Save actual CCF coordinates

[bjhardcastle]

I'm trying to use the ccf_channel_locations.json output from a GUI capsule duplicated 4 months ago, so apologies if this has already been changed.

It looks like the coordinates are saved in IBL xyz format, in mm, relative to bregma:

...
"channel_47": {
    "x": -3.3230860233306885,
    "y": 8.533195495605469,
    "z": -5.1742472648620605,
    "axial": 460.0,
    "lateral": 32.0,
    "brain_region_id": 463,
    "brain_region": "CA3"
  },
...

Given the filename, I was hoping they would be stored as CCF coordinates, in microns.

If this is intentional, how about adding the ccf_ap, ccf_ml, ccf_dv values as well, since the iblatlas with the conversion function is already available in this package?

[bjhardcastle]

I was wrong about the current format: ccf_channel_locations.json does save CCF coords, the x and z axes just need negating, and all values converted from mm to um.
This plot shows some the mean position of brain regions in some GUI values and in the DR dataset (brain regions share the same color in both columns):

so to get to CCF convention I think we can just use this mapping:

  ccf_ap: y * 1000
  ccf_ml: x * -1000
  ccf_dv: z * -1000