Hello,
I’m attempting to curate the ISH image and expression levels for a list of genes. The Allen brain atlas package for R has caught my attention, but I’m not sure how to download developing mouse brain ISH images for my gene list. Finding single genes is time-consuming and I have about 100 genes.
Any assistance would be greatly appreciated.
Thank you.
It would be greatly appreciated if anyone knew how to solve this issue.
Sorry for the lack of reply here! In case you’re still looking, or for the record for others, I’m assuming you’re referring to this package: GitHub - oganm/allenBrain: Acquiring images from allen brain atlas, mouse ISH experiments in R.
It looks very useful, but is not developed or maintained by us, so you’re better off reaching out to the developers. It looks to me like it is oriented primarily at the adult mouse brain atlas but could probably access developing mouse brain ISH data with some minor tweaks.
Of course, we also have a REST API for accessing these images, which the R package is built around (API - Allen Developing Mouse Brain Atlas), but using that directly is admittedly a bit complicated.