Comparison of cell density estimates from different tools. A) HT Colony Analyzer culture area estimate plotted against Colonyzer area estimate for the 384-format Sample4.jpg image from the Colonyzer example image collection hosted on SourceForge. Note that HT Colony Analyzer and several other high-throughput colony quantification tools are not designed to deal with the opacity and irregular morphology of spotted cultures and so this comparison is not completely fair. B) CellProfiler culture IOD estimate plotted against Colonyzer estimate for the 96-format yeast plate example from Figure 2E in Lamprecht et al. , downloaded from http://www.cellprofiler.org and analysed using the CellProfiler "Grid of Spots" demonstration pipeline. Pearson's correlation coefficient of 0.89, but with slope of 0.53. C) Two example cultures from the image in panel B with original images together with CellProfiler culture location (designated with a circle) in the left column. The right column shows the equivalent Colonyzer masks defining its estimates of cell locations CellProfiler incorrectly estimates culture location badly in three of the 96 cultures and erroneously trims ~5% of culture edge for almost all cultures. D) & E) Horizontal and vertical intensity slices through bottom and right sides of CellProfiler test image after correction by Colonlyzer (blue curve) and by CellProfiler (red curve).