treem - neuron morphology processing toolΒΆ

Module treem

Module provides data structure and command-line tools for accessing and manipulating the digital reconstructions of the neuron morphology in Stockley-Wheal-Cannon format (SWC).

Main classes

Access to morphological data from the source code is supported by the classes Tree, Node, Morph and SWC.

Tree Recursive tree data structure
Node Morphology data storage
Morph Neuron morphology representation
SWC Definitions of the data format

For the complete list of available functions, see API reference.

Commands

Common operations with SWC files are possible via the swc command-line tool:

swc <command> [options] file

List of swc commands:

check Test morphology reconstruction for structural consistency
convert Convert morphology to compliant SWC format
find Locate single nodes in the reconstruction
measure Calculate morphometric features
modify Manipulate morphology reconstruction
render Display 3D model of the reconstruction
repair Correct reconstruction errors
view Show morphology structure

For the detailed description of the commands and options, see Command-line interface.