Image analysis software for quantification of cell density in microbial cultures (e.g. S. cerevisiae) growing on solid agar plates. Specialises in detection of extremely low cell densities. Forms part of the Quantitative Fitness Analysis (QFA) workflow:

http://research.ncl.ac.uk/qfa/

Suitable for high-throughput, genome-wide analysis of culture libraries when combined with the following qfa R package:

http://qfa.r-forge.r-project.org/

This is the version presented, used and demonstrated in the following manuscripts:

Lawless et al. 2010 http://dx.doi.org/10.1186/1471-2105-11-287
Addinall et al. 2011 http://dx.doi.org/10.1371/journal.pgen.1001362
Chang et al. 2011 http://dx.doi.org/10.1534/g3.111.000216
Banks et al. 2012 http://dx.doi.org/10.3791/4018

Development has been moved to github, where Colonyzer has undergone several recent improvements, particuarly making installation easier and analysis faster:

https://github.com/CnrLwlss/Colonyzer

Features

  • Batch-capable automated image analysis
  • Image specific grid definition tool (Parametryzer)
  • Lighting correction
  • Low cell density measurements

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Additional Project Details

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Python, S/R

Registered

2009-03-02