morphio

A neuron morphology IO library

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Project description

MorphIO

Documentation

MorphIO documentation is built and hosted on readthedocs <http://morphio.readthedocs.org/>.

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 GNU Lesser General Public License version 3. Refer to COPYING.LESSER and COPYING for details.

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Release history Release notifications | RSS feed

3.4.0

Oct 11, 2024

3.3.10

Oct 11, 2024

3.3.9

Apr 24, 2024

3.3.8

Apr 24, 2024

3.3.7

Dec 11, 2023

3.3.6

Jul 4, 2023

3.3.5

Jun 7, 2023

3.3.4

Jan 17, 2023

3.3.3

Mar 3, 2022

3.3.2

Nov 9, 2021

This version

3.3.0

Jun 16, 2021

3.2.0

Jun 9, 2021

3.1.1

May 3, 2021

3.1.0

May 3, 2021

3.0.2

Apr 12, 2021

3.0.0

Mar 24, 2021

2.7.1

Mar 11, 2021

2.7.0

Feb 12, 2021

2.6.2

Feb 11, 2021

2.6.1

Feb 8, 2021

2.6.0

Feb 5, 2021

2.5.3

Feb 4, 2021

2.5.2

Feb 4, 2021

2.5.1

Feb 3, 2021

2.5.0

Jan 29, 2021

2.3.11

Sep 17, 2020

2.3.10

Jun 4, 2020

2.3.9

Apr 23, 2020

2.3.8

Mar 26, 2020

2.3.7

Mar 12, 2020

2.3.6

Mar 6, 2020

2.3.5

Mar 2, 2020

2.3.4

Jan 22, 2020

2.3.3

Jan 14, 2020

2.3.2

Jan 8, 2020

2.3.1

Jan 6, 2020

2.3.0

Sep 30, 2019

2.2.2

Sep 16, 2019

2.2.1

Sep 2, 2019

2.2.0

Jul 19, 2019

2.1.5

Jul 16, 2019

2.1.4

Jul 16, 2019

2.1.3

Jun 27, 2019

2.1.2

Jun 21, 2019

2.1.1

Jun 6, 2019

2.0.7

Mar 12, 2019

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