Workshop on Quantitative Microscopy 2021
We hope to run the Stereology workshop Bern in 2021.
Date: Mon 16 - Fri 20 August 2021
(VISIOPHARM newCAST hands-on: Sat 21. & Sun 22 August 2021)
Registration is open.
Due to COVID, the date cannot be guaranteed.
Stereology provides biomedical researchers with efficient and unbiased tools to obtain real 3D data like volume, surface, length, and number of organs, tissues, cells, and organelles from measurements done on microscopic sections.
If this is important for your research, this workshop is for you!
In collaboration with the Microscopy Imaging Center (MIC), University of Bern
This workshop provides an introduction to state-of-the-art stereology with emphasis on its practical application in biomedicine. Experimental design, sampling, use of stereological probes, estimation of stereological parameters, and the application of statistical methods appropriate for stereology are covered. The workshop encompasses lectures, classroom exercises with real biomedical images, and laboratory practicals demonstrating the implementation of proper sampling and processing techniques on real biological organs.
This workshop is intended for students and researchers from the field of biology and medicine interested in sampling and measurement of 3D structures. Applications involving any kind of microscopy (e.g. light microscopy, confocal laser scanning microscopy, multi-photon microscopy, electron microscopy) as well as non-invasive scanning techniques like CT and NMR are welcome.
Participants should bring their specific projects and questions. During the workshop, there will be ample opportunity for discussions with the instructors.
Presentation of projects by participants
Lecture: Definition of probes, sampling and basic statistics
Lecture: Volume estimation, Cavalieri principle
Exercise: Volume estimation
Practical: Agar embedding and slicing of organs
Lecture: The fractionator principle (systematic sampling)
Exercise: The fractionator
Lecture: The disector, counting and sampling in 3D
Exercise: Number estimation
Lecture: More disector sampling, including connectivity
Exercise: Alveolar number
Lecture: Length and Surface, IUR
Exercise: Length estimation
Lecture: Ratios, multilevel sampling design, reference trap
Lecture: Vertical sections
Exercise: Surface from vertical sections
Practical: Fractionator sampling, vertical sections; embedding, sectioning and staining
Lecture: Sampling and sizing of particles
Exercise: The Nucleator
Exercise: Point sampled intercepts
Lecture: Tissue deformation, slicing, tools and gadgets
Demonstration: Stereology and imaging machinery: newCAST
Demonstration: Stereology web-tool: the STEPanizer
Lecture: All the estimators of particle size
Final presentation of projects by participants
Hands-on computer based stereology and imaging machinery: newCAST (Visiopharm, DK)
Lectures: Introduction to stereology and newCAST, incl. volume estimation, Cavalieri principle
Exercises: Cavalieri volume, fractional volume
Lectures: Number estimation disector (physical and optical), surface area estimation, and length estimation
Exercises: Physical disector, optical disector, surface area, local volumes using nucleator / rotator
Exercises: Microscop setup, calibration, image acquisition
Exercises: Optical disector
Lectures: Automation in stereology software, new sampling techniques (Proportionator)
Exercises: Microimager, Auto disector, Point Sampled Intercept
Dr. Johnnie Bremholm Andersen
Visiopharm A/S, Hoersholm, Denmark
Prof. Heinz Fehrenbach
Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften (FZB), Borstel, Germany
Beat Haenni (head of laboratory)
Institute of Anatomy, Experimental Morphology, University of Bern, Switzerland
Prof. Christian Mühlfeld
Institute for Functional and Applied Anatomy, Hannover Medical School, Germany
Prof. Jens Randel Nyengaard
Stereology and EM Laboratory, University of Aarhus, Denmark
Prof. Matthias Ochs
Institut für Funktionelle Anatomie, Charité - Universitätsmedizin Berlin
PD Dr. Stefan Tschanz (Organizer)
Institute of Anatomy, IT- Department/Stereology, University of Bern, Switzerland
Stefan Tschanz, PD Dr. med., Software Eng.
Institute of Anatomy, Baltzerstrasse 2, CH-3000 Bern 9
Tel. +41 31 631 84 78
Institute of Anatomy. Baltzerstrasse 2, 3000 Bern 9, Switzerland
Entrance of the old building, Bühlstrasse 26
Lesesaal first floor (lectures), Room B 212 OPS (lab. demos)
2nd Edition (2010 reprint)
by C.V. Howard and M.G. Reed