swc_specification

Information about the SWC file specification. A video describing the specification can be found here: https://vimeo.com/853224668?share=copy

Specification of standard SWC - adapted from (3)

An SWC file (S.W.C. encodes for the last names of its initial designers Ed Stockley, Howard Wheal, and Robert Cannon) is a text file that starts with an optional header section in which each line starts with the symbol #. Some SWC-variants use this section to store information about the data in an orderly fashion, others treat is as a free-text field.

Below the header section, a points matrix with 7 columns follows. It contains the points traced along the neuronal tree. The seven numbers in each row are separated by spaces, and have the following meaning:

Column index	Field	Description
1	Index	Sample identifier. A sequential positive integer.
2	Type	Type identifier. A positive integer.
3	X	X-position in micrometers
4	Y	Y-position in micrometers
5	Z	Z-position in micrometers
6	R	Radius in micrometers (half the node thickness)
7	Parent	Parent sample identifier.

The basic set of types used in NeuroMorpho.org SWC files are:

Type	ID	Description
undefined	0	Structure type unknown or unspecified
soma	1	Soma of a neuron
axon	2	Axon of a neuron
basal dendrite	3	Basal dendrite of a neuron
apical dendrite	4	Apical dendrite of a neuron
custom	5	Custom type of cell component
unspecified neurite	6	An unspecified part of a neuron
glia processes	7	Glial processes
custom	>7	Custom type of cell component

Parent defines how points are connected to each other. In a tree, multiple points can have the same ParentID. The first point in the file must have a ParentID equal to -1, which represents the root point. Parent samples must be defined before they are being referred to. By counting how many points refer to the a given parent, the number of its children can be computed.

Soma representation

The soma in SWC can consist of a single root point or multiple points, the first of which is the root. The single-point representation approximates the soma as a sphere of radius R and centered in X, Y, Z. The multi-point representation approximates the soma as a sequence of nodes akin to a neurite branch. Note that representing the soma as a contour tracing of the soma perimeter or a series of contour tracings approximating the soma surface is not consistent with the SWC standard.

SWC Example - adapted from Ascoli et al, 2001

This extremely simplified neuronal structure was obtained by extensive pruning of a dentate gyrus granule cell in (4). The left panel shows the digital SWC representation: every node compartment is described by a row containing: - A label (ID or Index, the same numbers reported next to the branches in the right panel - A tag (T or Type, 1 for soma, 3 for dendrite), - Cartesion positions (X,Y,Z in micrometers), - Radius (R) and - Connectivity (C or Parent, representing the label of parent, -1 indicates no parent)

Syntax of basic SWC reconstruction in EBNF - from Nanda et al, 2018

newline = “:raw-latex:`\n`” ;

letter = “A” | “B” | “C” | “D” | “E” | “F” | “G” | “H” | “I” | “J” | “K” | “L” | “M” | “N” | “O” | “P” | “Q” | “R” | “S” | “T” | “U” | “V” | “W” | “X” | “Y” | “Z” | “a” | “b” | “c” | “d” | “e” | “f” | “g” | “h” | “i” | “j” | “k” | “l” | “m” | “n” | “o” | “p” | “q” | “r” | “s” | “t” | “u” | “v” | “w” | “x” | “y” | “z” ;

digit = “0” | “1” | “2” | “3” | “4” | “5” | “6” | “7” | “8” | “9” ;

symbol = “[” | “]” | “{” | “}” | “(” | “)” | “<” | “>” | “‘” |’”’ | “=” | “|” | “.” | “,” | “;” ;

integer = [+|-] digit{digit} ;

double = integer [“.”] {integer} ;

character = letter | double | symbol | “_” | ” “;

header = “#” character {character} newline [“#” character {character} newline] ;

Index = integer ;

Type = integer ;

X = double ;

Y = double ;

Z = double ;

Radius = double ;

Parent = integer ;

node = Index ” ” Type ” ” X ” ” Y ” ” Z ” ” Radius ” ” Parent ;

neuron_tree = node newline {node newline} ;

SWC = [header] neuron_tree ;

Header fields defined in Cannon et al 1998

The original publication that introduced SWC (4) described the header as containing the following fields, although these are not considered a required component of SWC:

Field	Description
ORIGINAL_SOURCE	File type delivered by digitisation equipment
CREATURE	Species from which the cell came
REGION	Brain region
FIELD/LAYER	Location within region
TYPE	Cell type
CONTRIBUTOR	Name, initials, organisation, e.g. Turner DA, Duke
REFERENCE	Where the data has been published
RAW	File name of original data
EXTRAS	Files containing further information on this cell
SOMA_AREA	Area of soma (in mm2)
SHRINKAGE_CORRECTION	x, y and z correction factors
VERSION_NUMBER	To identify different versions of the same raw data
VERSION_DATE	Date this version was created (yyyy-mm-dd)
SCALE	Used internally to record applied shrinkage corrections

References

Ascoli GA, Krichmar JL, Nasuto SJ, Senft SL. Generation, description and storage of dendritic morphology data. Philos Trans R Soc Lond B Biol Sci. 2001;356(1412):1131-1145. doi:10.1098/rstb.2001.0905 (PMCID: PMC1088507)
Nanda S, Chen H, Das R, et al. Design and implementation of multi-signal and time-varying neural reconstructions. Sci Data. 2018;5:170207. Published 2018 Jan 23. doi:10.1038/sdata.2017.207 (PMCID: PMC5779069)
https://neuroinformatics.nl/swcPlus/ “SWC plus (SWC+) format specification”
Cannon RC, Turner DA, Pyapali GK, Wheal HV. An on-line archive of reconstructed hippocampal neurons. Journal of Neuroscience Methods. 1998 Oct;84(1-2):49-54. DOI: 10.1016/s0165-0270(98)00091-0. PMID: 9821633.
https://en.wikipedia.org/wiki/Extended_Backus%E2%80%93Naur_form
http://neuromorpho.org/SomaFormat.html Soma format representation in NeuroMorpho.Org as of version 5.3

Contributors

Lydia Ng
Giorgio Ascoli
Bengt Ljungquist
Sumit Nanda