Module treem
Module treem
(pronounced as "trim") 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: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 cli:Command-line interface
.
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