Simple Neurite Tracer SWC loading problems

When I am trying to load SWC files (in Simple Neurite Tracer) I sometimes get this problem as best illustrated with this screen shot:
example.tif (5.9 MB)
As shown the SWC file is “attached” to the upper left corner. Why does it do that? How can I avoid that problem?

Can you please subscribe to the NeuroAnatomy and SciView update site and see if the problem persists?

Hi Tiago, did you ever hear more about this? I have a similar issue. I’ve subscribed to updates from NeuroAnatomy and SciView as you suggest, SNT is otherwise working perfectly, and I can export the .traces file. The .traces file loads with no issue, but I need an swc file for loading into CATMAID. When I export and import a .swc file it looks like the attached image. Any ideas?


There are several lines in the .swc file that look like this:

315 0 12.911416 128.191918 27.300000 0.000000 314
316 0 12.450294 128.191918 27.300000 0.000000 315
317 0 0.000000 0.000000 0.000000 0.000000 181
318 0 61.790349 114.358258 65.099999 0.000000 317
319 0 61.790349 114.819380 65.099999 0.000000 318

I should also mention that I did make a few mistakes during tracing and deleted some of the paths, which caused them to be renumbered. Otherwise things were smooth. I don’t know if that is meaningful, but could point to the issue. Thanks for the help.

If I just replace the 0000 lines with the right coordinates (e.g. line 181 in the example above) I should get the right shape, but why is it doing thi?

We need to develop an easier way to load data into CATMAID. Ah, I wish there would be 100hours in a day.

That is probably related. I don’t know what is causing that. It looks as if a deleted path (which presumably was connected to the node #181) was not properly deleted, and its nodes are saved with 0,0,0 coordinates. It is a nasty bug.
A workaround would be to run Path Manager’s Edit>Rebuild… command before saving an edited reconstruction. But now that the file is saved, I am not so sure the command is smart enough to prune those ‘null’ nodes. Can you please try?

Otherwise please feel free to share the file, to see if we can use to study the problem. In the interim we could write a script that culls such nodes. Sorry that it has to be that cumbersome.

Good thought. I just rebuilt the path and exported/imported the .swc file and I see the same issue. nuts. Looks like .swc and .traces files are not allowed for upload, so the .swc file is a text file. R22H10-20181211_63_A2-f-40x-VNC-GAL4-JRC2018_VNC_FEMALE-8195869-aligned_stack_red_right_T1_rebuilt-000.txt (80.0 KB)

Couple things about uploading to catmaid. 1) For an earlier version of SNT there was a radius measurement, using a tubeness algorithm that was only available on linux. I’m still getting accustomed to your new version, but is that still around? 2) I generally find the .swc file fairly straightforward, not too bad to move around into catmaid, but I’m curious if you have good ideas you’ve been thinking about. I predict we (the tuthill group at University of Washington, TUTHILL LAB) and others will be doing a fair bit of this in the near future, maybe we can help think about a good way?

But it may still be related to the deleted paths. If I do a better job on the next neuron and the .swc file turns out better, I’ll update.

@tazevedo,
On the artifact nodes: When you were editing the paths did you use the “Connect to” option on the contextual menu, by any chance? We are able to replicate a similar issue when connecting branches. We’ll try to release the fix soon.

Tubeness filtering is certainly around! (BTW, I am not aware of any linux exclusivity: Even in the early days it was always cross-platform). Have a look at the documentation on tracing and generating “Secondary Images”, including the super neat youtube tutorial by @arshadic

BTW: The original Simple Neurite Tracer remains available. You can access it using the “Legacy Commands” option in Plugins>Neuroanatomy>Neuroanatomy Shortcuts Window…

On CATMAID: Great! feel free to open a new discussion either here or on Github!

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@tazevedo, this issue of “ghost” nodes with zero coordinates upon editing of paths should now be fixed with SNT-3.1.113 released today. This issue has also been reported in another post.

Thanks! I’ll update and check it out.

i still facing the facing the after downloading gimp on my system