Optimization of FIB-SEM Tomography and Reconstruction for Soft, Porous, and Poorly Conducting Materials
Journal article, 2020

Tomography using a focused ion beam (FIB) combined with a scanning electron microscope (SEM) is well-established for a wide range of conducting materials. However, performing FIB-SEM tomography on ion- and electron-beam-sensitive materials as well as poorly conducting soft materials remains challenging. Some common challenges include cross-sectioning artifacts, shadowing effects, and charging. Fully dense materials provide a planar cross section, whereas pores also expose subsurface areas of the planar cross-section surface. The image intensity of the subsurface areas gives rise to overlap between the grayscale intensity levels of the solid and pore areas, which complicates image processing and segmentation for three-dimensional (3D) reconstruction. To avoid the introduction of artifacts, the goal is to examine porous and poorly conducting soft materials as close as possible to their original state. This work presents a protocol for the optimization of FIB-SEM tomography parameters for porous and poorly conducting soft materials. The protocol reduces cross-sectioning artifacts, charging, and eliminates shadowing effects. In addition, it handles the subsurface and grayscale intensity overlap problems in image segmentation. The protocol was evaluated on porous polymer films which have both poor conductivity and pores. 3D reconstructions, with automated data segmentation, from three films with different porosities were successfully obtained.

scanning electron microscopy


soft material


focused ion beam

poorly conducting material


Cecilia Fager

Chalmers, Physics, Nano and Biophysics

Magnus Röding

RISE Research Institutes of Sweden

Anna Olsson

AstraZeneca AB

Niklas Lorén

Chalmers, Physics, Nano and Biophysics

RISE Research Institutes of Sweden

Christian von Corswant

AstraZeneca AB

Aila Särkkä

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

Eva Olsson

Chalmers, Physics, Nano and Biophysics

Microscopy and Microanalysis

1431-9276 (ISSN) 1435-8115 (eISSN)

Vol. 26 4 837-845

Subject Categories


Textile, Rubber and Polymeric Materials

Materials Chemistry





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