napari-stress

napari-stress

Interactive surface analysis in napari for measuring mechanical stresses in biological tissues


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    License PyPI Python Version tests codecov pre-commit PyPI - Downloads napari hub DOI

    This plugin provides tools for the analysis of surfaces in Napari, such as utilities to determine and refine the surface-representation of objects using a ray-casting approach and calculate the curvature of surfaces. It re-implements code in Napari that was written for Gross et al. (2021): STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses and has been made open source in this repository.

    Usage

    For documentation on how to use napari-stress both interactively from the napari-viewer or from code, please visit the documentation

    Installation

    Create a new conda environment with the following command. If you have never used conda before, please read this guide first.

    conda create -n napari-stress Python=3.9 napari jupyterlab -c conda-forge
    conda activate napari-stress

    You can then install napari-stress using pip:

    pip install napari-stress

    Issues

    To report bugs, request new features or get in touch, please open an issue or tag @EL_Pollo_Diablo on image.sc.

    See also

    There are other napari plugins with similar / overlapping functionality

    Contributing

    Contributions are very welcome. Tests can be run with pytest, please ensure the coverage at least stays the same before you submit a pull request.

    License

    Distributed under the terms of the BSD-3 license, "napari-stress" is free and open source software

    Acknowledgements

    This project was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy – EXC2068 - Cluster of Excellence "Physics of Life" of TU Dresden.

    Version:

    • 0.1.2

    Release date:

    • 08 November 2022

    First released:

    • 02 June 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 10
    • Forks: 2
    • Issues + PRs: 31

    Python versions supported:

    Operating system:

    Requirements:

    • numpy
    • vedo (>=2022.4.1)
    • napari
    • vispy
    • matplotlib
    • tqdm
    • scipy
    • pandas
    • scikit-image
    • napari-tools-menu (>=0.1.15)
    • napari-process-points-and-surfaces (>=0.3.0)
    • aicsimageio
    • napari-segment-blobs-and-things-with-membranes
    • mpmath
    • pyshtools (<=4.10.0)
    • napari-matplotlib
    • pygeodesic

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