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The volume of holes can be obtained from a stack thresholded to show the voids.
 then the Z projected sum (ImageJ) gives the thickness in Z. The sum of the thickness for each void is its volume, which you can get from analyse particles in ImageJ
You also need to know where the voids starts in Z - perhaps the trickiest part, and remove areas outside the void from the analysis.

-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]] On Behalf Of Shanna Banman
Sent: den 7 mars 2014 18:33
To: [log in to unmask]
Subject: Re: Topographical pits volume

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Hi all, 

I would be interested in this reply too.  I have a client working with cuticle elevation and volume, as well as trichome volume and length from 3D stacks. 

THank you all!

Shanna Banman