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SWC reading error due to soma #213
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Do you mean that it's a contour as opposed to a set of stacked cylinders? |
No, it's not a contour, it's more like that (attempt to ASCII art!):
On the point |
Spec wise, it's quite hard to nail anything down, and people seem to put stuff out that isn't conformant with what little there is. For the soma; I have always referred to this: http://neuromorpho.org/SomaFormat.html as neuromorpho.org has the most clout (in a way). The original paper (R.C.Cannon et al.: Journal of Neuroscience Methods - 1998) with the spec says: What do you think @wizmer? Nice art :) |
Ping @wizmer |
I don't think this should be allowed if we don't understand the physical meaning of such thing. |
Hello,
I am having an issue parsing an SWC file and I think it's related to the soma being multipoint. The Python error I have is the following:
When I open the morph with my JS or custom Python parser, I can see that the soma is actually having a "star shape" and that one branch of the star is an actual section composed of the point
1
,5136
and5137
(on the file I'll provide you by email). I admit it's a bit weird to have a soma designed like that, but to my understanding, it's still somehow compliant with the SWC pseudo-spec (very loose spec imo).As a side note, I haven't tested all the files but on the about 100 files I have tested, this happens only once.
Best.
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