Thank you for answering so fast!
I also ended finding this answer from you in another topic.
Using the 3D maximum seems to do the trick, but it is very very slow.
With the 3D Maxima Finder I could find all my nuclei. I was hoping to use that information to simply redraw all of them as spheres of a defined radius. If I try to use 3D draw shape it seems that I would have to enter the info one by one. I was hoping for an automated way to simply redefine all the ROIs into the spheres (read: a couple of buttons to click). I couldn’t find that. Is there a way? Maybe a macro alternative for feeding the ROIs obtained from 3D Maxima Finder into the 3D draw shape?
As for the nuclei segmentation solutions you mentioned, they might be a bit overkill for my current application. At this point I am not really interested in nuclear architecture. I just have quite round nuclei with nuclear localized red and green fluorescent proteins on them, and just want to know how much of red and how much of green I have. I am also interested in having object based colocalization done on the red and green. Essentially trying to answer: how many of my nuclei are both red and green, does presence of green always lead to absence of red.
Once again, thank you for the help.