I am trying to come up with a good way to count neurons from the set of images below. The cell cultures consist of both neurons and progenitors. We stained neurons with Tuj1 (red channel). nuclei with DAPI (blue channel), and neuronal progenitor with Sox2 (pink channel). I guess I could use nuclei as masks for defining “positive” areas. However, I don’t quite know how to set up the masks accurately because of the coexistence of progenitor cells and the fact that masks like that can include neurites in those “positive” areas (because some areas belong to the progenitors). Is there any other idea for counting neurons by using those channels? Thank you.