Stereology Workshop

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.


Week: Stereology


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: 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
Lunch break
Final presentation of projects by participants


Hands-on computer based stereology and imaging machinery: newCAST (Visiopharm, DK)

(start 09:00):

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

(end 17:00):

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

Unbenanntes Dokument

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)