Hi List,
 
I have found a solution for my problem. Thanks for all the on and off list responses. One thing i probably should have mentioned in my first post. The images are taken with a 60x NA1.4 Oil lens on samples mounted in DPX. So there is no refractive index mismatch. Also cubic voxels were captured (in most cases 0.25x0.25x0.25 um).
 
As to why not use imageJ or other free programs. We have MetaMorph that i am much more familar with and we have Imaris as well. So it woudl be best to use the programs that we have paid a lot of money for if possible.
 
Kevin- I tried the Gaussian filtering and it didn't really work very well, it always made things a bit too fuzzy.
 
So onto the solution. Basically i had to tell Imaris to stop making things pretty and smooth. My masks from MetaMorph were fine, it was just imaris trying to fill in gaps that was causing all my problems. Once i disabled smoothing when generating my 3D surfaces based on my Metamorph binary masks it worked like a dream. I can now create a 3D version of what i could do in 2D in MetaMorph. And better yet the data it seems to be producing frmo our samples is exactly what we were looking for.
 
 
Once again thaks to all for their suggestions.
 
 
 
Cheers
 
 
Cam
 
 
 
Cameron J. Nowell
Microscpy Manager
Central Resource for Advanced Microscopy
Ludwig Insttue for Cancer Research
PO Box 2008
Royal Melbourne Hospital
Victoria, 3050
AUSTRALIA
 
Office: +61 3 9341 3155
Mobile: +61422882700
Fax: +61 3 9341 3104
 
http://www.ludwig.edu.au/branch/research/platform/microscopy.htm