Package: napari-zelda
napari-zeldaZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napariAuthors: Rocco D'Antuono, Giuseppina PisignanoArticle: Front. Comput. Sci., 04 January 2022 |https://doi.org/10.3389/fcomp.2021.796117Examples of 2D and 3D data sets:https://doi.org/10.5281/zenodo.5651284What you can do with ZELDA plugin for napariThe plugin can be used to analyze 2D/3D image data sets.Multidimensional images (each channel corresponding to a napari layer) can be used to:Segment objects such as cells and organelles in 2D/3D.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)ActinMitochondriaMergeParent cell cytoplasmsChildren mitochondriaChildren labelled by ParentsThe images shown above are available in thedocsfolder of this repository and were segmented using ZELDA with the following parameters:Parent objectsGB: sigma=2.0-> Th_parents=60.0-> DistMap-> Maxima: min_dist=10Children objectsGB: sigma=0.3-> Th_children=450.0 -> DistMap-> Maxima: min_dist=2For small monitors it may be convenient to float the protocol panelFloat a panel in napariPlot results within napari interface.HistogramScatterplotCustomize an image analysis workflow in graphical mode (no scripting knowledge required).Custom image analysis workflowImport and Export Protocols (image analysis workflows) in graphical mode (share with the community!).Import and Export of ZELDA ProtocolsInstallationOption A.The easiest option is to use the napari interface to install ZELDA (make sure napari!=0.4.11):Plugins / Install/Uninstall Package(s)Choose ZELDAZELDA is installedLaunch ZELDAOption B.You can installnapari-zeldaalso viapip. 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
conda install napari pyqt  
pip install napari-zeldaOption C.Alternatively, clone the repository and install locally viapip:pip install -e .Option D.Get the latest code withgitandpip:conda create -y -n napari-env python=3.8 git
conda activate napari-env
conda install napari pyqt
pip install git+https://github.com/RoccoDAnt/napari-zelda.gitSpecificationsThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.The GUI has been developed usingmagicguiwidgets, while the image analysis and processing include functions fromscikit-image,SciPy, andNumPy. Results are handled withpandasanddatatable. Plots are obtained withmatplotlib.ContributingContributions are welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.Users can add new protocol steps to their local installation usingmagicguiwidgets.
Code can be added at the end of napari_zelda.py file:###Add here new functionalities for ZELDA ######@magicgui(layout="vertical")###def new_functionality_widget(viewer: 'napari.Viewer'):###...###End###LicenseDistributed under the terms of theBSD-3license,
"napari-zelda" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.