G'day,
 
>1.) Reconstruction: therefore we not only want a nice picture of a single
>stack of optical sections, but we would have to combine different stacks
>like a mosaic or puzzle to get the whole reconstruction. The stacks used
>for this stem as well from the same histological section as from adjacent
>ones.
 
Some WWW resources for 3D reconstruction:
 
        http://biocomp.arc.nasa.gov:80/3dreconstruction/
        http://www.cs.ubc.ca/spider/ladic/confocal.html
 
 
>2.) The measurements we would like to make (volumes, neurite length, angles
>between neurites,...) should not be done on a 2D-projection of the data,
>but in the 3D-data.
 
It is often useful to start by skeletonizing the structures that you want
to measure, i.e. thinning to single pixel/voxel wide representations.
I've just developed some software to do this.  Let me know if you're
interested.
 
Regards,
______________________________________________________________________________
Chris Pudney                    Biomedical Confocal Microscopy Research Centre
[log in to unmask]                 Department of Pharmacology
http://www.cs.uwa.edu.au/~chrisp           The University of Western Australia
PH: (+61 9) 346 4571 FAX: (+61 9) 346 3469        Nedlands, WA 6907, AUSTRALIA