Counting speckles per nucleus but filtering for oversaturation


I am trying to count the number of white specles in the nucleus in a grayscale image. I’ve tweaked the speckle counting pipeline provided and it is picking up the nuclei and speckles well, however, it is counting oversaturated nuclei (completely white as opposed to gray with structures in it) as a large clump of speckles. Is there a way to filter out oversaturated cells such as this so that they are not picked up as specks? Thank you!

Welcome! And yes, you can definitely do this.

Just add a MeasureObjects module to measure some property that would be useful to separate the speckles from the nuclei: I’m guessing area or intensity would do the trick?

Then, use the FilterObjects module to get rid of the objects that are not true speckles.