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I created a PDF that shows the steps with Fiji/ImageJ: 
http://microscopy.tamu.edu/lab-protocols/Measuringpitvolume.pdf

In summary (without pictures):
1. generate TOPO projection with TopoJ plugin. Use the Quadratic 
Refinement option for more precise result.  The result is a 32-bit file where 
pixel value corresponds to surface height (in the calibrated units, e.g, 
micrometers) 
 
2. Crop the image as needed to remove processing artifacts on the edges 
of the image
3. display the interactive 3D surface plot to check if there are any outliers 
(hot or black pixels). If  necessary, remove the outliers (process-Noise-
Remove Outliers)
 
4. Level the TOPO image (Plugins-TopoJ-Level)
5. Threshold the image to highlight the flat surface. Measure the mean 
pixel value of the surface (make sure the Analyze- Set Measurements-Limit 
to Threshold is set and that you have sufficient number of decimal places 
for the result) , subtract this value from the image (Process-Math-
Subtract).  The flat surface now have pixel values close to zero.
 
6. Threshold the resulting image to highlight the pits.   
 
7. Analyze-Set Measurements – make sure to check the Integrated 
Density. Then  Process-Analyze Objects  (EXCLUDE ON EDGES, INCLUDE 
HOLES, SHOW OUTLINE).  The IntDen corresponds to the well volume. 

In this case, measuring an AFM test target with ~1.4 micron square wells 
~1 micron deep, the volume is about two cubic micrometers each well.
 
Results:(in micrometers)
#	label		  Area	mean	         IntDen	RawIntDen
-----------------------------------------------------------------------------
1	QR_AFT-	2.0430	-0.9844	-2.0110	-461.6724
2	QR_AFT-	2.0691	-1.0024	-2.0740	-476.1324
3	QR_AFT-	2.0604	-0.9930	-2.0460	-469.7013
4	QR_AFT-	2.0647	-0.9901	-2.0443	-469.3108
5	QR_AFT-	2.0430	-0.9811	-2.0043	-460.1183
6	QR_AFT-	2.0647	-0.9914	-2.0469	-469.9020
7	QR_AFT-	2.0560	-0.9771	-2.0090	-461.1930
8	QR_AFT-	2.0430	-0.9807	-2.0036	-459.9545
9	QR_AFT-	2.0299	-0.9745	-1.9781	-454.1175

I hope this helps.

Stan Vitha
Microscopy and Imaging Center
Texas A&M University
  
On Wed, 5 Mar 2014 11:28:11 +0800, Tong Yan 
<[log in to unmask]> wrote:

>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>Dear All,
>
>We have one user working on dentine slice with osteoclasts and 
interested in the resorption pits volume on the surface.
>
>We used reflection mode to generate 3D images for the dentine slice on 
our LSM 510 Meta confocal system and showed the topographical profiles 
and depth coding map in Fiji by using 3D shape and SurfCharJ plugin.
>
>Could you kindly suggest Fiji plugin to calculate the pits volume? Or any 
other software is able to do this job?
>
>Thank you for your advice and help in advance.
>Kind regards,
>
>TONG Yan (Ms)
>Senior Scientific Officer:: NUS Centre for BioImaging Sciences :: 
Department of Biological Sciences :: National University of Singapore :: 14 
Science Drive 4, Singapore 117543 :: (65) 6516 7202 (DID) :: (65) 6779 
2486 (Fax) ::) :: [log in to unmask]<mailto:[log in to unmask]> 
(E) :: www.nus.edu.sg<http://www.nus.edu.sg/> (W)Company 
Registration No: 200604346E