cortex-lab
Registration for ICR mice and SD rats implanted with multi-electrode arrays
Hi, this is very impressive work and tool developed by the authors. Thank you!
We in our lab use Multi-electrode arrays to record from awake freely interacting SD rats and ICR mice. As I see, the brain coordinates for this program are derived from Allen brain atlas which is a C57 mouse atlas. Thus, would be useful to find regions using your method for ICR mice and do u have any suggestions on how to use your method for SD Rats?
I'm not sure how different ICR and C57 brains are, but it'd be worth it to test if the Allen atlas provides a good fit for your ICR brain slices using SHARP-Track. If it doesn't, you could look into some of the non-linear tools mentioned in the biorxiv paper (see readme) introduction.
For rats, I don't think that the data out there are of the same quality as the mouse brain atlas. However, there are a couple 3D labeled atlases. If you're able to get them into the same form as the variables used in this tool (i.e. 3D matlab arrays), I'm sure that would be useful for other users as well.
