2D in green, 3D in red (H3-647). 
Z images are collapsed down into single plane. It looks like brightness differences are substantial, better contrast total photons from 2D imaging (might have expected reverse, 3D apparently doesn’t compensate for photon loss of out of focal plane pixels to correct for what would be received
Zoom in and separate out the channels for a better look.
Now running analysis with different parameter file with higher thresholds to see comparison.