Hi two questions:
I have started to play with the IBL BWM dataset and two things came up.
- Why is are the probe points (from the “electrodeSites.brainLocationIds_ccf_2017.npy”) not on a line when plotted in the CCFv3?
- 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.
Hello, it is great to see you using the dataset! To answer your questions:
- 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)
- Thank you for noticing this ; indeed it is incorrect. We have a fix and will update the website soon.
Ok. I was suspecting something like this. Very cool!
I 'll start digging in then!