*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Nate

Rebuild your surface wizard, 
select an ROI around the cavity
choose a high smoothing factor
at the threshold step (set 4 of 5), set the minimum value to 0 and the max value to quite low so that you select the inside of your cavity
finish the wizard
then at the top menu edit/preferences/statistics/surface, deselect everything except volume.
Now going back to your surface object, you can go to the statistic tab/selection/specific value
select your cavity in the image to find out what its volume is.

The ability of the threshold to identify your cavity will of course depend on your signal to noise ratio but I guess your cavity is black.

Hope that helps :)

Med vänlig hälsning / Best regards
 
Sylvie
 
@@@@@@@@@@@@@@@@@@@@@@@@
Sylvie Le Guyader
Live Cell Imaging Unit
Dept of Biosciences and Nutrition
Karolinska Institutet
Hälsovägen 7
Novum, G lift, floor 6
14157 Huddinge
Sweden
office: +46 (0) 8 5248 1107 
LCI room 1: +46 (0) 8 5248 1172
LCI room 2: +46 (0) 8 5248 3542
mobile: +46 (0) 73 733 5008


> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[log in to unmask]] On Behalf Of Nate Jowett
> Sent: 07 November 2013 11:16
> To: [log in to unmask]
> Subject: Measurement of cavity/void volume in Imaris?
> 
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
> 
> Hello
> 
> I am trying to measure cavity/void volume in Imaris.
> 
> The cavity was created by laser ablation of a tissue surface - the tissue was
> subsequently surfaced stained and z-stacked LSM imaged.  The cavity is clearly
> visible in Imaris 3D Surpass view.  I can define an ROI and create a surface that
> outlines the walls of the cavity adequately (the cavity is open to the surface
> superiorly, otherwise it is lined by tissue on all other sides).  I simply want to know
> what is the volume contained within the Imaris generated surface (i.e.
> where the intensity is zero, or close to zero).  Can this be done in Imaris?  Or do I
> need Imaris Measurement Pro?  Can Volocity do this if Imaris cannot?
> 
> I realize one solution is to manually trace out the cavity margins on each z-stack
> image frame, then reconstruct the volume.  However, this is extremely time
> consuming, and prone to significant error.
> 
> Thanks
> 
> Nate