sorry for not being more specific and thanks for the help. My main problem is that the neun staining is very “dirty” and that’s why its harder to first identify the nuclei with the neun channel. So i’m thinking maybe the best way is to identify the nuclei with the dapi, than see which ones are also neun positive (green) and only measure their dapi intensity?
Only i am not so sure what is the way to recognize nuclei that are also neun positive after identifying with dapi. Should i recognize them using ID secondary objects? and once i do that, do they become merged, or i can measure the intensity only in the dapi channel and only in the cells that were found to be neun positive? should i first filter any cells?
I am attaching three pictures. ch1 is neun in green, ch3 is dapi in blue and ch4 merge.
I would really appreciate if i can get some help with this.