https://github.com/bluebrain/tmd

A python package for the topological analysis of neurons.

Science Score: 72.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
○
.zenodo.json file
✓
DOI references
Found 9 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
10 of 14 committers (71.4%) from academic institutions
✓
Institutional organization owner
Organization bluebrain has institutional domain (portal.bluebrain.epfl.ch)
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary

Keywords

analyze morphology morphology-analysis

Keywords from Contributors

neurons morphologies neuroscience genetic-algorithm evolutionary-algorithms optimisation transformers parameters computational-neuroscience biological-simulations

Last synced: 5 months ago · JSON representation ·

Repository

A python package for the topological analysis of neurons.

Basic Info

Host: GitHub
Owner: BlueBrain
License: other
Language: Python
Default Branch: master
Homepage: https://tmd.readthedocs.io/en/latest/
Size: 462 KB

Statistics

Stars: 28
Watchers: 7
Forks: 23
Open Issues: 11
Releases: 17

Archived

Topics

analyze morphology morphology-analysis

Created over 7 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog Contributing License Citation Authors

README.md

[!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/TMD

TMD

A python package for the topological analysis of neurons.

The TMD performs the topological analysis of neuronal morphologies and extracts the persistence barcodes of trees.

This Python module includes:

Basic loading of neuronal morphologies in swc and h5 file format.
Extraction of the topological descriptors of tree morphologies.
Visualization of neuronal trees and neurons.
Plotting persistence diagrams, barcodes and images.

Installation

This package should be installed using pip:

bash pip install TMD

For installation of optional viewers:

bash pip install TMD[viewer]

