Single-molecule localization microscopy analysis with ImageJ

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ImageJ is a versatile and powerful tool for quantitative image analysis in microscopy. It is open-source software, platform-independent and enables students and researchers to obtain an easy but thorough introduction into image analysis. Especially the image processing package Fiji is a valuable and powerful extension of ImageJ. Several plugins and macros for single-molecule localization microscopy (SMLM) have been developed during the last decade. These novel tools cover the steps from single-molecule localization and image reconstruction to SMLM data postprocessing such as density analysis, image registration or resolution estimation. This article describes how ImageJ/Fiji can be used for image analysis, reviews existing extensions for SMLM, and aims at introducing and motivating novices and advanced SMLM users alike to explore the possibilities of ImageJ/Fiji for automated and quantitative data analysis.
Original languageEnglish
Article number203002
Number of pages11
JournalJournal of Physics D: Applied Physics
Issue number20
Early online date21 Feb 2019
Publication statusPublished - 13 Mar 2019


  • ImageJ
  • Fiji
  • image analysis
  • super-resolution
  • quantitative imaging
  • SMLM

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