title: Automated analysis of time-lapse fluorescence microscopy images: from live cell images to intracellular foci.
abstract: BACKGROUND
  Complete, accurate and reproducible analysis of intracellular foci from fluorescence microscopy image sequences of live cells requires full automation of all processing steps involved: cell segmentation and tracking followed by foci segmentation and pattern analysis. Integrated systems for this purpose are lacking.
  
  
  RESULTS
  Extending our previous work in cell segmentation and tracking, we developed a new system for performing fully automated analysis of fluorescent foci in single cells. The system was validated by applying it to two common tasks: intracellular foci counting (in DNA damage repair experiments) and cell-phase identification based on foci pattern analysis (in DNA replication experiments). Experimental results show that the system performs comparably to expert human observers. Thus, it may replace tedious manual analyses for the considered tasks, and enables high-content screening.
  
  
  METHODS
  The described system was implemented in MATLAB (The MathWorks, Inc., USA) and compiled to run within the MATLAB environment. The routines together with four sample datasets are available at http://celmia.bigr.nl/. The software is planned for public release, free of charge for non-commercial use, after publication of this article.
authors: Biomedical Imaging Group Rotterdam, Department of Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands.
authors: Oleh
authors: O
authors: Dzyubachyk
authors: Jeroen
authors: J
authors: Essers
authors: Wiggert A
authors: WA
authors: van Cappellen
authors: Céline
authors: C
authors: Baldeyron
authors: Akiko
authors: A
authors: Inagaki
authors: Wiro J
authors: WJ
authors: Niessen
authors: Erik
authors: E
authors: Meijering
mesh_terms: D000465:Algorithms; D001331:Automation; D004249:DNA Damage; D007090:Image Interpretation, Computer-Assisted; D008856:Microscopy, Fluorescence / Q000379:methods*; D010363:Pattern Recognition, Automated; D012984:Software; D059008:Time-Lapse Imaging / Q000379:methods*