Information about the SWC file specification
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 squential 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 cylinder thickness) |
| 7 | Parent | Parent sample identifier. |
The basic set of types used in NeuroMorpho.org SWC files are:
| TypeID | Description |
|---|---|
| -1 | root |
| 0 | undefined |
| 1 | soma |
| 2 | axon |
| 3 | (basal) dendrite |
| 4 | apical dendrite |
| 5 | custom |
| 6 | unspecified neurite |
| 7 | glia processes |
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.
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 cylinders 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.
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 cylindrical 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 = "\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 ;
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 |
- 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