Hello,
Is there a way to export the Original 2017 mouse brain atlas and not just the Rainbow 2017 atlas?

Thanks,
Jacob

Hi Jacob,

The simplest workaround is to download VisuAlign ( https://www.nitrc.org/projects/visualign... ), as it saves both kind of overlay images. VisuAlign opens JSON files saved by QuickNII.

I hope this helps,
Gergely

Perfect - thanks for the tip Gergely. 

I know that this is the wrong place to ask, but is there a way to propagate transformations in the VisuAlign program?  

Jacob

Originally posted by Jacob Bumgarner: There is none at the moment.
I can imagine a way, but haven't even tried it yet. The main issue is that in the general case the position and orientation of the actual tissue on a slide is a bit random. So if I just copy markers from one image to another directly, there may not be tissue at the given image position at all. But in fact the QuickNII-step does provide information about these irregularities, so in theory it may be possible to do the copy in "atlas-space" (which is uniform), and then transform it back into "image-space" (which has the randomness). But I don't know for sure if it would work, so I can't promise anything.

Best regards,
Gergely

Fair enough. Seems like a difficult issue.

Thanks for the work you've put in on this project Gergely. It has been extremely helpful!

Jacob