Table 3.

List of specification checks and corresponding error correction (in the order of execution) to ensure SWC standardization

Check	Action/Correction
Missing Field	If the SWC points matrix does not have seven columns, then return an error. All further checks are omitted.
Number of Lines	- Generate an error if no samples are detected. All further checks are omitted. - If fewer than 20 lines, generate a warning to check file integrity.
Number of soma Samples	Generate warning if no soma samples detected.
Invalid Parent	If the Parent points to an Index value that does not exist, then make the sample with the invalid Parent a root point, and generate a warning to check file integrity.
Index/Parent Integer	If Index and/or Parent are float-formatted integer (e.g., “1.00”), format them as integers. If they are non-integer values (e.g., “1.34”) or non-numerical entries (e.g., “abc”), generate an error.
XYZ Double	Ensure X, Y, and Z coordinates are float/double values. Any NaN or NA values detected in the ASCII text file are treated as 0.0. Generate a warning to check file integrity, and add a footer to the file to note inserted values.
Radius Positive Double	- Ensure sample Radius is a double/float value. - If radius is negative, zero, NaN, or NA, then set to 0.5. Generate a warning to check file integrity, and add a footer to the file to note inserted values.
Non-Standard Type	- If Type is float-formatted integer, format as integer. - If it is non-integer value or non-numerical entry, change to Type 0 indicating ‘undefined’. - If bifurcation and terminal points have non-standard Types, set them to that of parent.
Sequential Index	If the Index values are not in sequential order (starting from 1), then sort and reset Index and Parent numbering.
Sorted Order	- If parent samples are referred to before being defined, then sort and reset Index and Parent numbering. - Sort indices to ensure that the first sample in the file is a root point. If no sample point is a root, generate an error.
Soma Contours	Detect soma contour(s), and replace each with a single point.