A neuron morphology IO library

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  • License: Apache License 2.0
  • Author: Blue Brain Project, EPFL
  • Tags computational neuroscience, morphology, neuron, neurolucida, neuromorphology
  • Requires: Python >=3.8
  • Provides-Extra: docs
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Project description

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license documentation status

MorphIO

Documentation

MorphIO documentation is built and hosted on readthedocs.

Introduction

MorphIO is a library for reading and writing neuron morphology files. It supports the following formats:

  • SWC

  • ASC (aka. neurolucida)

  • H5 v1

  • H5 v2 is not supported anymore, see H5v2

It provides 3 C++ classes that are the starting point of every morphology analysis:

  • Soma: contains the information related to the soma.

  • Section: a section is the succession of points between two bifurcations. To the bare minimum the Section object will contain the section type, the position and diameter of each point.

  • Morphology: the morphology object contains general information about the loaded cell but also provides accessors to the different sections.

One important concept is that MorphIO is split into a read-only part and a read/write one.

H5v2

Starting at version 2.6.0, the file format h5v2 is no longer supported. If you have morphologies in this format, you can convert them to h5v1 with:

pip install "morphio<2.6" "morph-tool==2.3.0"

and then:

# single file, OUTPUT must end with `.h5`
morph-tool convert file INPUTFILE OUTPUT
# bulk conversion
morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR

Contributing

If you want to improve the project or you see any issue, every contribution is welcome. Please check the contribution guidelines for more information.

Acknowledgements

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

This research was supported by the EBRAINS research infrastructure, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).

License

MorphIO is licensed under the terms of the Apache License 2.0. See LICENSE.txt for further details.

Copyright (c) 2013-2024 Blue Brain Project/EPFL

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Avatar for bbp.opensource from gravatar.com bbp.opensource Avatar for GianlucaFicarelli from gravatar.com GianlucaFicarelli Avatar for mgevaert from gravatar.com mgevaert

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  • License: Apache License 2.0
  • Author: Blue Brain Project, EPFL
  • Tags computational neuroscience, morphology, neuron, neurolucida, neuromorphology
  • Requires: Python >=3.8
  • Provides-Extra: docs
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