Our article describing a new, sensitive image analysis tool for quantifying the density of micro-organism cultures growing on solid agar plates has been accepted for publication in BMC Bioinformatics, you can access it here.

Colonyzer is largely written in Python using the Python Imaging Library, but also uses the rgenoud genetic optimisation package in R (via RPy).

Colonyzer has a website here and if you want to use or develop the code, it is freely available from its sourceforge page.

DOI: 10.1186/1471-2105-11-287.