SEM3De: image restoration for FIB-SEM.

Area of Science:

• Microscopy and Imaging Science
• Materials Science
• Biological Imaging

Background:

• Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) is a powerful technique for generating high-resolution 3D images of samples.
• The technique involves sequential imaging and material removal, enabling the acquisition of extensive image stacks.
• However, FIB-SEM imaging is prone to various artifacts, such as milling stripes, detector saturation, and sample drift, which hinder accurate image interpretation and analysis.

Purpose of the Study:

• To address the challenges posed by artifacts in FIB-SEM imaging.
• To develop a user-friendly software solution for artifact correction and data enhancement in FIB-SEM acquisitions.
• To improve the overall usability and reliability of 3D imaging data obtained from FIB-SEM.

Main Methods:

• Development of SEM3De, a freeware plugin for ImageJ.
• Implementation of state-of-the-art artifact correction algorithms within SEM3De.
• Integration of image inpainting techniques to replace artifact-affected image slices with data from adjacent slices.

Main Results:

• SEM3De effectively corrects common artifacts encountered in FIB-SEM imaging.
• For uncorrectable artifacts, SEM3De provides a robust method for replacing corrupted slices using image inpainting.
• The software significantly enhances the quality and interpretability of 3D FIB-SEM datasets.

Conclusions:

• SEM3De offers a valuable solution for mitigating artifacts in FIB-SEM microscopy.
• The freeware improves the usability of FIB-SEM data for scientific research across various fields.
• SEM3De is readily available as an ImageJ plugin, promoting wider adoption and accessibility.