Using CellX to Quantify Intracellular Events

Christian Mayer1, Sotiris Dimopoulos1, Fabian Rudolf1, Jörg Stelling1

1 Swiss Institute of Bioinformatics, Basel, Switzerland
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 14.22
DOI:  10.1002/0471142727.mb1422s101
Online Posting Date:  January, 2013
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

Methods to quantify features of individual cells using light microscopy have become widely used in biology. A multitude of computational tools has been developed for image analysis; however, they are often only for specific cell types and microscopy techniques. This unit describes CellX, an open‐source software package for cell segmentation, intensity quantification, and cell tracking on a variety of microscopy images. CellX can perform cell segmentation largely independently of cell shapes, and can also cope with images that are crowded with cells. The basic protocol describes how to use CellX for cell segmentation and quantification. This protocol remains the same whether there is a collection of images to be analyzed or whether cell tracking on a sequence of images is to be performed. The CellX output comprises control images for visual validation, text files for post‐processing statistics, and MATLAB objects for advanced subsequent analysis. Curr. Protoc. Mol. Biol. 101:14.22.1–14.22.20. © 2013 by John Wiley & Sons, Inc.

Keywords: image analysis; segmentation; tracking; microscopy; single cell quantification

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol 1: CellX Installation, Calibration, and Batch Processing
  • Alternate Protocol 1: Run in Terminal
  • Alternate Protocol 2: Run on Cluster
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Carpenter, A.E., Jones, T.R., Lamprecht, M.R., Clarke, C., Kang, I.H., Friman, O., Guertin, D.A., Chang, J.H., Lindquist, R.A., Moffat, J., Golland, P., and Sabatini, D.M. 2009. CellProfiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7:R100.
   Collins, T.J. 2007. ImageJ for microscopy. BioTechniques 43:S25‐S30.
   Gordon, A., Colman‐Lerner, A., Chin, T.E., Benjamin, K.R., Yu, R.C., and Brent, R. 2007. Single‐cell quantification of molecules and rates using open‐source microscope‐based cytometry. Nat. Methods 4:175‐181.
   Kvarnstrom, M., Logg, K., Diez, A., Bodvard, K., and Kall, M. 2008. Image analysis algorithms for cell contour recognition in budding yeast. Opt. Express 17:12943–12957.
   Locke, J.C.W. and Elowitz, M.B. 2006. Using movies to analyse gene circuit dynamics in single cells. Nat. Rev. Microbiol. 7:383–392.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library