[Histonet] embedding in agarose then paraffin

[Judith L. Williams]

Hi- I will be trying to embed entire mouse lungs and heart to do a 3-D reconstruction using paraffin sections stained H&E. I am thinking that filling the lungs with agarose and then embedding it in agarose will help inflate the lungs and keep cell/tissue continuity. Then I want to slice the agarose into rather thick sections - say four per lung- and put these into cassettes for paraffin processing. Each block will then be serially sectioned and slides stained and scanned for reconstruction.
so questions are:
1.  is  Matrigel, Extragel or agarose (4 to 10%) best?
2.  has anyone ever filled lungs, heart with melted agarose gel prior to embedding?
3. will the agarose- gel stay in the tissue throughout the paraffin processing?
4. will the gel stain differently in the blocks embedded in paraffin and stained with H&E?
I would appreciate hearing from those of you doing whole embryos or large parts that need orientation and sectioning.  
Thank you!

Judy Williams, HT, PhD
Dept. of Comparative Medicine
University of Washington