atlas coordinates for probes sliced perpendicular to shank

[DanEgert]

Hi, great tool, well coded and explained, this is so useful!

My experimental setup is a little different from the one used in the cookbook. I work with multi-shank silicon probes and slice perpendicular to insertion, ie horizontal in my case. The individual shanks show as dots in the sections. Is there a good way to determine their coordinates in atlas space?

Thanks for any clue,
Dan

[DanEgert]

By the way, I can't find the 'scale slider' to increase resolution on my non 'czi' histology images (the cookbook says it's not supposed to be there). Is there a workaround? The images get really pixelated after matching with an atlas.

[DanEgert]

Seems like the histology sections get down-sampled to the atlas resolution. So a workaround would be to up-sample the atlas slice.