In collaboration with Chris Potter in Liqun Luo's lab and Torsten Rohlfing (at SRI) I have developed/applied techniques for mapping different fly brains into a common frame of reference and then using this for analysing the spatial relationships between different neurons. The software and approaches are likely to be of general relevance in neuroanatomy.
The key software component is a suite of tools that Torsten has written for 3D image registration and analysis. On top of this I have built a variety of data analysis tools in R along with some very simple visualisation scripts in Amira.
I think an instruction manual would be very helpful. For example, a manual showing how one goes from a sample raw image, warping it with the standard brain, tracing the neuron, warping the neuron trace, and then assembling everything into Amira. Would it be possible to put something like that together?
Alternatively, you could take the text you've written for each of the website pages, and just add figures to those pages illustrating the various steps. Seeing a real-life example is always the best and easiest way to learn how a new technique is done.
The original Cell paper and Supplemental Information
Richard Axel's recent paper (Datta, Vasconcelos et al.) using a similar warping technique, including their Supplemental Information
Colours: Purple:1, Red: 2, Orange: 3, Yellow: 4, Green: 5.