Well said! I agree and you are correct that the software used for this stuff pretty much sucks. The thing is that a lot of scientists don't know that the software could be better, and they are reluctant to try new software considering it is so expensive (We just spent $5k on a licence for software that is subpar. I've seen this 91203091283 times and it's disappointing). New software will change the game.
To add to that list, http://www.brain-map.org/ is a reallllllllly nice tool. I love what this company is doing in terms of automating gene expression within the brain and look forward to their software going through some revisions.