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).
[](https://badge.fury.io/py/treem)
[](https://github.com/a1eko/treem/blob/master/LICENSE)
[](https://codecov.io/gh/a1eko/treem)
[](https://treem.readthedocs.io/en/latest/?badge=latest)
[](https://doi.org/10.5281/zenodo.4890844)
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
or sometimes more convenient as
swc <command> file [file ...] [options]
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+https://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](https://treem.readthedocs.io/en/latest/).
Funding
-------
Horizon 2020 Framework Programme (785907, HBP SGA2); Horizon 2020 Framework Programme (945539, HBP SGA3); Vetenskapsrådet (VR-M-2017-02806, VR-M-2020-01652); Swedish e-science Research Center (SeRC); KTH Digital Futures.
We acknowledge the use of Fenix Infrastructure resources, which are partially funded from the European Union's Horizon 2020 research and innovation programme through the ICEI project under the grant agreement No. 800858.
The computations and testing were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at PDC KTH partially funded by the Swedish Research Council through grant agreement no. 2018-05973.
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"description": "\ntreem - neuron morphology processing tool\n=========================================\n\nModule provides data structure and command-line tools for accessing and\nmanipulating the digital reconstructions of the neuron morphology in\nStockley-Wheal-Cannon format (SWC).\n\n[](https://badge.fury.io/py/treem)\n[](https://github.com/a1eko/treem/blob/master/LICENSE)\n\n[](https://codecov.io/gh/a1eko/treem)\n[](https://treem.readthedocs.io/en/latest/?badge=latest)\n[](https://doi.org/10.5281/zenodo.4890844)\n\n\n\nMain classes\n------------\n\nAccess to morphological data from the source code is supported by the\nclasses ``Tree``, ``Node``, ``Morph`` and ``SWC``.\n\n* ``Tree`` - Recursive tree data structure\n* ``Node`` - Morphology data storage\n* ``Morph`` - Neuron morphology representation\n* ``SWC`` - Definitions of the data format\n\n\nCommands\n--------\n\nCommon operations with SWC files are possible via the ``swc`` command-line\ntool:\n\n swc <command> [options] file\n\nor sometimes more convenient as\n\n swc <command> file [file ...] [options] \n\nList of ``swc`` commands:\n\n* ``check`` - Test morphology reconstruction for structural consistency\n* ``convert`` - Convert morphology to compliant SWC format\n* ``find`` - Locate single nodes in the reconstruction\n* ``measure`` - Calculate morphometric features\n* ``modify`` - Manipulate morphology reconstruction\n* ``render`` - Display 3D model of the reconstruction\n* ``repair`` - Correct reconstruction errors\n* ``view`` - Show morphology structure\n\n\nInstallation\n------------\n\nInstall the latest stable release:\n\n pip3 install treem\n\nInstall a development version:\n\n pip3 install git+https://github.com/a1eko/treem\n\nSee also ``pip3`` documentation for installation alternatives.\n\n\nDependencies\n------------\n\nModule ``treem`` has minimal runtime dependencies:\n\n* ``python`` >= 3.7\n* ``matplotlib``\n* ``numpy``\n* ``PyOpenGL`` (optional) enables ``swc render`` command\n\nFor testing and documentation, ``treem`` needs development packages with\nthird-party extensions:\n\n* ``sphinx`` with ``napoleon`` and ``programoutput``\n* ``pytest`` with ``pytest-cov``\n* ``coverage``\n\n\nDocumentation\n-------------\n\nDocumentation is available online at [Read the Docs](https://treem.readthedocs.io/en/latest/).\n\n\nFunding\n-------\n\nHorizon 2020 Framework Programme (785907, HBP SGA2); Horizon 2020 Framework Programme (945539, HBP SGA3); Vetenskapsr\u00e5det (VR-M-2017-02806, VR-M-2020-01652); Swedish e-science Research Center (SeRC); KTH Digital Futures.\n\nWe acknowledge the use of Fenix Infrastructure resources, which are partially funded from the European Union's Horizon 2020 research and innovation programme through the ICEI project under the grant agreement No. 800858.\n\nThe computations and testing were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at PDC KTH partially funded by the Swedish Research Council through grant agreement no. 2018-05973.\n",
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