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Tree-like morphology data processing

Project description

treem - neuron morphology processing tool

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).

PyPI version License: MIT Documentation Status Build Status Coverage Status

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

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

Installation

Install the latest stable release:

pip3 install treem

Install a development version:

pip3 install git+git://github.com/a1eko/treem

See also pip3 documentation for installation alternatives.

Dependencies

Module treem has minimal runtime dependencies:

  • python >= 3.7
  • matplotlib
  • numpy
  • PyOpenGL (optional) enables swc render command

For testing and documentation, treem needs development packages with third-party extensions:

  • sphinx with napoleon and programoutput
  • pytest with pytest-cov
  • coverage

Documentation

Documentation is available online at Read the Docs.

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