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On Wed, 30 Apr 2008, Badri Roysam wrote:

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> Dear Colleagues,
>
> I am interested in learning about tissue sectioning equipment that is capable
> of accurately preserving the geometry of the slices (so successive sections can
> be aligned), and transferring the slices to slides. Any suggestions?
>

Are you talking about cutting from paraffin blocks?

I hate to tell you this, but whatever you use probably won't work if you are going to try to do 3D reconstruction with multiple optical slices through each thick section.  The knife introduces non-affine warping, and you will get non-affine deformation in the Z-axis as well, depending on the type of tissue.  When we did this with glomeruli, the tufts would stick up out of the plane of the section, being pulled up by the knife.

Since the initial alignment of sections is pretty simple in terms of rotation, translation, and shear, (and there are lots of tricks for automating it -- I used embedded fiducials) the hard part is the nonaffine deformation.  Thus, I would concentrate most of my effort in getting a clean cut rather than worrying about getting a pre-aligned ribbon.

As an aside, I would suggest looking at the ITK toolkit for developing registration software, if you haven't already.  See: www.itk.org

billo
http://www.billoblog.com/billoblog