I’ve been working with the yeast pipeline, and after a rough start, I’ve gotten it to process my images without any problems except one- the program is counting very tiny light spots (dust, the area around any writing, the edges, etc) as colonies. Thus, on a plate that clearly only has around 5 or 6 colonies, is being counted as having anywhere from 200- 2000 colonies. The closest I’ve been able to get it, by playing with the image quality and the type of surface I use for a background, has been in the mid 80s. I’m thinking that I need to add something like the Filter by Object Measurement module, so that I can give it a minimum and maximum colony size to prevent it from counting background objects.
Pictures are attached below.
So I am asking, first, if this would be a correct approach, and if not, what should I do? Second, if this module is what I need, I need to know how to go about inserting it. I’ve gone through the manual a few times, and I don’t really have much experience yet with this program, so I’m quite lost on how to do that.
Please let me know,