Colonyzer
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Image analysis software for estimating cell density in arrayed microbial cultures growing on solid agar.

Website describing current, stable release:
http://research.ncl.ac.uk/colonyzer/

Open access manuscript describing Colonyzer algorithms:
http://dx.doi.org/10.1186/1471-2105-11-287

Open access video and manuscript demonstrating the use of Colonyzer within a Quantitative Fitness Analysis workflow
http://www.jove.com/video/4018