Hi there,
I downloaded the morphology data and opened them as suggested in this notebook Mouse Patch-seq Demo . Specifically the _transformed.swc files
When i plot the distribution of the somas for VISp cells, I get the histograms attached. This seems very strange to me. Are these in CCF coordinates?
Thanks
The “transformed” SWC files have been rotated so that the y-axis of the coordinate space is in the pial surface to white matter direction. The y-coordinate of the soma consequently reflects the depth from the pial surface. The x-coordinate and z-coordinate are more-or-less arbitrary, though, since they reflect the original coordinates of the image from which the reconstruction was made (and then are rotated). They are not CCF coordinates.
Thankyou ! Are the _raw.swc files in CCF coordinates?
No, those files are in the original image coordinates (scaled to micron units, rather than pixel units). I don’t believe that CCF-aligned SWC files for those cells have been made publicly available anywhere, but I can check in case they have.
