Pipeline for counting E. coli colonies

I have not used CellProfiler before but have just downloaded it to use on an urgent project to count bacterial colonies from photographs (please see an enclosed example). Setting up a suitable pipeline for a new user seems daunting and I wonder if anyone has a suitable example? It would be greatly appreciated.

Tom Brown, Professor of bio-organic chemistry, University of Southampton, UK.


Hi Tom

(I’ve moved this topic to a more appropriate forum).

I have two comments:

  • I would recommend looking at the ExampleYeastColonies pipeline from our Examples
    page. It seems very similar to your assay. - I’ve put together a quick pipeline based on your image to get you started. The central portion of the dish had to manually estimated for the Crop module, but it can be done automatically using the approach in the ExampleYeastColonies pipeline.

Hope this helps!
-Mark
2011_01_10.cp (6.24 KB)