Probe display in CCFv3 - IBL BWM dataset

1

Hi two questions:

I have started to play with the IBL BWM dataset and two things came up.

  1. Why is are the probe points (from the “electrodeSites.brainLocationIds_ccf_2017.npy”) not on a line when plotted in the CCFv3?
  2. I think the probe display in https://viz.internationalbrainlab.org/app is a bit off, all the other plot windows match the anatomical regions but not the 3D display.

Capture d’écran 2022-12-01 à 15.00.05
Capture d’écran 2022-12-01 à 15.00.051920×670 64.1 KB

2

Hello, it is great to see you using the dataset! To answer your questions:

  1. the electrode channels are not distributed along a straight line in CCF space, but rather are distributed along the user traced trajectory of the probe - this trajectory is not perfectly linear, but has wobbles.

To give you a sense of where these wobbles may come from, I am enclosing here a screenshot from a traced probe trajectory (the blue line ; the green is the imaged brain sample, the yellow the probe track covered in the fluorescent dye DiI)
Screenshot 2022-12-01 at 16.40.22

  1. Thank you for noticing this ; indeed it is incorrect. We have a fix and will update the website soon.
3

Ok. I was suspecting something like this. Very cool!

I 'll start digging in then!

Cheers,

Pierre