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. 2023 Sep 6;3(1):vbad119.
doi: 10.1093/bioadv/vbad119. eCollection 2023.

SEM3De: image restoration for FIB-SEM

Rayane Hamdane Serir  1 , Aurelie Deliot  2 , Caroline Kizilyaprak  3 , Jean Daraspe  3 , Christine Walczak  1 , Françoise Canini  2 , Amandine Leleu  2 , Sergio Marco  2 , Frederic Ronzon  2 , Cedric Messaoudi  1
Affiliations

SEM3De: image restoration for FIB-SEM

Rayane Hamdane Serir et al. Bioinform Adv. .

Abstract

Motivation: FIB-SEM (Focused Ion Beam-Scanning Electron Microscopy) is a technique to generate 3D images of samples up to several microns in depth. The principle is based on the alternate use of SEM to image the surface of the sample (a few nanometers thickness) and of FIB to mill the surface of the sample a few nanometers at the time. In this way, huge stacks of images can thus be acquired.Although this technique has proven useful in imaging biological systems, the presence of some visual artifacts (stripes due to sample milling, detector saturation, charge effects, focus or sample drift, etc.) still raises some challenges for image interpretation and analyses.

Results: With the aim of meeting these challenges, we developed a freeware (SEM3De) that either corrects artifacts with state-of-the-art approaches or, when artifacts are impossible to correct, enables the replacement of artifactual slices by an in-painted image created from adjacent non-artifactual slices. Thus, SEM3De improves the overall usability of FIB-SEM acquisitions.

Availability and implementation: SEM3De can be downloaded from https://sourceforge.net/projects/sem3de/ as a plugin for ImageJ.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Example of use of inpainting to restore data using different implemented algorithms. Two slices from a FIB-SEM volume are shown in A (no-artifactual, slice 283) and B (artifactual, slice 293). The slice in B is strongly out of focus. C and D are the slices corresponding to A and B after the deconvolution step. The gain in the spot’s definition is visible in C but for D the defocus was too strong to be compensated. E and F (corrected) are the slices corresponding to C and D after removal and inpainting of slice D. E was not changed compared to C. F shows an image with same definition as E and in accordance with densities visible in D.
See this image and copyright information in PMC

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