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Volume Electron Microscopy by Automated Serial SEM

October 20, 2019 - October 25, 2019

(Deadline: July 29, 2019)

Course Overview

Recent developments in scanning electron microscopes (SEM) have led to ground-breaking opportunities in volume imaging of cells and tissues. The aim of the course is to provide extensive theoretical and practical knowledge on the 3 main techniques for automated serial imaging based on SEM (ASI-SEM): microtome-based serial block-face SEM, focused ion beam SEM and array tomography. At the issue of the course, the participants will be able to assess the potentials of each technique and which fit best to their own scientific project. The participants will acquire the theoretical background to understand the different techniques as well as to optimize the imaging conditions. Data processing, analysis and management will be covered extensively, as they are inherent key considerations to all ASI-SEM techniques. An important fraction of the course will be devoted to hands-on experimentation on i) sample preparation adapted to each ASI-SEM technique ii) operation of the hardware (SEMs, automated microtomes) iii) image processing software (stack registration, segmentation, tracing).

The course will bring together some of the world experts in this new imaging field for biologists. They will share their expertise and trigger a new network of scientists that will together contribute to a better dissemination and use of ASI-SEM.


This course will address a large audience in the life science community, in particular (but not exclusively) cell and developmental biology, neurosciences, etc. Participants should preferably have prior experience in cellular electron microscopy, not necessarily in volume EM. The course is open to early career researchers (PhD students and post-docs) as well as facility staff who are starting or intend to start working with volume SEM techniques.


  • Serial Blockface SEM (SBEM)
  • Focused Ion Beam SEM (FIB-SEM)
  • Array Tomography
  • Biological sample preparation
  • Image post-processing and analysis

*Extensive hand-on experimentation in all modules.

Learning Outcomes

Dissemination of the ASI-SEM techniques across the Life Sciences community. Extensive theoretical and practical knowledge on the main techniques for automated serial imaging based on SEM (ASI-SEM).