Recognition of clumps and single colonies in a single plate


#1

I need to perform a simple (!) colony count on a large number of agar plate photos. I am very impressed with the versatility of this software, but I am having a difficult time getting the software to recognize both large, well formed colonies and clumps of small colonies within the same plate. A typical plate often looks like this:

http://jo.labs.googlepages.com/home

If I am able to get the software to recognize the larger, single colonies, it completely ignores the large clump in the middle of the plate. The more recognition of pieces of the clump I get, the more background noise I pick up. I have tinkered with the settings in the IdentifyPrimAutomatic module for several days and not gotten very far. Any suggestions? My pipeline is as follows:

LoadImages
ColorToGray
Crop
SaveImages
CorrectIllumination_Calculate
CorrectIllumination_Apply
IdentifyPrimAutomatic
OverlayOutlines

Thank you in advance,
Jo


#2

Issue resolved.