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Hi Keith,

You should take a look at ImageJ or Fiji.  It sounds like you have a grasp on the basics of image processing, and you have an idea of what you are looking for so I would give it a shot.  Here are a few advantages to the ImageJ/Fiji approach.

-freely available

-bioreader has many proprietary formats available to read raw data as well as metadata

-easy to get started writing macros with the "record macro" function 

-access to hundreds of niche programs and macros that could cost thousands of dollars is purchased via commercial route

Disadvantage to ImageJ/Fiji:

-some programs may not work as expected or at all depending on how you files are labeled or formatted

-customer support is on a voluntary basis so find a friend to help bail you out if you get stuck.

FIJI has more 3d applications for making the measurements you are looking to do included with the initial download than does ImageJ so I would check this out first.

Enjoy!
Justin  

On Mar 14, 2013, at 10:15 AM, Keith Prater <[log in to unmask]> wrote:

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> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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> 
> Dear list,
> 
> I've recently become involved in a project that is going to require a large
> number of images to be analyzed for multiple antigens. The images will be
> section series (approx. 6 - 12 um deep) of porcine tissue captured on a
> Leica confocal system, indirectly stained using 3 different fluorophores. I
> will need to retrieve volume measurements from the section series. From the
> number of tissues I will receive, I will be acquiring hundreds of images.
> 
> My usual method for smaller workloads has been to load the raw .tiff files
> into Nikon Elements, and go through the time-consuming process of telling
> the software how to handle the series (wavelengths, steps, etc.), manually
> calibrate the image from the Leica text output, apply median filter,
> threshold and run measurements. I have as many of those steps as possible
> rolled into one macro. Also, Elements has the ability to automatically
> reconstruct the section series based on file name, but this is unreliable
> with files captured using a sequential scan.
> 
> Does anyone out there have experience with a similar situation and found a
> method that is more efficient for dealing with such a large number of
> images? Is there a better software alternative? I think the biggest
> time-hog is having to take raw image files from a Leica system and
> reconstruct them in Nikon Elements. Perhaps Leica has an analysis package
> better suited for this?
> 
> Just wanted to see if anyone else has fought this battle.
> 
> Thank you all in advance.
> 
> Keith Prater
> Research Technician II
> Center for Environmental Biotechnology
> University of Tennessee-Knoxville