Thanks for the images. I take it what you are trying to do is determine the size of the fungal mass, correct?
If so, coming up with a solution that fits the full range of fungus you have here would be difficult since the primary challenge is coming up with a way to distinguish the fungus from the dish itself. This might be possible in the cases where the fungus occupies the center of the dish; the reddish agar could then be used to distinguish the fungus. But in the Day9 image, the fungus takes up the entire dish and no agar is visible, so this approach would not work.
The best approach I think would be the one illustrated in the yeast colony example available from our Examples page. The example pipeline simply uses a binary image in the size/shape of the agar area; you will need to make one approapriate for your dishes.
I’m attaching a pipeline and first pass at a template image (which you should adjust). Another warning: the Day4 images seems to have different dimensions than the others. For this to work properly, your images should be the same size, acquired in exactly the same way (magnification, zoom, etc). This template image will work with the Day6, 7 and 9 images since they are the same size.
2011_01_04.cp (8.55 KB)