treem 1.0.0a1

Tree-like morphology data processing

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).

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 repair Correct reconstruction errors view Show morphology structure ========= =========================================================

Installation

Basic installation

Install the latest stable release::

    pip3 install treem

Install a development version::

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

See ``pip3`` documentation for installation alternatives.


Dependencies
~~~~~~~~~~~~

Module ``treem`` has minimal runtime dependencies:

* ``python`` >= 3.7
* ``matplotlib``
* ``numpy``

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 <https://readthedocs.org/>`_.