OpenCFU, a new free and open-source software to count cell colonies and other circular objects

PLoS One. 2013;8(2):e54072. doi: 10.1371/journal.pone.0054072. Epub 2013 Feb 15.


Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Colony Count, Microbial / methods*
  • Software*
  • Staphylococcus aureus / isolation & purification*
  • User-Computer Interface

Grant support

This study is part of the project “Multidrug resistance and the evolutionary ecology of insect immunity” ( funded by the European Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.