automatic or fixed threshold to compare more images?

[Davide.Priori]

Dear all, I have a doubt and I need help.
My aim is comparing more images about positive pixels and intesity of pixels in tissue staining. I think it should be better to set a fixed threshold value over the background for all of them, but it seems to me that this method is not very realistic to give me the realistic threshold for each image. For this reason I shift on automatic threshold but I'm not sure it is right.
What is your opinion??

Thank you!

Davide