Cell cluster measurement

Hi everybody,
I am trying to count cell clusters. I have the problem that I can’t manage to only measure these clusters but always have many cells included in my analysis that I do not want. The goal is to not only get the amount of clusters but also their average size. To make it more clear what I mean, I included a picture, where I manually marked all the structures that I want to analyze.
Thanks in advance for any tips on this issue.

Best,
Jana

@JanaN

Well, this is a tough one. This is a case where our eyes - your eyes - are much better trained for finding such regions than any computer. You can try using Trainable Weka Segmentation - to see if you can train a classifier to pick up these clusters. But this will be difficult - as they are even extremely difficult to delineate by eye.

Do you have any specific markers/antibodies that you could use in your staining protocol to highlight these areas? This is where your experimental set-up can perhaps better help. What stain is this? The tissue/cells? Do you have other channels you are using?

Hi,
thank you for your suggestion! I will try that out.

I did stain with other colors, however, there I do not see these clusters very clearly. So far I did not find any other antibody that stains them but I am still looking to see if I can find anything.

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