads
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 LSFM; Applications and limitations of OPT and LSFM.
Mercader Huber N. (ANA)Downloads
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)Downloads
Transmission Electron Microscopy
Basic knowledge:
Basic properties of electromagnetic waves (wavelength, interference, diffraction, resolution limit); Elementary knowledge about atomic nuclei and electron shells as well as atomic mass.
Learning objectives:
Basic building blocks of an electron microscope and lens aberration; Electron-material scattering; Contrast formation by elastic interactions and inelastic interactions; Obtaining analytical information.
Vanhecke D. (AMI)Downloads
30.11.2018MIC Symposium 2018:
From Organoids to Organisms - Multiscale imaging
Replaces the regular lecture!
From 10.00 am to 4.00 pm
Further information:
The microscopy imaging center (MIC) invites all students of the lecture Advanced Microscopy to participate at the MIC Symposium 2018. Please register to this event, because we have to order lunch (cost-free for you!). Looking forward to meeting you all at this exciting event.
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)Downloads
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. (ANA)
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. (ANA)
Written exam.
Entrance at 7.50 am.
Written exam from 8.00 - 10.00 in the Lecture Hall of building G. Woker Strasse 5.
Lyck R. (TKI)

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