TMA analysis--some of the cores were skipped

I am analyzing positive cell counts on TMA slides.
When I performed the whole slides, some of the cores were skipped.
Why does this happen?

Were the cores skipped or were perhaps no cells detected based on your parameters? The yellow outlines definitely looks like all cores were selected

Could you try and select one the skipped cores and run your cell detection only on it. I suspect this is possible due to that fact that the skipped cores are so dark brown and you are using the haematoxylin OD to pick up cells. If you look at the skipped cores with only this channel selected (can use the ‘2’ key) does it looks like nuclei could be picked up?

Of course, I may be wrong but then we’d be a step closer to figuring out what’s giong on.

Thank you so much!
I think I can try the skipped cores only. (I tried the optical sum to pick up cells also, but the problem happened again.)

Have you tried turning off Background radius/setting it to zero?

Thank you so much for your help.
Now I tried turning off the background radius it to zero.
I think the results are better.
Thank you!

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One last thing, the default setting of “2” for Max background Intensity is usually high enough that with a good “Background” set, the Background radius does not cause a problem. It looks like your image background is quite dark already (might be something to look at on the scanner itself, it probably needs to be white balanced or the slide needs more wash steps), but have you adjusted for that by setting the background and stain vectors?

In your case, the Background will be quite a bit lower than the default 255 255 255 if you use Estimate stain vectors.