Mis-registration of EM image coordinates using Cloudvolume for mm^3 (minnie) volume

Technical
, ,
1

I am pulling the electron micrograph image data from the minnie volume (mm^3) using modified version of the tutorial notebook ImageAndSegmentationDowload.ipynb.

I have used this successfully on the Layer 2/3 volume (pinky).

However, when attempting to make a similar notebook for the minnie volume, the image data pulled from cloudvolume is mis-registered, that is, it doesn’t match the same coordinates as displayed in neuroglancer.

The cell of interest is: 864691134964446239
The x,y,z, position is: 172695, 135328, 20958
Here is the neuroglancer link and here is a screenshot on my github repo.

I have posted my code here in my debug folder on github, and you can see that it is pulling different coordinates than Neuroglancer, even though the xyz should be the same. I can’t figure out what I’m doing wrong. Any help would be greatly appreciated.

Shawn

2

This is caused because the coordinates you were entering were in 4,4,40 coordinates, but the segmentation’s base segmentation level was in 8,8,40 at mip 0. See cv.resolution and the units on the coordinates in the upper left of your neuroglancer link.