CMTK or Natverse for initial reg to template space

[Molly Kirk]

Hello, 

My name is Molly Kirk, I am doctoral candidate in Kristin Scott's lab. I am really excited to start using this system for my registrations and bridging registrations. I usually use the CMTK image j gui and have found your step by step protocol very helpful in the past! 

 Is there a way to run CMTK registrations from a sample nc82 or BrpSnapf data through the Natverse? Or, should I be first registering my brains through the CMTK image j gui  and then performing my bridging registrations between templates in the Natverse? If you have a detailed protocol to do this that would be amazing! 

All the best,  

Molly Jane Kirk 

[Greg Jefferis]

Dear Molly,

Thanks for your interest in the natverse. We use the CMTK registration GUI or the underlying munger command line tool to run the light level registrations.

Then we use natverse tools to apply those registrations to e.g. neurons or surface models that have been traced out of a confocal stack. We do have a number of protocols, but to offer further advice, you would need to say a bit more about what you want to do.

All the best,

Greg.

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[Molly Kirk]

Thank you so much for your quick response. I figured that you were using the GUI as I couldn't find documentation on actually performing CMTK registration in Natverse. Makes much more sense. 

To be honest, I think you answered my question. I will continue running my registrations in the CTMK GUI and then transferring them to natverse to do the bridging registrations I need.

As for the protocol. Ideally, we would like to be able to take light level images from Gal4 and Split-Gal4 lines and register them to template space for subsequent use in nblast and identification in EM datasets.  Do you have a protocol that could take us from .Tiff or .Nrrd stacks to nblast and EM in the natverse?  We would love to try it out. 

Thanks,

Molly 

[Greg Jefferis]

Dear Molly,

On 10 Sep 2020, at 22:18, Molly Kirk <molly...@gmail.com> wrote:

As for the protocol. Ideally, we would like to be able to take light level images from Gal4 and Split-Gal4 lines and register them to template space for subsequent use in nblast and identification in EM datasets.  Do you have a protocol that could take us from .Tiff or .Nrrd stacks to nblast and EM in the natverse?  We would love to try it out. 

You can try to see if this package helps

https://jefferislab.github.io/jimpipeline/reference/index.html

I'm afraid it wasn't really written for external use, but we use this function, skeletonise_nrrds

https://jefferislab.github.io/jimpipeline/reference/skeletonise_nrrds.html

to process a folder full of NRRD files into the dotprops format used by NBLAST.

Once you have the dotprops objects in R then there are several recent examples in the list archives of moving neurons to EM space and doing NBLAST e.g,

https://groups.google.com/g/nat-user/c/8fdQiflCidQ/m/wdAyUYIIBAAJ

https://groups.google.com/g/nat-user/c/zNaCyQnZeVg/m/mStE5zbcAgAJ

All the best,

Greg.

[Molly Kirk]

Thanks so much! This was very helpful! I will try it out and pass it along to the rest of the lab. I appreciate your help. Hope you have a great weekend. 

Best, 

Molly Kirk