In the Brain Explorer there are nodes and edges in the mouse connectivity data. I think I’m able to obtain the nodes’ data in the SDK, but I’m not sure if the edges’ data is available in the SDK (see below image).
For example, to obtain the nodes’ data, e.g. to get the projection density at Caudoputamen (CP), I believe what we need to do is to take average for
myData within the CP region (please let me know if it’s not):
from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache experiment_id = 298179622 mcc = MouseConnectivityCache() myData, data_info = mcc.get_projection_density(experiment_id)
But how about the edges from/to CP? How can I obtain the edges (of the projection) that would flow from/to CP? How are those edges drawn in the Brain Explorer? Should I get the edges in the data, or should I get them from the template/reference atlas? Or the edges are unavailable in the SDK? Thanks for your help in advance!