skeleton stops unexpectedly

[neurologic]

Hi,
Do you know why the skeleton might be stopping before the end of the dendrite on the left in this picture?

I thought it might be because the branch got thinner, so I reduced scale and const and it did not change where it stopped. Also, there are many processes that are thinner in the neuron that the skeleton does traverse. There are no discontinuities in the mesh at that point.

I used igneous to get the skeleton after meshing, but I assume this is a kimimaro question (and not necessarily an issue with the program).

Thank you,

Krista

[william-silversmith]

Hi Krista,

In an earlier version, I would have said that it's possible an off-screen invalidation sphere from another branch could be affecting the tip, but in the most recent version I believe I fixed that (and you also tried reducing scale and const).

One other possibility is if you have "remove ticks" set and there is a tiny branch, both of the branches could be removed. Make sure that parameter is set to zero.

[neurologic]

--tick-threshold is set to 0 (a skeleton merge parameter, correct? -- I am doing this through igneous):
Running UnshardedSkeletonMergeTask(cloudpath='file:///Users/.....',prefix=48,crop=0,dust_threshold=1000.0,max_cable_length=None,tick_threshold=0.0,delete_fragments=False)

[william-silversmith]

That's right, sorry I should have mentioned its a merge parameter.

[ekchapman]

I ran into this issue on a 2D image and got around it by setting fix_borders=False.