Image Analysis Tools for Scanning Electron Microscopy

Scanning Electron Microscopy (SEM) is widely used in many scientific fields, particularly in life sciences, offering high-resolution information on the ultrastructure of biological organisms. Accurate characterization of SEM image quality is important for assessing the SEM tool performance, in addition to sample preparation protocol, imaging conditions, etc. This paper provides an overview of tools we developed as plugins for the popular image processing package Fiji (ImageJ) (1). These tools include signal-to-noise ratio analysis, contrast evaluation, and resolution analysis, as well as the capability to import images acquired on custom FIB-SEM instruments (2). We have also made these tools available in Python, with both versions available on GitHub.