DOI: 10.1002/cpz1.849 ISSN: 2691-1299

Basic Image Analysis and Manipulation in ImageJ/Fiji

Fabio Stossi, Pankaj K. Singh
  • Medical Laboratory Technology
  • Health Informatics
  • General Pharmacology, Toxicology and Pharmaceutics
  • General Immunology and Microbiology
  • General Biochemistry, Genetics and Molecular Biology
  • General Neuroscience


Microscopy‐generated images contain quantitative information that can be extracted using a variety of analysis methods and automated pipelines. In this protocol, basic aspects of image analysis are outlined, including software installation, data import, image processing functions, and analytical tools that can be used to extract information from microscopy data using the open‐source software ImageJ/Fiji. Step‐by‐step protocols for analyzing objects (i.e., nuclei) in a fluorescence image are included, focusing on segmentation routines. © 2023 Wiley Periodicals LLC.

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