I have had an issue with masking. Can someone take a look at my slice and its mask and inform me as to what structure im observing and how best to troubleshoot?
The mask is warped
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Hi,
Thank you for your question. Below is our response:
You can find the structures in the 2D atlas plate (the attached file) and on our web portal (https://atlas.brain-map.org/atlas?atlas=602630314#atlas=602630314&plate=576986571&structure=35&x=6577.036946614583&y=3849.037136501736&zoom=-3&resolution=8.89&z=3). In fact, CCFv3 is not a stereotaxic atlas. We recommend that you get the coordinates from the Paxinos mouse brain atlas.
-Quanxin
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Could you post the code you’re using to generate the image and the mask? It could help with reproducing and troubleshooting the issue.
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