Neuroscience: News and Discussions.
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Allen Brain Map question (self.neuroscience)
submitted 11y ago by markelliott
Hey, all.
I know this is a bit of an unconventional post, and it might seem like "do my homework," but it's only sort of that. I feel like a lot of us could use this technique in a lot of different contexts.
I would really like to use the Allen Insitute for Brian Science's brain atlas to compare gene expression between different genes within the same region.
I know it's likely that with the ISH they're doing there's experiment-experiment variation to the point that it's impossible to talk in meaningful units, I feel like even comparing relative distributions could be interesting.
But I can't figure out how to do it, despite a fair amount of fiddling, and Google is no help.
Should I just ImageJ the sections?
I know this is a bit of an unconventional post, and it might seem like "do my homework," but it's only sort of that. I feel like a lot of us could use this technique in a lot of different contexts.
I would really like to use the Allen Insitute for Brian Science's brain atlas to compare gene expression between different genes within the same region.
I know it's likely that with the ISH they're doing there's experiment-experiment variation to the point that it's impossible to talk in meaningful units, I feel like even comparing relative distributions could be interesting.
But I can't figure out how to do it, despite a fair amount of fiddling, and Google is no help.
Should I just ImageJ the sections?
theGolgiApparatus 1 points
If you are viewing the data from the microarray page it gives you a normalized z-score. What it is normalized to I don't know.
markelliott [OP] 1 points
wow. how did you even find this post?
I can't seem to find those microarray data w/ z-scores.. could you point me in the right direction?
I can't seem to find those microarray data w/ z-scores.. could you point me in the right direction?
theGolgiApparatus 1 points
i was searching r/neuroscience looking for anyone talking about the somewhat recent press release for Allen Institute funding for brain mapping. I am not sure where you are starting from. But if you start from the website and not the explorer software you can get to a page like this. Then if you click on any part of the heat map the z-score is under gene information.
veils1de 1 points
I remember doing this in neuro lab, but gosh I wish I remembered how I did it (you aren't by any chance taking this from UCLA are you?). I do remember having to use ImageJ to get area selections.
markelliott [OP] 1 points
naw. doing it for a project in lab.
ucsd alum, though =]
ucsd alum, though =]
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