Tree format (.ntr) description
The file completely describes the cells geometry.
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the description can be found in teh following paper: J. Neurosci
Methods 88, 3, 727-739, 1998
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the file starts with header lines describing the types of segment points
present in the file
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# ORIGINAL_SOURCE
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# CREATURE
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# REGION
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# FIELD/LAYER
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# TYPE
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# CONTRIBUTOR
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# REFERENCE
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# RAW
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# EXTRAS
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# SOMA_AREA
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# SHRINKAGE_CORRECTION
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# VERSION_NUMBER
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# VERSION_DATE
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# SCALE
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# SEGMENT_TYPE 1
1.60 Rad Thick Smooth
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several of this lines describes the possible segment types present in the
file and used at the descrition of the points
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first field: code
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seconf field: diameter of the given type
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third field: decription of the given type
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the header is followed by one line of data for each point in the structure
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each line has the same seven fields:
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numbered point index
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user defined flag denoting the specific part of the structure (cell
body, dendrite, axon et. al.)
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three-dimensional position (x, y, z, in micrometers)
- diameter (r, in $\mu m$) NOTE: I think the original SWC format wrote
radius, but I put here DIAMETER
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and the parent point index.
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one point in any file has a parent point index of -1, indicating it is
the root point, which is generally part of the soma
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all other points have one, and only one parent. Thus, multiple branches
at a single point are possible but provided each point has a parent of
lower index than itself, loops and unconnected branches are excluded.
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the user defined flag contains information on the type of subsegment the
point belongs to (subsegment codes are detailed in the header)