I like the 3D Objects Counter in ImageJ. I'm not sure it is in the standard imageJ, but it is in the Fiji version under the "Analyze" menu. That will let you measure a number of parameters in 3D data sets such as volume, surface area, intensity, etc.

Here is a link to the user manual: http://imagejdocu.tudor.lu/lib/exe/fetch.php?media=plugin:analysis:3d_object_counter:3d-oc.pdf

Thank you! do you do the analysis under maximum projection or each individual z stack separately?

Are you looking for 3D information like volume and surface area? If so, you need to analyze them as a volume with 3D Objects Counter. If you are looking for 2D information, then you don't need the 3D Objects Counter plugin and you can do standard 2D measurements. If the projection isn't too filled with structures (which can happen in large z stacks filled with dense structures), then I prefer to measure in the sum intensity projection rather than the maximum intensity projection. A max projection is only selectively displaying some brightest pixels from the volume and skews the measurements. The Sum projection shows the integrated value of all pixels, so especially if you are quantifying intensity this is important. or, if the information you need is contained within individual planes then you can measure a representative plane or planes.