If you click on Plugin -> Analyze -> Cell Counter Notice, you'll see that the software will guide you to the new place of the plugin. There is a multi-point tool on the panel below (it has plusses "+" in its icon). If you click that, you can count the cells.
Hi Vatamanu Sergiu-Marian . Have you tried thresholding your images and just using the Analyze Particles command? This would be be a more automated way of counting cells instead of doing it manually.