https://github.com/kvslab/morphman
A collection of tools for manipulation of morphological features in patient-specific geometries
https://github.com/kvslab/morphman
biomedical geometric-algorithms morphology vascular
Last synced: 8 months ago
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A collection of tools for manipulation of morphological features in patient-specific geometries
- Host: GitHub
- URL: https://github.com/kvslab/morphman
- Owner: KVSlab
- License: other
- Created: 2018-07-03T12:46:02.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-09-26T14:07:35.000Z (over 1 year ago)
- Last Synced: 2025-10-17T23:33:08.071Z (8 months ago)
- Topics: biomedical, geometric-algorithms, morphology, vascular
- Language: Python
- Homepage: https://morphman.readthedocs.io/en/latest/
- Size: 59.5 MB
- Stars: 33
- Watchers: 6
- Forks: 13
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
## [morphMan - Morphological Manipulation](https://morphman.readthedocs.io)
[](https://morphman.readthedocs.io/en/latest/?badge=latest)
[](https://doi.org/10.21105/joss.01065)
[](https://codecov.io/gh/KVSlab/morphMan)
[](https://anaconda.org/conda-forge/morphman)
[](https://github.com/kvslab/morphman/actions/workflows/lint_and_test.yaml)
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](https://en.wikipedia.org/wiki/Internal_carotid_artery)
, 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](https://morphman.readthedocs.io/en/latest/).
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](https://morphman.readthedocs.io/en/latest/getting_started.html) 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