Download the outlines of brain areas

Technical
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1

Hi,

I am new user and I am using the Interactive Atlas Viewer to download the images from the Mouse Brain
http://atlas.brain-map.org/atlas?atlas=1#atlas=1&plate=100960224&structure=549&x=5280.25390625&y=3744.012887137277&zoom=-3&resolution=11.97&z=5

In the annotations, I add the outlines which thickens the black lines defining the brain areas. But when I try to download the same image I do not get the outlines.

I would like to just have the black outlines and no colors (i.e. white/transparent) in the different brain areas. Is there a way to do this via the allensdk api or directly via the website?

Thank you!

Best Regards,

Johanna

2

Hi Johana,

There isn’t direct way of doing what you want in the SDK or website.

One solution would be to download the images and SVG from the API and do the manipulate in an SVG editor like Illustrator or Inkscape.

Some documentation regarding downloading atlas, images and SVG
https://help.brain-map.org/display/api/Atlas+Drawings+and+Ontologies
https://help.brain-map.org/display/api/Downloading+and+Displaying+SVG