CCF locations packaged in NWBs on DANDI!

[rcpeene]

Greetings all,

for approx. ~30 sessions, we have uploaded CCF regions in the NWBs. These are not totally final; the locations might have minor adjustments in the future and more NWBs will be reuploaded with CCF as we continue.

In the community spreadsheet, you can view the status of the CCF on DANDI for a session using the 'CCF on DANDI?' column (col W at the moment)

The information is in the nwb.electrodes table. The columns 'location', 'x', 'y', and 'z' are the ones that have been updated.

[Sarruedi]

That's awesome! Just to clarify the x, y, and z coordinates are measured in relation to what exactly? Bregma or Lambda or how do we need to read these numbers to infer the location of a given channel/unit?

[rcpeene]

the coordinates are relative to the allen CCF atlas space, which I think is a bounding box surrounding the brain with an origin in one of the corners. x,y,z can basically just be treated as relative coordinates rather than anything absolute with respect to specific structures.

The location label is produced through a manual alignment process. human operators view and consider certain markers in the firing rate, LFP, the targeted location (determined via ISI mapping), CCF coords, among others.

Perhaps @severine2305 has more to say.

[severine2305]

x, y, z are coordinates in ccf brain (the ccf brain has a border box around it and the upper left corner is 0, 0, 0). These coordinates are AP, ML and depth, I don't know which one is x and y though. This is useful to 1)know which area you are 2) can replot trajectories in ccf brain.