MSE-704 | 3D Electron Microscopy and FIB-Nanotomography

Electron microscopes deliver only 2D information in a single image. The 3rd dimension is often left to the interpretation by the observer. Different techniques have been developed to use 2 or more images to reconstruct the 3rd dimension. To investigate and analyze the complex structures produced by micro- and nano-technology 3D electron microscopy is offering powerful methods. The resolution of modern electron microscopes and the possibility to choose between different signals make them versatile tools for the exploration of the micro- and nano-cosmos.

In this course the principles of 3D surface (SEM) reconstruction and its limitations will be explained. 3D volume reconstruction and tomography methods by electron microscopy (SEM/FIB and TEM) will be explained and compared with x-ray tomography. This course is intended for researchers who have a background in electron microscopy.


This 1 credit 3D Electron Microscopy and FIB-Nanotomography doctoral school MSE-704 is held once per year in the spring semester.

The next running of the course will take place in Spring 2024.

The schedule and course material will be made available on Moodle.

Please register via IS-Academia, or contact [email protected].


  • Understand the principles of 3D surface (SEM) and volume (SEM/FIB and TEM) reconstruction by electron microscopy.
  • Know the possibilities and limitations of the different techniques for materials science applications.


  • Physics of the different signals generated by electron beams and focused ion beams.
  • Underlying physical principles for the acquisition of data sets for 3D reconstruction: interaction volumes, voxel (3 dimensional “pixel”) size, mechanical stability issues for successful recon-struction.
  • Surface reconstruction (SEM), serial (parallel) sectioning (SEM/FIB and TEM), tilt series tomo-graphy (TEM).
  • Introduction to the use of software packages for 3D surface and volume reconstruction.
  • Practical session about 3D volume reconstruction by FIB nano-tomography.

Required prior knowledge

  • Background in electron microscopy: electron microscopy lecture 5 sem.
  • Bachelor level or doctoral school SEM&TEM or equivalent.

Links to download useful software


Monte Carlo simulation of electron trajectory in solids

ImageJ, ‘Fiji package’

An open platform for scientific image analysis