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.