A universal approach to analyzing transmission electron microscopy with imagej

Jacob Lam, Prasanna Katti, Michelle Biete, Margaret Mungai, Salma Ashshareef, Kit Neikirk, Edgar Garza Lopez, Zer Vue, Trace A. Christensen, Heather K. Beasley, Taylor A. Rodman, Sandra A. Murray, Jeffrey L. Salisbury, Brian Glancy, Jianqiang Shao, Renata O. Pereira, E. Dale Abel, Antentor Hintonjr.

Research output: Contribution to journalArticlepeer-review


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 devel-oped 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 reproduci-ble measurements and visualizations of mitochondria and ER.

Original languageEnglish (US)
Article number2177
Issue number9
StatePublished - Sep 2021


  • Cristae
  • Image J
  • Image analysis
  • Image processing
  • Mitochondria
  • Mitochondria endoplasmic reticulum contacts (MERCs)
  • TEM analysis
  • TEM quantification

ASJC Scopus subject areas

  • Medicine(all)


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