UNIT 14.18 Using Cell-ID 1.4 with R for Microscope-Based Cytometry

  1. Ariel Chernomoretz1,
  2. Alan Bush2,
  3. Richard Yu3,
  4. Andrew Gordon4,
  5. Alejandro Colman-Lerner2

Published Online: 1 OCT 2008

DOI: 10.1002/0471142727.mb1418s84

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Chernomoretz, A., Bush, A., Yu, R., Gordon, A. and Colman-Lerner, A. 2008. Using Cell-ID 1.4 with R for Microscope-Based Cytometry. Current Protocols in Molecular Biology. 84:14.18:14.18.1–14.18.27.

Author Information

  1. 1

    Physics Department, FCEN, University of Buenos Aires and CONICET, Buenos Aires, Argentina

  2. 2

    IFIByNE-CONICET and Department of Physiology, Molecular and Cellular Biology, FCEN, University of Buenos Aires, Buenos Aires, Argentina

  3. 3

    Molecular Sciences Institute, Berkeley, California

  4. 4

    Brookhaven National Laboratory, Upton, New York

Publication History

  1. Published Online: 1 OCT 2008
  2. Published Print: OCT 2008

This is not the most recent version of the article. View current version (1 OCT 2012)


This unit describes a method for quantifying various cellular parameters (e.g., volume, total and subcellular fluorescence localization) from sets of microscope images of individual cells. It includes procedures for tracking cells over time. One purposefully defocused transmission image (sometimes referred to as bright-field or BF) is acquired to locate each cell. Fluorescent images (one for each of the color channels to be analyzed) are then acquired by conventional wide-field epifluorescence or confocal microscopy. This method uses the image processing capabilities of Cell-ID (Gordon et al., 2007) and data analysis by the statistical programming framework R (R-Development-Team, 2008), which we have supplemented with a package tailored to analyze Cell-ID output. Both programs are open-source software packages. Curr. Protoc. Mol. Biol. 84:14.18.1-14.18.27. © 2008 by John Wiley & Sons, Inc.


  • image processing;
  • fluorescence microscopy;
  • Cell-ID, R