Nikon Elements Image Quality vs Fiji

Hello all,
Apologies if this is overly simplistic or has already been asked. I am trying currently to do a FRAP experiment on a Nikon Eclipse Ti2. The acquisition software is Nikon Elements, but I’m doing all of the analysis in Fiji. For my experiment, I take snapshots in elements and then define the regions I am going to FRAP. What I’ve noticed is that images I take tend to look a lot better in Fiji, and I am also able to discern good FRAPpable regions in the Fiji representation of the image that I cannot see well in elements. Is there any reason for this discrepancy. Can anyone with elements experience offer some tips to optimize image quality? It would help save a lot of time.