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lydiang authored Mar 10, 2022
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## 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. According to the original publication (4) that introduced SWC, the header contains the following prescribed fields:

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 some (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.
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.

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:

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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:

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 some (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/))
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