Usage

```python

Import the TMD toolkit in IPython

import tmd

Load a neuron

neuron = tmd.io.loadneuron('inputpathtofile/input_file.swc')

Extract the tmd of a neurite, i.e., neuronal tree

pd = tmd.methods.getpersistencediagram(neuron.neurites[0]) ```

Citation

If you use this software or method for your research, we kindly ask you to cite the following publication associated to this repository:

A Topological Representation of Branching Neuronal Morphologies

Cite this article as:

Kanari, L., Dłotko P., Scolamiero M., et al., A Topological Representation of Branching Neuronal Morphologies, Neuroinformatics 16, nᵒ 1 (2018): 3‑13. https://doi.org/10.1007/s12021-017-9341-1.

Related publications

Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex, Cerebral Cortex

Cite this article as:

Deitcher Y., Eyal G., Kanari L., et al., Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex, Cerebral Cortex, Volume 27, Issue 11, November 2017, Pages 5398–5414, https://doi.org/10.1093/cercor/bhx226

Objective Morphological Classification of Neocortical Pyramidal Cells:

Cite this article as:

Lida Kanari, Srikanth Ramaswamy, Ying Shi, Sebastien Morand, Julie Meystre, Rodrigo Perin, Marwan Abdellah, Yun Wang, Kathryn Hess, Henry Markram, Objective Morphological Classification of Neocortical Pyramidal Cells, Cerebral Cortex, Volume 29, Issue 4, April 2019, Pages 1719-1735, https://doi.org/10.1093/cercor/bhy339

Developed in Blue Brain Project.

Funding & Acknowledgment

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.

For license and authors, see LICENSE.txt and AUTHORS.md respectively.

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

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  A Topological Representation of Branching Neuronal
  Morphologies.
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - family-names: Kanari
    given-names: Lida
    orcid: 'https://orcid.org/0000-0002-9539-5070'
  - family-names: Dłotko
    given-names: Paweł
  - family-names: Scolamiero
    given-names: Martina
  - family-names: Levi
    given-names: Ran
  - family-names: Shillcock
    given-names: Julian
    orcid: 'https://orcid.org/0000-0002-7885-735X'
  - given-names: Kathryn
    family-names: Hess
    orcid: 'https://orcid.org/0000-0003-2788-9754'
  - family-names: Markram
    given-names: Henry
    orcid: 'https://orcid.org/0000-0001-6164-2590'
  - family-names: Arnaudon
    given-names: Alexis
    orcid: 'https://orcid.org/0000-0001-9486-1458'
identifiers:
  - type: doi
    value: 10.1007/s12021-017-9341-1
    description: The DOI of the related article.
repository-code: 'https://github.com/BlueBrain/TMD'
abstract: >-
  Many biological systems consist of branching
  structures that exhibit a wide variety of shapes.
  Our understanding of their systematic roles is
  hampered from the start by the lack of a
  fundamental means of standardizing the description
  of complex branching patterns, such as those of
  neuronal trees. To solve this problem, we have
  invented the Topological Morphology Descriptor
  (TMD), a method for encoding the spatial
  structure of any tree as a 'barcode', a unique
  topological signature. As opposed to traditional
  morphometrics, the TMD couples the topology of
  the branches with their spatial extents by tracking
  their topological evolution in 3-dimensional space.
  We prove that neuronal trees, as well as
  stochastically generated trees, can be accurately
  categorized based on their TMD profiles. The
  TMD retains sufficient global and local
  information to create an unbiased benchmark test
  for their categorization and is able to quantify
  and characterize the structural differences between
  distinct morphological groups. The use of this
  mathematically rigorous method will advance our
  understanding of the anatomy and diversity of
  branching morphologies.
keywords:
  - Branching morphology
  - Clustering trees
  - Neuronal morphologies
  - Topological data analysis
license: LGPL-3.0

GitHub Events

Total

Issues event: 1
Watch event: 1
Issue comment event: 1
Push event: 1
Pull request event: 1
Fork event: 2
Create event: 2

Last Year

Issues event: 1
Watch event: 1
Issue comment event: 1
Push event: 1
Pull request event: 1
Fork event: 2
Create event: 2

Committers

Last synced: 12 months ago

All Time

Total Commits: 146
Total Committers: 14
Avg Commits per committer: 10.429
Development Distribution Score (DDS): 0.479

Past Year

Commits: 3
Committers: 3
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.667

Top Committers

Name	Email	Commits
kanari	l**i@e**h	76
Adrien Berchet	a**t@e**h	29
Eleftherios Zisis	e**s@e**h	10
Benoît Coste	b**e@e**h	10
Alexis Arnaudon	a**n@g**m	8
dependabot[bot]	4****]	5
Erik Heeren	e**n@o**g	1
MikeG	m**t@e**h	1
Oren Amsalem	o**1@m**l	1
alex4200	a**z@e**h	1
nadavyayon	3****n	1
Benoit Coste	b**e@p**m	1
Julien Francioli	j**i@e**h	1
Stanislav Schmidt	s**t@c**h	1

Committer Domains (Top 20 + Academic)

epfl.ch: 7 cbdhcp-2-242.epfl.ch: 1 mail.huji.ac.il: 1 openbraininstitute.org: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 14
Total pull requests: 86
Average time to close issues: 8 months
Average time to close pull requests: about 1 month
Total issue authors: 11
Total pull request authors: 13
Average comments per issue: 1.36
Average comments per pull request: 1.34
Merged pull requests: 74
Bot issues: 0
Bot pull requests: 9

Past Year

Issues: 1
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.5
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 2

View more stats

Top Authors

Issue Authors

riddick-the-furyan (2)
Sepulcrum89 (2)
lidakanari (2)
dokato (1)
Visdoom (1)
Romane1234 (1)
adrien-berchet (1)
yanyanming77 (1)
silentsilence1 (1)
Adlily (1)
wizmer (1)

Pull Request Authors

adrien-berchet (33)
lidakanari (14)
dependabot[bot] (14)
wizmer (9)
arnaudon (8)
eleftherioszisis (7)
Stannislav (2)
alex4200 (1)
orena1 (1)
bbpgithubaudit (1)
nadavyayon (1)
mgeplf (1)
BCJongbloets (1)

Top Labels

Issue Labels

enhancement (1) bug (1)

Pull Request Labels

dependencies (14)

Packages

Total packages: 1
Total downloads:
- pypi 537 last-month

Total dependent packages: 1
Total dependent repositories: 1
Total versions: 17
Total maintainers: 4

pypi.org: tmd

A python package for the topological analysis of neurons.

Homepage: https://TMD.readthedocs.io
Documentation: https://tmd.readthedocs.io/
License: GNU Lesser General Public License v3.0
Latest release: 2.4.3
published almost 2 years ago

Versions: 17
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 537 Last month

Rankings

Dependent packages count: 4.7%

Forks count: 7.8%

Downloads: 8.4%

Average: 10.9%

Stargazers count: 12.0%

Dependent repos count: 21.7%

Maintainers (4)

bbp.opensource mgevaert GianlucaFicarelli obi.maintainer

Last synced: 6 months ago

Dependencies

.github/workflows/commitlint.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite

.github/workflows/publish-sdist.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish release/v1 composite

.github/workflows/run-tox.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
awalsh128/cache-apt-pkgs-action latest composite
codecov/codecov-action v3 composite
mikepenz/action-junit-report v3 composite

package.json npm

pyproject.toml pypi

setup.py pypi