Download/generate top-down cortical fluorescence image data

Technical
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1

I have a question regarding the top-down image of mouse connectivity experiment data.

image
image902×745 517 KB

http://connectivity.brain-map.org/projection/experiment/cortical_map/146077302 (left image)

  1. What is this showing (is it a max intensity projection of all signals in the cortex, and is it a simple projection in DV axis or is it projecting orthogonal to the surface curvature)
  2. Is there a way to download/generate this image data?
2

Hello @mmori

This is a projection of all signal in the cortex curved with the structure of the cortex. There is more information about this image in the Connectivity Atlas help, linked here: http://help.brain-map.org/display/mouseconnectivity/Projection#Projection-CorticalMapViewer .

The code that we used to generate these images is very specific to our environment and is not publicly available.

Best regards,
Wayne

3

Hi @wayne
Thanks for your response. So to clarify, we cannot download this image, in data formats such as tiff?

4

The background images themselves can be downloaded using the API.

As an example, for this experiment:
http://connectivity.brain-map.org/projection/experiment/cortical_map/543679575

You can get information about the file with this API call:
http://connectivity.brain-map.org/api/v2/data/WellKnownFile/query.json?wrap=true&criteria=%5Bwell_known_file_type_id$in501029518],[attachable_id$eq543679575]

Replace the id 543679575 with other experiment ids if needed.

In the JSON that is returned, precede the ‘download_link’ value with ‘http://api.brain-map.org’ to get a URL that will download the PNG image to your computer.

So, for this example the full download URL is http://api.brain-map.org/api/v2/well_known_file_download/550319947

5

thanks a lot!