“So does the algorithm use color information at this stage and if so, how?”
It’s bee a long while and people has come and go. My best recollection is that the color information get converted to single “intensity” value during the segmentation process.
“Are these accessible via the API? That is, is the range which the jet map represents available via the API?”
Yes, they are. Have a look at these places first and follow up with questions
http://help.brain-map.org/display/mousebrain/API
http://api.brain-map.org/examples/foldchange/index.html
“Do these numbers have any physical meaning, or are they arbitrary?”
They are again local average of the gray scale value using that formula over “expression pixels” (see the whitepaper pdf)
“, do you know if the luminosity of the stain in the ISH image is roughly linear with the number density of mRNA strands that code for the given protein, or is it some other relationship, such as exponential?”
No, I do not. ISH is semi-quantitative (!) with the quantitative part being good spatial resolution but they color aspect is not so much.