A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ

TLDR

Transmission electron microscopy provides high‑resolution imaging of subcellular structures, with mitochondria and the endoplasmic reticulum being key organelles studied in metabolic disorders. This protocol presents a straightforward method to quantify and characterize mitochondrial and ER morphology using the open‑source ImageJ software. It details how to measure mitochondrial length, width, area, and circularity, assess cristae morphology, and quantify mito‑ER interactions within ImageJ. The resulting procedures enable accurate and reproducible measurements and visualizations of mitochondrial and ER sub‑cellular morphology.

Abstract

Transmission electron microscopy (TEM) is widely used as an imaging modality to provide high-resolution details of subcellular components within cells and tissues. Mitochondria and endoplasmic reticulum (ER) are organelles of particular interest to those investigating metabolic disorders. A straightforward method for quantifying and characterizing particular aspects of these organelles would be a useful tool. In this protocol, we outline how to accurately assess the morphology of these important subcellular structures using open source software ImageJ, originally developed by the National Institutes of Health (NIH). Specifically, we detail how to obtain mitochondrial length, width, area, and circularity, in addition to assessing cristae morphology and measuring mito/endoplasmic reticulum (ER) interactions. These procedures provide useful tools for quantifying and characterizing key features of sub-cellular morphology, leading to accurate and reproducible measurements and visualizations of mitochondria and ER.