treem - Neuron Morphology Processing Tool

Module treem

The treem module (pronounced “trim”) provides data structures and command-line tools for accessing and manipulating digital reconstructions of neuronal morphology in the Stockley-Wheal-Cannon (SWC) format.

Main classes

Access to morphological data from the source code is provided through 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 can be performed using the swc command-line tool:

swc <command> [options] file

Alternatively:

swc <command> file [file ...] [options]

List of swc commands:

check	Tests the morphology reconstruction for structural consistency
convert	Converts morphology data to a compliant SWC format
find	Locates individual nodes in the reconstruction
measure	Calculates morphometric features
modify	Modifies morphology reconstruction
render	Displays a 3D model of the reconstruction
repair	Corrects reconstruction errors
view	Displays the morphology structure

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