Adding a template brain

[LauraAnn Schmidberger]

Hi Greg,

I've been using nat and nat.nblast for comparison of traced zebrafish neurons, and once I figured out how to import the .swc files and dataframes it's been working great-- thank you for this resource!

I was wondering if there is a way to add a template brain to the 3D plot of neurons. We already have a registered fish brain, we just want to be able to superimpose the neurons, which are now different colors based on their proximity in the dendrogram, onto our registered brain. Is there a way to do this using your packages?

Thank you!

LauraAnn

[Gregory Jefferis]

Dear Laura, thanks for your message and interest in nat. It’s great to hear that it’s proving useful for fish neurons. 

You can read in a surface mesh representation of your template brain for 3d plots. nat has built in support for Amira surfaces. You can use the readobj package to read in wavefront obj format surfaces (a very standard format) - make sure to choose the rgl mesh3d as your return type. You can the plot the surface with rgl functions like shade3d or wire3d. 

Best,

Greg. 

Sent from my iPhone

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[LauraAnn Schmidberger]

Thank you for your rapid response and your help!

Best,

LauraAnn

On Friday, March 22, 2019 at 5:43:33 PM UTC-4, Gregory Jefferis wrote:

Dear Laura, thanks for your message and interest in nat. It’s great to hear that it’s proving useful for fish neurons. 

You can read in a surface mesh representation of your template brain for 3d plots. nat has built in support for Amira surfaces. You can use the readobj package to read in wavefront obj format surfaces (a very standard format) - make sure to choose the rgl mesh3d as your return type. You can the plot the surface with rgl functions like shade3d or wire3d. 

Best,

Greg. 

Sent from my iPhone

On 22 Mar 2019, at 20:33, LauraAnn Schmidberger <lauraann.s...@gmail.com> wrote:

Hi Greg,

I've been using nat and nat.nblast for comparison of traced zebrafish neurons, and once I figured out how to import the .swc files and dataframes it's been working great-- thank you for this resource!

I was wondering if there is a way to add a template brain to the 3D plot of neurons. We already have a registered fish brain, we just want to be able to superimpose the neurons, which are now different colors based on their proximity in the dendrogram, onto our registered brain. Is there a way to do this using your packages?

Thank you!

LauraAnn

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