Michael A Kuluz  wrote:
> 
> What part of the neuron does this substance stain to show degenerating
> neurons?  I have searched high and low and have yet to learn this "trade
> secret".   Thanks in advance...
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The published papers about this secret substance
describe it as a fluorescent anionic xanthene dye.
Eosin is such a dye; so is fluorescein. Such dyes
bind most strongly to basic proteins, which seem
to occur at high concentrations in the nuclei and
cytoplasm of dead cells.

Here are a few refs that might help you to decide
what to do.

Acidophilia of dead neurons:

   Kiernan JA, Macpherson CM, Price A, Sun T (1998) 
   A histochemical examination of the staining of 
   kainate-induced neuronal degeneration by anionic 
   dyes. Biotech. Histochem. 73: 244-254. (This includes
   references to earlier papers on the subject.)
   
"Fluoro-jade" for dead neurons:

   Schmued LC, Albertson C, Slikker W (1997) Fluoro-Jade: 
   a novel fluorochrome for the sensitive and reliable 
   histochemical localization of neuronal degeneration. 
   Brain Res. 751: 37-46.

   Schmued LC, Hopkins KJ (2000) Fluoro-Jade: novel 
   fluorochromes for detecting toxicant-induced neuronal 
   degeneration. Toxicologic Pathology 28: 91-99.

"Fluoro-jade" is not specific for dead neurons:

   Colombo JA, Puissant VI (2002) Fluoro jade stains early 
   and reactive astroglia in the primate cerebral cortex. 
   J. Histochem. Cytochem. 50: 1135-1137.
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John A. Kiernan
Department of Anatomy and Cell Biology
The University of Western Ontario
London,   Canada   N6A 5C1
   kiernan@uwo.ca
   http://publish.uwo.ca/~jkiernan/
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