napari-zelda

ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari


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    ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari

    Authors: Rocco D'Antuono, Giuseppina Pisignano

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

    What you can do with ZELDA plugin for napari

    1. Segment objects such as cells and organelles in 2D/3D.

    2. Segment two populations in 2D/3D (e.g. cells and organelles, nuclei and nuclear spots, tissue structures and cells) establishing the "Parent-Child" relation: count how many mitochondria are contained in each cell, how many spots localize in every nucleus, how many cells are within a tissue compartment.

    Example: cell cytoplasms (parent objects) and mitochondria (child objects)


    Actin

    Mitochondria

    Merge

    Parent cell cytoplasms

    Children mitochondria

    Children labelled by Parents
    1. Plot results within napari interface.


      Histogram

      Scatterplot
    2. Customize an image analysis workflow in graphical mode (no scripting knowledge required).


      Custom image analysis workflow
    3. Import and Export Protocols (image analysis workflows) in graphical mode (share with the community!).


      Import and Export of ZELDA Protocols

    Installation

    Option A. You can install napari-zelda via pip. For the best experience, create a conda environment and use napari!=0.4.11, using the following instructions:

    conda create -y -n napari-env python==3.8  
    conda activate napari-env  
    pip install "napari[all]"  
    pip install napari-zelda  

    Option B. Alternatively, clone the repository and install locally via pip:

    pip install -e .

    Option C. Another option is to use the napari interface to install it (make sure napari!=0.4.11):

    1. Plugins / Install/Uninstall Package(s)

    2. Choose ZELDA

    3. ZELDA is installed

    4. Launch ZELDA

    Contributing

    Contributions are 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, "napari-zelda" is free and open source software

    Issues

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

    Version:

    • 0.1.10

    Release date:

    • 26 January 2022

    First released:

    • 17 October 2021

    License:

    • BSD-3-Clause

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 11
    • Forks: 3
    • Issues + PRs: 4

    Python versions supported:

    Operating system:

    Requirements:

    • Information not submitted

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