search

int-brain-lab / iblapps

pyqt5 dependent applications for IBL sessions
MIT License
23 stars 15 forks source link

Question about how coronal atlas slice is selected #123

Open Lozanoda opened 4 months ago

Lozanoda commented 4 months ago

Hello,

I am just curious how this coronal section is selected/made in the program. Does it account for slant in the AP direction somehow or just select the best normal Allen atlas section slice. I know the real underlying fit does take into account all 3 dimensions, just curious if this example slice is a slice perfectly along the probe track or a normal AP coronal slice?

Thank you! image

mayofaulkner commented 4 months ago

Hello! The coronal slice displayed is a slice that follows perfectly along the probe track. For each coordinate it finds the corresponding pixel in the allen volume and then finds the row in the allen volume that matches this pixel. It then builds up the slice in this way. If you have large discontinuities in the probe tracing this can therefore make the slice looks quite distorted. Let me know if that makes sense

Lozanoda commented 4 months ago

Thank you!! That is incredible. Would it be possible to somehow access this image and save it as an svg file?

mayofaulkner commented 4 months ago

Hello!

Sorry for the delayed reply. On the slice image on the GUI you can right click and then select export. An option menu then appears which allows you to export the image in the format that you would like. Let me know if that helps!