YeastCountingPIPE can not normally work


Hi, everyone
My YeastCountingPIPE can not normally work. I don’t konw why.
Give me some advice.Thank you.

I present my sample image and an output figure in attachment.
ModifiedGrayYeast0918PIPE.mat (1.79 KB)


Give my output figure.



Your pipeline is not performing as well as it should because the thresholding in IdentifyPrimAutomatic is not set appropriately for your image.

One way to see this is that the lower bound which is pre-set for the threshold is set 0.001. The output of IdentifyPrimAutomatic shows that the threshold automatically found is also 0.001, which means that IdentifyPrimAutomatic thinks that the threshold is lower but is stopped at the pre-set lower bound. But since the output shows that the threshold should actually be higher (since there are too many objects being identified), you can conclude that this thresholding method is not appropriate for this image.

Each thresholding method works best under certain circumstances, depending on the image quality or the amount of foreground to background. If one thresholding method doesn’t seem to work well, you can try any of the others until you find one that works best. With the image you provided, it seems that Otsu Global or RidlerCalvard Global do a good job.