https://github.com/bluebrain/morphio

A python and C++ library for reading and writing neuronal morphologies

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
21 of 44 committers (47.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.1%) to scientific vocabulary

Keywords

glia mitochondria morphology neuron neurons python reticulum

Keywords from Contributors

neuroscience morphologies build-tools hpsf radiuss spack parameter optimisations genetic-algorithm electrophysiology

Last synced: 5 months ago · JSON representation

Repository

A python and C++ library for reading and writing neuronal morphologies

Basic Info

Host: GitHub
Owner: BlueBrain
License: apache-2.0
Language: C++
Default Branch: master
Homepage: https://morphio.readthedocs.io
Size: 7.59 MB

Statistics

Stars: 28
Watchers: 12
Forks: 24
Open Issues: 41
Releases: 50

Archived

Topics

glia mitochondria morphology neuron neurons python reticulum

Created over 8 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog Contributing License Authors

README.rst

.. warning::
   The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
   Future development will take place at: https://github.com/openbraininstitute/MorphIO

.. image:: doc/source/logo/BBP-MorphIO.jpg


|license| |docs|

MorphIO
=======

Documentation
-------------

MorphIO documentation is built and hosted on `readthedocs `_.

* `latest snapshot `_
* `latest release `_

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:

.. code-block:: bash

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

and then:

.. code-block:: bash

   # 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

.. |license| image:: https://img.shields.io/pypi/l/morphio
                :target: https://github.com/BlueBrain/morphio/blob/master/COPYING.LESSER

.. |docs| image:: https://readthedocs.org/projects/morphio/badge/?version=latest
             :target: https://morphio.readthedocs.io/
             :alt: documentation status

Owner

Name: The Blue Brain Project
Login: BlueBrain
Kind: organization
Email: bbp.opensource@epfl.ch
Location: Geneva, Switzerland

Website: https://portal.bluebrain.epfl.ch/
Repositories: 226
Profile: https://github.com/BlueBrain

Open Source Software produced and used by the Blue Brain Project

GitHub Events

Total

Issues event: 2
Delete event: 3
Issue comment event: 9
Push event: 6
Pull request review event: 5
Pull request event: 9
Create event: 4

Last Year

Issues event: 2
Delete event: 3
Issue comment event: 9
Push event: 6
Pull request review event: 5
Pull request event: 9
Create event: 4

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 757
Total Committers: 44
Avg Commits per committer: 17.205
Development Distribution Score (DDS): 0.699

Top Committers

Name	Email	Commits
Benoit Coste	b**e@e**h	228
MikeG	m**t@e**h	88
Benoit Coste	b**e@p**m	79
Stefan Eilemann	S**n@e**h	78
Juan Hernando Vieites	j**o@e**h	58
Daniel Nachbaur	d**r@e**h	48
asanin-epfl	5**l@u**m	27
Eleftherios Zisis	e**s@e**h	24
Juan Hernando	j**o@f**s	15
Stefan Eilemann	e**n@g**m	15
Matthias Wolf	m**t@s**t	10
Matthias Wolf	m**f@e**h	9
Mohamed-Ghaïth Kaabi	k**g@u**m	8
snigdha	s**r@g**m	7
Daniel Nachbaur	d**r@g**m	5
Raphael Dumusc	r**c@e**h	4
Arseny V. Povolotsky	c**s@y**u	4
Jafet Villafranca	j**z@e**h	4
tomdele	4**e@u**m	4
Chevtchenko Grigori	g**o@e**h	4
Ben Beasley	c**e@m**t	3
Nicolas Cornu	n**u@e**h	3
Adrien Devresse	a**e@e**h	2
Tristan Carel	t**l@g**m	2
wizmer	b**e@g**m	2
Fernando Pereira	f**e@g**m	2
Benoit Jean-Albert Coste	b**e@b**h	2
haleepfl	4**l@u**m	2
Robin De Schepper	r**3@g**m	2
Coste Benoît Jean-Albert	b**e@b**h	2
and 14 more...

Committer Domains (Top 20 + Academic)

epfl.ch: 19 upm.es: 1 urjc.es: 1 bluebrain351.epfl.ch: 1 bluebrain354.epfl.ch: 1 musicinmybrain.net: 1 yandex.ru: 1 sushinara.net: 1 fi.upm.es: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 50
Total pull requests: 118
Average time to close issues: 8 months
Average time to close pull requests: about 2 months
Total issue authors: 20
Total pull request authors: 16
Average comments per issue: 5.24
Average comments per pull request: 1.11
Merged pull requests: 97
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 2
Pull requests: 14
Average time to close issues: 25 days
Average time to close pull requests: 7 days
Issue authors: 2
Pull request authors: 6
Average comments per issue: 12.5
Average comments per pull request: 0.5
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 1

View more stats

Top Authors

Issue Authors

arnaudon (8)
Helveg (7)
eleftherioszisis (6)
mgeplf (5)
adrien-berchet (4)
wizmer (3)
1uc (2)
marwan-abdellah (2)
matz-e (2)
ssssarah (1)
DexterAntonio (1)
jaehongpark-neuro (1)
musicinmybrain (1)
st4rl3ss (1)
NadirRoGue (1)

Pull Request Authors

mgeplf (69)
eleftherioszisis (23)
1uc (16)
matz-e (7)
bbpgithubaudit (5)
NadirRoGue (3)
adrien-berchet (3)
musicinmybrain (3)
Helveg (2)
rowleya (2)
dependabot[bot] (2)
ferdonline (2)
penguinpee (1)
sanjayankur31 (1)
alex4200 (1)

Top Labels

Issue Labels

cpp (1) good first issue (1)

Pull Request Labels

dependencies (2)

Packages

Total packages: 2
Total downloads:
- pypi 14,190 last-month

Total dependent packages: 15
(may contain duplicates)
Total dependent repositories: 9
(may contain duplicates)
Total versions: 46
Total maintainers: 5

pypi.org: morphio

A neuron morphology IO library

Homepage: https://github.com/BlueBrain/MorphIO/
Documentation: https://morphio.readthedocs.io/
License: Apache License 2.0
Latest release: 3.4.0
published over 1 year ago

Versions: 46
Dependent Packages: 15
Dependent Repositories: 9
Downloads: 14,190 Last month

Rankings

Dependent packages count: 1.0%

Downloads: 3.0%

Dependent repos count: 4.8%

Average: 5.9%

Forks count: 8.2%

Stargazers count: 12.3%

Maintainers (4)

bbp.opensource mgevaert GianlucaFicarelli obi.maintainer

Last synced: 6 months ago

spack.io: py-morphio

Python library for reading / writing morphology files

Homepage: https://github.com/BlueBrain/MorphIO
License: []

Versions: 0
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Forks count: 21.0%

Stargazers count: 25.3%

Average: 26.2%

Dependent packages count: 58.6%

Maintainers (1)

tristan0x

Last synced: 6 months ago

Dependencies

setup.py pypi

numpy >=1.14.1

tests/requirement_tests.txt pypi

h5py >=2.9.0 test
numpy >=1.14.2 test
pytest >=6.0 test

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