morphometrics

A plugin for quantifying shape and neighborhoods from images.

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

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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

If you are on Mac OS or Linux install the following:

Mac:

conda install -c conda-forge ocl_icd_wrapper_apple

Linux:

conda install -c conda-forge ocl-icd-system

Development installation

To install latest development version :

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

Example applications

<table border="0"> <tr><td>

<img src="https://github.com/kevinyamauchi/morphometrics/raw/main/resources/surface_distance_measurement.gif" width="300"/>

</td><td>

measure the distance between surfaces

</td></tr><tr><td>

<img src="https://github.com/kevinyamauchi/morphometrics/raw/main/resources/region_props_plugin.png" width="300"/>

</td><td>

napari plugin for measuring properties of segmented objects (regionprops)

</td></tr><tr><td>

<img src="https://github.com/kevinyamauchi/morphometrics/raw/main/resources/object_classification.png" width="300"/>

</td><td>

object classification

</td></tr><tr><td>

<img src="https://github.com/kevinyamauchi/morphometrics/raw/main/resources/mesh_object.png" width="300"/>

</td><td>

mesh binary mask

</td></tr></table>

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.