What does SWC stand for?

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basjanzandt

What does SWC stand for?

Post by basjanzandt »

The .SWC file format is a widely used open format, and describes a reconstruction as a list of points with a.o. their coordinates, diameter and parent.
Out of curiosity, does anyone know what SWC stands for? I cannot seem to find this anywhere. My guess would be the C stands for Cvapp?

Best regards,
Bas-Jan

ted
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Re: What does SWC stand for?

Post by ted »

SWC are the initials of the last names of E.W. Stockley, H.V. Wheal, and H.M. Cole, who developed a system for generating morphometric reconstructions of neurons that is described in

Stockley, E. W.; Cole, H. M.; Brown, A. D. & Wheal, H. V.
A system for quantitative morphological measurement and electronic modelling of neurons: three-dimensional reconstruction.
J Neurosci Methods, 1993, 47, 39-51

PLEASE NOTE THAT THE SWC FILE FORMAT IS NOT DESCRIBED IN THAT PAPER!
Indeed, I have not been able to find a paper by any one, two, or three of these authors, alone or with other co-authors, that describes an "SWC file format." It should come as no surprise that there is a bit of uncertainty about the SWC file format itself. In particular, there is some ambiguity about how the soma should be handled.

basjanzandt

Re: What does SWC stand for?

Post by basjanzandt »

Thanks Ted!

ted
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Re: What does SWC stand for?

Post by ted »

Different groups use slightly different standards for SWC. See
http://www.neuromorpho.org/myfaq.jsp
under the question "What is SWC format?"
and also
http://research.mssm.edu/cnic/swc.html
and
http://www.neuronland.org/NLMorphologyC ... /Spec.html

bsuter
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Re: What does SWC stand for?

Post by bsuter »

Hi Ted,
The neuromorpho FAQ that you linked below cites "Cannon 1998" for the SWC format. That seems to be this paper, which includes at least the presumed "W", aka Wheal. Whether Cannon or Cole (or both) are the "C" remains a mystery for now ...

Cannon RC, Turner DA, Pyapali GK, and Wheal HV. An on-line archive of reconstructed hippocampal neurons. 1998, JNeurosciMethods. https://doi.org/10.1016/S0165-0270(98)00091-0

Interesting to read their plan for well-defined metadata properties in the header section.

The earlier (Stockley, Cole, Brown, Wheal, 1993) paper appears to have stored the reconstructions as a linked-list data structure, probably not in text files, but I'm not sure about the details. Fig. 5B is a quite impressive surface rendering of a detailed reconstruction. https://doi.org/10.1016/0165-0270(93)90020-R

ted
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Re: What does SWC stand for?

Post by ted »

The most authoritative answers to such questions might be obtainable from the authors of one or both of these papers, at least a few of whom are probably still alive.

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