diff --git a/README.md b/README.md index 7caa73e..0ad2ca1 100644 --- a/README.md +++ b/README.md @@ -3,26 +3,7 @@ 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. 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: @@ -113,6 +94,28 @@ neuron_tree = node newline {node newline} ; 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/))