In the PNAS paper, I counted cell bodies that contained photoactivated GFP after photoactivating the fan-shaped body. To do this, I followed this procedure: Acquire z-stacks before and after photoactivation, then align the first stack to the second stack using brainAligner (instructions here).
Next, download and install the Cell Counter plugin for imageJ.
Open both z-stacks. Make sure they have the same dimensions. (If not, scale them.)
Go to Plugins>Cell Counter
initialize Cell Counter on the after-activation stack.
Make sure the Counter Window (after activation z-stack) has focus, then click Analyze>Tools>Sync Windows
Now you can go through and click cell bodies that are greener in the after-activation stack than the before-activation stack.