morphometrics

A plugin for quantifying shape and neighborhoods from images.


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    A plugin for quantifying shape and neighborhoods from images.


    This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

    Installation

    conda environment file

    You can install morphometrics via our conda environment file. To do so, first install anaconda or miniconda on your computer. Then, download the environment.yml file (right click the link and "Save as..."). In your terminal, navigate to the directory you downloaded the environment.yml file to:

    cd <path/to/downloaded/environment.yml>

    Then create the morphometrics environment using

    conda env create -f environment.yml

    Once the environment has been created, you can activate it and use morphometrics as described below.

    conda activate morphometrics

    Development installation

    To install latest development version :

    pip install git+https://github.com/kevinyamauchi/morphometrics.git

    Example applications

    measure the distance between surfaces

    napari plugin for measuring properties of segmented objects (regionprops)

    object classification

    mesh binary mask

    Contributing

    Contributions are very welcome. Tests can be run with tox, 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, "morphometrics" is free and open source software

    Issues

    If you encounter any problems, please file an issue along with a detailed description.

    Version:

    • 0.0.5

    Release date:

    • 02 June 2022

    First released:

    • 17 March 2022

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 0
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • leidenalg
    • napari-clusters-plotter
    • napari-skimage-regionprops
    • napari[all]
    • numpy (<1.22)
    • pyclesperanto-prototype
    • pymeshfix
    • scanpy
    • scikit-image (>0.19.0)
    • scikit-learn
    • tqdm
    • trimesh[easy]

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