Image analysis tools for Electron Microscopy

janelia7_blocks-janelia7_biblio_header | block
bioRxiv. 2026-03-14;. doi: 10.64898/2026.03.11.711125
Image analysis tools for Electron Microscopy Hess Lab
Shtengel DH, Shtengel G, Xu CS, Hess HF
janelia7_blocks-janelia7_biblio_abstract | block

Abstract

Electron Microscopy (EM) is widely used in many scientific fields, particularly in life sciences, offering high-resolution information on the ultrastructure of biological organisms. Accurate characterization of EM image quality is important for assessing the EM 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.

janelia7_blocks-janelia7_biblio_authors | block

Janelia Authors

Gleb Shtengel
Harald Hess
janelia7_blocks-janelia7_biblio_tools | block