search

VirtualBrainLab / Pinpoint

Multi-probe trajectory planning in an intuitive 3D environment
https://data.virtualbrainlab.org/Pinpoint/
GNU General Public License v3.0
45 stars 3 forks source link

add Kim atlas #655

Open WeissShahaf opened 7 months ago

WeissShahaf commented 7 months ago

Is your feature request related to a problem? Please describe. A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] Please add Kim atlas, important for brainstem implants such as PAG.

Describe the solution you'd like A clear and concise description of what you want to happen.

https://data.mendeley.com/datasets/2svx788ddf/1 also implamented in Brainglobe: https://brainglobe.info/documentation/bg-atlasapi/usage/atlas-details.html

Describe alternatives you've considered A clear and concise description of any alternative solutions or features you've considered.

Additional context Add any other context or screenshots about the feature request here.

Thanks, Shahaf

dbirman commented 7 months ago

Hi Shahaf -- the BrainGlobe implementation of the Kim atlas has a bug that prevents it from being used in Pinpoint. I'm working with the people who uploaded it to try to fix the issue.

Thanks!

WeissShahaf commented 6 months ago

any news on fixing the issue to get Kim atlas on Pinpoint?

dbirman commented 6 months ago

The issue is fixed on the BrainGlobe side, but they haven't pushed it as an updated package yet. As soon as it is, I'll run the pipeline on my side and we should be good to go.

StempelLab commented 6 months ago

we are using Brainglobe for registering the probes. is there a bug we should know about or is it only an issue of formatting to get the data into pinpoint?

dbirman commented 6 months ago

@StempelLab Is this a question related to the Kim atlas, or something else?

StempelLab commented 6 months ago

@StempelLab Is this a question related to the Kim atlas, or something else?

the Kim atlas

dbirman commented 6 months ago

So you're using BrainGlobe to register the probes to the Kim atlas, and then wondering whether there will be an issue when you transfer those registrations to Pinpoint? I haven't personally used BG for probe registration so I assume there will be some kind of rotation necessary to get the angles matched with Pinpoint's system.

For AP/ML/DV coordinates the Kim atlas is just the CCF, so even without the Kim atlas functional in Pinpoint you can use the standard CCF atlas with the transform set to null and the coordinates should correspond to what you get from the Kim atlas.