Finding White Areas

[helia_ziaei]

Hi

I am trying to identify white areas in my photos. I have created a pipeline to do so but it does not work properly.

I used Image math and rescale intensity to increase contrast. I also used Image math again to invert the image so white areas become black.
Then I used “identify primary objects” with Otsu thresholding to find the black areas.

But the result is not correct, it just identifies a little part of the area.

I appreciate any thought which can help me to improve the pipeline.
(This is the first question I have ever asked in an online forum. Please let me know if there is something more I should include in the post.)

M_388_L_better_4.tif (9.0 MB)

[helia_ziaei]

this is the pipeline I have used.
White_area.cpproj (844.9 KB)

[lee.marshall]

Hi Helia

White_area.cpproj (652.4 KB)

I have attached a pipeline for you to mask the white areas. Your image looks like a H&E stain, so I extracted the stains. It is easier to identify the white areas as a primary object, so instead of identifying what you stained, it is easier to identify what isn’t stain, so keep the white areas as primary. Otsu wants to separate your image to foreground and background (~50%), but as you will likely have variable white proportions, I would manually set the threshold and invert mask to remove. However be careful as this assumes that your images are white balanced, but personally I have found this method to be very reproducible.

Best
Lee