Experimenters' guide to colocalization studies: finding a way through indicators and quantifiers, in practice

Methods Cell Biol. 2014;123:395-408. doi: 10.1016/B978-0-12-420138-5.00021-5.


Multicolor fluorescence microscopy helps to define the local interplay of subcellular components in cell biological experiments. The analysis of spatial coincidence of two or more markers is a first step in investigating the potential interactions of molecular actors. Colocalization studies rely on image preprocessing and further analysis; however, they are limited by optical resolution. Once those limitations are taken into account, characterization might be performed. In this review, we discuss two types of parameters that are aimed at evaluating colocalization, which are indicators and quantifiers. Indicators evaluate signal coincidence over a predefined scale, while quantifiers provide an absolute measurement. As the image is both a collection of intensities and a collection of objects, both approaches are applicable. Most of the available image processing software include various colocalization options; however, guidance for the choice of the appropriate method is rarely proposed. In this review, we provide the reader with a basic description of the available colocalization approaches, proposing a guideline for their use, either alone or in combination.

Keywords: Cell biology; Coincidence; Colocalization indicators; Colocalization quantifiers; Fluorescence microscopy.

Publication types

  • Review

MeSH terms

  • Image Processing, Computer-Assisted
  • Microscopy, Fluorescence
  • Protein Transport
  • Research Design
  • Single-Cell Analysis / methods*