How to download images from the Ivy Glioblastoma Atlas Project

I’m trying to download all the images on IvyGAP (ISH, H&E, TumorFeature). I was able to locate the APIs page (http://help.brain-map.org/display/glioblastoma/API), but it seems that this either has to be done through website GUI or there are some id’s that I could not associate to the proper images. Is there any direct way (such as FTP) to download all of these images?

There is no built-in functionality to download all the images for the Ivy Glioblastoma Atlas project. However, with a bit of programming effort, the generic image download functionality of the Allen Brain Atlas API can be leveraged to do so.

The Glioblastoma API page ( http://help.brain-map.org/display/glioblastoma/API ) lists general API calls in the “Experimental Overview and Metadata” section to get information about specimens (Note that you can change the ‘xml’ to ‘json’ if that is easier for you to work with).

Using the example for “All ISH SectionDataSets in sub-block Specimen “W32-1-1-K.01””, you can collect the ids of “sub image” records that are of interest to you.

http://api.brain-map.org/api/v2/data/query.xml?criteria=

model::SectionDataSet

,rma::criteria,specimen[external_specimen_name$eq’W32-1-1-K.01’],treatments[name$eq’ISH’]

,rma::include,genes,sub_images

sub_image_id = msg.2.sub_images.0.id = 278272303

This value can be used in an additional call to download the image:

http://api.brain-map.org/api/v2/image_download/278272303

This variation will get the annotated version of the same image:

http://api.brain-map.org/api/v2/image_download/278272303?view=tumor_feature_annotation

This variation will get the boundary version of the same image:

http://api.brain-map.org/api/v2/image_download/278272303?view=tumor_feature_boundary

This help page describes the general API functions available to download Allen Brain Atlas images: http://help.brain-map.org/display/api/Downloading+an+Image