Hi everybody!

I’m working on Cell profiler and I don’t understand how can I use the module Morph.I would like to remove an important noise.Apparently, I have to apply a threshold before the tophat.But how can I do if I don’t want to apply this threshold?

thanks for your help

We are considering adding a top hat filter that works on grayscale images rather than binary images. We will post here if/when that feature is added and the new CellProfiler version is released.

In the meantime, perhaps there is another way to ‘remove noise’ in your image? If you want advice on it, feel free to post images on a public website and describe here what exactly you are trying to analyze.


Right now, the Morph module works only on binary images, which means you need to threshold your images into binary ones before applying any morphological operations using the Morph module.

The best thing would be to expand the capability of the Morph module to handle grayscale images too. Like Anne Carpenter said, we will post here if/when that feature (grayscale morphological op including tophat) is added and the new CellProfiler version is released.

When you remove noise in your images, another (or the best) way to do would be applying the Smooth module to them.



Tophat filtering has been added as part of the functionality of CellProfiler. It may be found in the SmoothOrEnhance module (which was included as of release 5122). Look for the option “Enter the smoothing method you would like to use” and select “Enhance BrightRoundSpeckles.” For proper use, the filter size should be the diameter (in pixels) of the objects you would like to enhance, or larger.