napari-zelda

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

Authors: Rocco D'Antuono, Giuseppina Pisignano¶

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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

3. Plot results within napari interface.

   Histogram	Scatterplot

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

   Custom image analysis workflow

5. 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.