SWC specification

The SWC data format specification used by the treem package.

Format

Field	Column	Description	Values
I	0	Node ID	int: 1 (root), 2, 3, …
T	1	Point type	int: 1 (soma), 2 (axon), 3 (dend), 4 (apic)
X/Y/Z	2/3/4	Coordinates	float (micrometers)
R	5	Radius	float (micrometers)
P	6	Parent node ID	int: -1 (parent of root), 1, 2, …

Node IDs:
- Start at 1, increment sequentially by 1.
- Unique, positive integers.
Root:
- Exactly one root: I=1, T=1, P=-1.
Parent-child:
- All non-root nodes have only one parent and P < I (no loops).
- Parent IDs must exist in the file (except P=-1 for root).
Soma (type 1):
- Must be represented as one of the following:
  - Single node (root only).
  - Single section starting from the root.
  - Two sections from root (e.g., 3-point soma).
Non-somatic nodes (types 2/3/4):
- Each non-soma branch (neurite) originates in root.
- Non-soma branches must maintain consistent type P within a branch. First node of a neurite (stem) has parent root.
Validity:
- File must have >=1 data rows.
- T in {1, 2, 3, 4} (other types invalidate the file).

Term	Definition
Tree	Hierarchical structure with no loops. Each node has <=1 parent.
Branch	A maximal sub-tree of the same type `P` (a neurite).
Node	Single SWC line (point in 3D).
Root	Node with no parent (`I=1`, `T=1`, `P=-1`).
Child	Node with a parent.
Parent	Node with >=1 child.
Leaf	Node with no children (degree=0).
Fork	Non-root node with >1 child (degree>1). Bifurcation if degree=2.
Depth	Ancestor count from root (root depth=0).
Height	Max edges from node to any leaf in its sub-tree.
Size	Total nodes in (sub-)tree.
Breadth	Total leaves in (sub-)tree.
Width	Nodes at same depth as current node.
Segment	Line connecting two nodes (parent and child).
Section	Continuous chain of segments between fork/root/leaf nodes.
Stem	First node of non-somatic branch.