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

  1. Alan Bush1,
  2. Ariel Chernomoretz2,
  3. Richard Yu3,
  4. Andrew Gordon4,
  5. Alejandro Colman-Lerner1

Published Online: 1 OCT 2012

DOI: 10.1002/0471142727.mb1418s100

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Bush, A., Chernomoretz, A., Yu, R., Gordon, A. and Colman-Lerner, A. 2012. Using Cell-ID 1.4 with R for Microscope-Based Cytometry. Current Protocols in Molecular Biology. 100:14.18:14.18.1–14.18.26.

Author Information

  1. 1

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

  2. 2

    Physics Department, FCEN, University of Buenos Aires and CONICET and Fundación Instituto Leloir, IIB-BA and CONICET, Buenos Aires, Argentina

  3. 3

    Molecular Sciences Institute, Berkeley, California

  4. 4

    Renaissance Technologies, East Setauket, New York

Publication History

  1. Published Online: 1 OCT 2012
  2. Published Print: OCT 2012


This unit describes a method for quantifying various cellular features (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 purposely defocused transmission image (sometimes referred to as bright-field or BF) is acquired to segment the image and locate each cell. Fluorescence 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 and data analysis by the statistical programming framework R, which is supplemented with a package of routines for analyzing Cell-ID output. Both Cell-ID and the analysis package are open-source. Curr. Protoc. Mol. Biol. 100:14.18.1-14.18.26. © 2012 by John Wiley & Sons, Inc.


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