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morphMan

morphMan: Automated manipulation of vascular geometries - Published in JOSS (2019)

https://github.com/kvslab/morphman

Science Score: 93.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

biomedical geometric-algorithms morphology vascular

Scientific Fields

Mathematics Computer Science - 37% confidence
Last synced: 6 months ago · JSON representation

Repository

A collection of tools for manipulation of morphological features in patient-specific geometries

Basic Info
Statistics
  • Stars: 33
  • Watchers: 6
  • Forks: 13
  • Open Issues: 15
  • Releases: 6
Topics
biomedical geometric-algorithms morphology vascular
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License

README.md

morphMan - Morphological Manipulation

Documentation Status DOI codecov Conda Version CI

Create a stenois

Manipulation of the internal carotid artery, by introducing an artificial stenosis.

Description

morphMan (morphological manipulation) is a collection of tools for automated and objective manipulation and reconstruction of morphological features of patient-specific vascular geometries. In the tutorials we examplify the usage by manipulating internal carotid arteries , but the tool can be applied to any geometry with a tubular shape.

The goal of morphMan is to provide research groups, and other individuals, with a set of tools to investigate the impact of altering morphological features in patient-specific geometries. For instance, morphMan can be used to investigate how cross-sectional area, bifurcation angles, and over all curvature change the local hemodynamics.

Authors

morphMan is developed by

  • Aslak W. Bergersen
  • Henrik A. Kjeldsberg

Licence

morphMan is licensed under the GNU GPL, version 3 or (at your option) any later version.

morphMan is Copyright (2016-2022) by the authors.

Documentation

For an introduction to morphMan, and tutorials, please refer to the documentation.

If you use wish to use morphMan for journal publications, please cite the following the following journal article for the methods:

Bergersen, Aslak W., Henrik A. Kjeldsberg, and Kristian Valen‐Sendstad. "A Framework for Automated and Objective Modification of Tubular Structures: Application to the Internal Carotid Artery." International Journal for Numerical Methods in Biomedical Engineering (2020): e3330.

And the journal article from JOSS for the software:

Kjeldsberg et al., (2019). morphMan: Automated manipulation of vascular geometries. Journal of Open Source Software, 4(35), 1065, https://doi.org/10.21105/joss.01065

Installation

For reference, morphMan requires the following dependencies: VTK 9.1, Numpy 1.23, SciPy 1.8.1, and VMTK 1.5. If you are on Windows, macOS or Linux you can install all the general dependencies through conda-forge. First install Anaconda or Miniconda, then add conda-forge to your channels with: conda config --add channels conda-forge conda config --set channel_priority strict

Once the conda-forge channel has been enabled, morphman can be installed with conda:

conda create -n your_environment morphman

or with mamba:

mamba create -n your_environment morphman

You can then activate your environment with morphman by running

source activate your_environment

You are now all set, and can start manipulating your geometries. To get started, we have created some tutorials for the different modules within morphMan.

Contact

The latest version of this software can be obtained from

https://github.com/KVSlab/morphMan

Please report bugs and other issues through the issue tracker at:

https://github.com/KVSlab/morphMan/issues

Owner

  • Name: KVSlab
  • Login: KVSlab
  • Kind: organization

JOSS Publication

morphMan: Automated manipulation of vascular geometries
Published
March 20, 2019
DOI
Volume 4, Issue 35, Page 1065
Authors
Henrik A. Kjeldsberg
Department of Computational Physiology, Simula Research Laboratory
Aslak W. Bergersen ORCID
Department of Computational Physiology, Simula Research Laboratory
Kristian Valen-Sendstad ORCID
Department of Computational Physiology, Simula Research Laboratory
Editor
Tania Allard ORCID
Tags
geometric-algorithms morphology vascular biomedical
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 3
  • Watch event: 2
  • Issue comment event: 5
  • Fork event: 1
Last Year
  • Issues event: 3
  • Watch event: 2
  • Issue comment event: 5
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 669
  • Total Committers: 4
  • Avg Commits per committer: 167.25
  • Development Distribution Score (DDS): 0.366
Past Year
  • Commits: 17
  • Committers: 1
  • Avg Commits per committer: 17.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
hkjeldsberg h****g@l****o 424
Aslak Bergersen a****n@g****m 225
henrik.kjeldsberg h****g@b****o 19
Arfon Smith a****n 1
Committer Domains (Top 20 + Academic)
bankaxept.no: 1 live.no: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 35
  • Total pull requests: 53
  • Average time to close issues: 6 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 13
  • Total pull request authors: 3
  • Average comments per issue: 1.69
  • Average comments per pull request: 0.25
  • Merged pull requests: 51
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 hours
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • aslakbergersen (11)
  • SMSadat98 (5)
  • rlizzo (4)
  • hkjeldsberg (3)
  • michaelbernini (2)
  • mdsiamahmed26 (2)
  • keiyamamo (2)
  • myousefi2016 (1)
  • johannesring (1)
  • MartinaSchena (1)
  • JonathanPham (1)
  • DucoG (1)
  • JIsaacW (1)
Pull Request Authors
  • hkjeldsberg (46)
  • aslakbergersen (8)
  • arfon (1)
Top Labels
Issue Labels
enhancement (10) refactor (2) bug (1) good first issue (1)
Pull Request Labels
enhancement (2) refactor (1)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
conda-forge.org: morphman
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 24.3%
Average: 41.8%
Forks count: 43.8%
Stargazers count: 47.5%
Dependent packages count: 51.6%
Last synced: 6 months ago

Dependencies

.github/workflows/lint_and_test.yaml actions
  • actions/cache v3 composite
  • actions/checkout v4 composite
  • actions/checkout v3 composite
  • actions/setup-python v5 composite
  • codecov/codecov-action v3 composite
  • mamba-org/setup-micromamba v1 composite
docs/requirements.txt pypi
  • docutils <0.18
  • sphinx ==5
  • sphinx_rtd_theme *
pyproject.toml pypi
  • scipy *
environment.yml conda
  • python 3.10
  • vmtk