Injection site coordinates


I’m in the mouse connectivity dataset and I have the precise coordinates of the injection site [8870 , 860 , 792]. I know that the injection is in the primary visual area but is it possible to precisely know with allensdk in which layer it happened ?

Thanks !

Hi Margaux,

From the injection site coordinate [8870,860,792] you provided, I believe you are referring to experiment 263780729.

From the experiment page you can see that the injection site is large and spans multiple cortical layers.

The coordinates [8870,860,792] should be interpreted as point inside of a 0.22 mm^3 injection volume.

While it is possible use AllenSDK (start with this tutorial) to figure out what cortical layer CCF coordinate [8870,860,762] lies in, it cannot be interpreted that the injection site is localized to that layer.

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