Update README.md

README.md

@@ -3,14 +3,14 @@ Information about the SWC file specification
 
 ## Specification of standard SWC - adpated 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 a 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.
+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 positive integer.
-2 | Type | Type identifier
+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
@@ -32,6 +32,9 @@ TypeID | Description
 
 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 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.
+
 ## SWC Example - adapted from Ascoli et al, 2001
 
 ![image](https://user-images.githubusercontent.com/8552673/157725540-a49e8ab7-e930-401c-938b-713dd093dc2c.png)
@@ -92,7 +95,7 @@ SWC = [header] neuron_tree ;
 
 ## Header fields defined in Cannon et al 1998
 
-According to the original publication (4) that introduced SWC, the header contains the following prescribed fields:
+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 
 --- | --- 
@@ -105,17 +108,17 @@ 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 some (in mm2)
+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
 
-However, these fields are not present in the NeuroMorpho.org SWC format and therefore cannot be considered a required component of SWC.
 
 ## References
 1. 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](https://www.ncbi.nlm.nih.gov/sites/ppmc/articles/PMC1088507/))
 2. 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://www.ncbi.nlm.nih.gov/sites/ppmc/articles/PMC5779069/))
 3. https://neuroinformatics.nl/swcPlus/ "SWC plus (SWC+) format specification"
 4. 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://europepmc.org/article/MED/9821633).
 5. https://en.wikipedia.org/wiki/Extended_Backus%E2%80%93Naur_form
+6. http://neuromorpho.org/SomaFormat.html Soma format representation in NeuroMorpho.Org as of version 5.3