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janelia-flyem / NeuTu

Software package for neuron reconstruction and visualization
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How to use skeletonize? #371

Closed william-silversmith closed 3 years ago

william-silversmith commented 3 years ago

Hi Ting!

I was interested in trying out the TEASAR implementation in NeuTu / Neu3, but I've been having trouble finding documentation for how to do it (I tried to ctrl-F "skeleton" in the manuals). I looked through the code and found some references to DVID, but I didn't find the code in the DVID repo. I think I found a --skeletonize option, but it's not clear how to use it.

Thanks for any help. ^_^

Will

tingzhao commented 3 years ago

Hi Will,

You can run neutu as a command line to perform skeletonization.

neutu --command --skeletonize -o <output.swc> <input.tif>

neutu --command --skeletonize --bodyid <body id> '<dvid_server_address>?uuid=<uuid>&segmentation=<segmentation_name>'

The result will be saved under the keyvalue data _skeletons in DVID.

william-silversmith commented 3 years ago

Thank you Ting! I'll give this a try.

On Wed, Feb 24, 2021, 5:21 PM tingzhao notifications@github.com wrote:

Hi Will,

You can run neutu as a command line to perform skeletonization.

  • To skeletonize a binary TIF file:

neutu --command --skeletonize -o

  • To skeletonize a body in DVID:

neutu --command --skeletonize --bodyid '?uuid=&segmentation='

The result will be saved under the keyvalue data

_skeletons in DVID. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or unsubscribe .
william-silversmith commented 3 years ago

Thank you Ting! I was able to run it.