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Greetings Ioana,
Mario makes a very good point about the potential size of the dataset
you wish to create.  I have ended up with larger than 2 gigabyte
datasets just from tiling 24bit images of histological sections in 2D
(about 1cm square, 63x oil, 1024x1024 resolution).  Todays consumer
grade 32-bit "workstations" will likely choke on data this big--I know
that Windows NT couldn't deal with it.  Also, I think 32 bit platforms
are unable to address more than 2 gigs of memory.
    Approaches to handling large multidimensional datasets are a very
active area of research, and if you have a full-time geek on staff to
help, there are parallel volume rendering libraries and cluster based
solutions which can be employed.  Heavy duty workstations sporting 4 or
more 64 bit processors and many gigabytes of ram are available from Sun
and SGI--these boxes typically run upwards of $40K and specialized
software and operating systems knowledge would be required to configure
such a system to render confocal datasets for interactive data
exploration and rendering of regions of interest.
    In short, we are starting to see "stitching" type applications hit
the consumer-grade desktop in 2-D for microscopy, some confocal
manufacturers provide some ability to aquire stitched 3-D data, but the
handling of giant multidimensional datasets is still in the research
phase.  Newer chips from intel and AMD will be 64bit chips capable of
addressing lots of memory, but turn-key applications to analyze large
3-D datasets probably won't be available for a while yet.
Regards,
Karl

Ioana Coman wrote:

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Does anybody know about an automated program to combine multiple
>physical sections (say 100 micron thick) of the same sample (say 10 mm
>in diameter and 10 mm long)  to create a single 3D object (10 mm in
>diameter and 10 mm long). Each section is imaged with confocal
>microscopy with high resolution, so the whole 3D object is rendered
>with the same high resolution.
>
>Thanks in advance.
>I. Coman
>
>