Crate swc_neuron

Rust library for reading, writing, and manipulating SWC files for neuronal morphology. Also includes a CLI for basic validation, sorting, and reindexing (with optional feature cli).

The format was originally proposed in Cannon, et al. 1998, with an implementation in dohalloran/SWC_BATCH_CHECK.

While commonly used, many variants exist; this implementation tries to cover the “standardised” version described here, with some ambiguities resolved by the SWCplus specification.

The header is a series of #-prefixed lines starting at the beginning of the file. Blank lines (i.e. without a # or any other non-whitespace content) do not interrupt the header, but are also not included in the parsed header. All other #-prefixed and all whitespace-only lines in the file after the first sample are ignored. Samples define a sample ID, a structure represented by that sample, its location, radius, and the sample ID of the sample’s parent in the neuron’s tree structure (the root’s parent is -1).

The SwcNeuron is generic over implementors of StructureIdentifier and Header, and can be parsed from [Read]ers and dumped to Writers. StructureIdentifier is implemented for some known sub-specifications. Header is implemented for String (i.e. a free-text header field). AnySwc is a SwcNeuron with any structure integer and string header.

Re-exports

• pub use crate::structures::AnyStructure;
• pub use crate::structures::StructureIdentifier;
• pub use crate::header::Header;

Modules

• header
  Module for metadata contained in the header of the SWC file.
• structures
  Module for types represented by the structure ID field of a SWC sample.

Macros

• neuromorpho_ext
  Thin wrapper around the structure_mapping macro for producing enums which extend the Neuromorpho SWC standard (i.e. have additional structure types in the Custom block, 5+).
• structure_mapping
  Macro for creating a public enum implementing StructureIdentifier.

Structs

• MissingSampleError
  Error where a sample refers to an unknown parent sample.
• SwcLines
  Iterator which eagerly reads the header on construction and then lazily reads the remaining lines.
• SwcNeuron
  Struct representing a neuron skeleton as a tree of SwcSamples.
• SwcSample
  Struct representing a row of a SWC file (a single sample from the neuron), which gives information about a single node in the tree.

Enums

• InconsistentNeuronError
  Error where a neuron represented by a SWC file is inconsistent.
• SampleParseError
  Error in parsing a SWC sample (row).
• SwcLine
  Line in a SWC file, which might be a comment or sample.
• SwcParseError
  Error for a SWC file which cannot be parsed

Functions

• parse_swc_lines
  Parse lines from a SWC file.

Type Aliases

• AnySwc
  Maximally flexible SwcNeuron with any structure specification and a free-text header.
• Precision
  Float type used for locations and radii.
• SampleId
  Type used for sample IDs.