SWC

Overview

One of the most widely used formats (in particular, a standardized version of this format is used by the neuromorpho archive ).

Format specification:     

Encoding:  ASCII text
Limitations: no markers, no spines.

Comment lines begin with character '#'.

Subsequent non-empty lines each represent a single neuron sample point with seven data items.


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 8
data type
 Sample number
 Structure Identifier
 x position
 y position
 z position
 radius
 parent sample
data value
 integer value, generally continuous, starting from '1',
though this is not required. 



Standardized swc files (www.neuromorpho.org) - 
0 - undefined
1 - soma
2 - axon
3 - (basal) dendrite
4 - apical dendrite
5+ - custom

A lot of data does not conform exactly to this standard however e.g.

CNIC data -
0 - undefined
1 - soma
2 - axon
3 - (basal) dendrite
4 - apical dendrite
5 - fork point
6 - end point
7 - custom

VNED data -  seems to be standard, but uses 
10 - related to soma ?

Gulyas data - each number represents structure with same diameter.


Other data has been observed with 
-1 -  also possibly related to soma ?


 'x', 'y', 'z' are spatial co-ordinates, given in micrometers.
'radius' is half the dendrite thickness, also given in micrometers (note this is one of the few formats which use radius instead of diameter)


 The sample number.
Connectivity is expressed with this value.

Parent samples should appear before any child samples.


References

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Links

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Examples

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