Substitute to editobjectsmanually

Hi, I´m quite new with this cell profiler and I have a Little problem:

I have some objects that i can´t get rid of by putting up a threshold for the intensity of the staining or by size exclusion. The only module i´ve found so far is the Editobjectsmanually but since i have more than 300 pictures this procedure will take a very long time.

Do you have any suggestion of a corresponding module?

// Thanks in advance


Could you please post a sample set of images and your current pipeline? There are a lot of options depending on your image context.



Sure no problem, here are two pictures from my samples including outlines of the measured objects in them.
I would like the program only to detect Brown staining (DAB) but it pics up black areas which are just tissue that has been folded.

In the picture “CD146 5000 203 meninges” it pics up, in the left upper side, some thin strips which aren’t staining and for “CD146 5000 202 meninges” it pics up some false staining in the middle of the big vessel and some black parts above it.

Thanks for the help!

// Kind regards Anton

CD146_pipeline.cppipe (11.1 KB)

Hi Anton,

Try my attached pipeline. I think you are very close, but here are some key issues:
(1) ApplyThreshold - I removed as it wasn’t doing anything. I assume you were just testing it, but it doesn’t add much beyond IdentifyPrimaryObjects
(2) IdentifyPrimaryObjects – I disabled your version, but kept it as a reference. My IdentifyPrimaryObjects has a few changes:

  • Global Otsu thresholding. Avoid Manual thresholds as they won’t be robust across samples, especially for histology
  • Three class thresholding helps when there are background, lighter staining, and darker staining. Since you want to only include the darker staining (to my eye), then you can set the middle class to be included with the “Background”
  • Threshold Correction Factor. This is your main adjustment for thresholding here. Please adjust accordingly – Test across other images. I set this empirically to my eye, but you will almost certainly want to adjust this.

The rest of the settings are fine if you only care about measuring overall intensity of the dark DAB regions.

DLpipeline.cppipe (11.8 KB)

Thank you David!

I tried it on a dozen pictures and it seems to work pretty good and as you said the correction factor is varying a lot between the pictures.

// Kind regards Anton

Great! Thanks for the reply.