Colonyzer is an image analysis tool developed at CISBAN which is part of the Institute for Ageing and Health in Newcastle University.
Colonyzer is primarily designed for quantifying the cell density of arrays of independent micro-organism cultures growing on solid agar. It specialises in being sensitive enough to detect the presence of cultures with extremely low cell density arising after dilute liquid inoculation onto agar from photographs of plates. In order to achieve its high levels of sensitivity, it relies on sophisticated algorithms for the identification and detection of lighting gradients in the photograph, and for the detection of thin, opaque developing cultures in the corrected images.
Colonyzer is suitable for high-throughput screening of libraries of yeast mutants for example, and has proven extremely useful in the estimation of phenotypes such as exponential growth rate, appropriate for genome-wide investigations of genetic interaction.
You can find a detailed description of Colonyzer, its algorithms, the motivation for its development, and some example analysis here.
Colonyzer is an open source tool and is available for download from SourceForge:
http://sourceforge.net/projects/colonyzer/At the SourceForge site above you can find Colonyzer source code, installation instructions, a library of example images, and some auxiliary scripts for setting up Colonyzer to analyze batches of images, and some tools for analyzing the output data
If you use Colonyzer in research leading to a publication, please cite our open access article:
Conor Lawless, Darren J Wilkinson, Alexander Young, Stephen G Addinall and David A Lydall Colonyzer: automated quantification of micro-organism growth characteristics on solid agar BMC Bioinformatics 2010, 11:287