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fiji / SNT

Legacy project superseded by https://github.com/morphonets/SNT
GNU General Public License v3.0
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Conver SWC to skeletonized volume #70

Open jpgard opened 4 years ago

jpgard commented 4 years ago

Hi, thanks for the great software. I would like to generate a "rasterized" version of a neuronal trace, which is currently in SWC format. It seems that previously this functionality existed in SNT, as described in the Methods section of this paper. However, the procedure described here no longer seems to exist in the SNT plugin menus.

Is there a way to convert from SWC file to a 3D output, where each voxel in the output is zero if it is not an "active" voxel in the network described by the SWC, and 1 otherwise?

I have also posted this question here if it is easier to answer there!

ctrueden commented 4 years ago

@tferr Thoughts? I also invited you to the corresponding Image.sc Forum issue.

tferr commented 4 years ago

@jpgard, Sorry for the late reply. We are currently migrating SNT to its own organization here.We wanted to make a unique umbrella on all things NeuroAnatomy (with SciView and Cx3D integration) but things have been more tedious to finalize then anticipated. Yes. rasterization has been improved with the latest patches! It is as easy as (in Groovy):

import sc.fiji.snt.Tree
tree = new Tree("/path/to/swc/file")
tree.getSkeleton().show() // 3D skeleton
tree.getSkeleton2D().show() // MIP of rasterized skeleton

There are also methods to skeletonize a collection of reconstructions into a common image. The easiest way is to subscribe Fiji's updater to Neuroanatomy-Unstable (https://imagej.net/Neuroanatomy-Unstable) to get the latest builds of SNT. As we move things around things keep breaking in one way or the other, but that core functionality should not be affected at this point. We are also working on a website at