# napari-zelda
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[](https://pypi.org/project/napari-zelda)
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[](https://codecov.io/gh/RoccoDAnt/napari-zelda)
## ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari
#### Authors: Rocco D'Antuono, Giuseppina Pisignano
###### Article: Front. Comput. Sci., 04 January 2022 | https://doi.org/10.3389/fcomp.2021.796117
###### Examples of 2D and 3D data sets: [https://doi.org/10.5281/zenodo.5651284](https://zenodo.org/record/5651284#.YYgn_WDP2Ch)
----------------------------------
## What you can do with ZELDA plugin for napari
The plugin can be used to analyze 2D/3D image data sets.
Multidimensional images (each channel corresponding to a napari layer) can be used to:
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)
 <br> **Actin** |  <br> **Mitochondria**|  <br> **Merge**
------ | ------| -----
 <br> **Parent cell cytoplasms** |  <br> **Children mitochondria**|  <br> **Children labelled by Parents**
The images shown above are available in the [**docs**](https://github.com/RoccoDAnt/napari-zelda/tree/main/docs) folder of this repository and were segmented using ZELDA with the following parameters:
| **Parent objects** | **GB: sigma=2.0-> Th_parents=60.0-> DistMap-> Maxima: min_dist=10** |
| -----| ----|
| **Children objects** | **GB: sigma=0.3-> Th_children=450.0 -> DistMap-> Maxima: min_dist=2**|
For small monitors it may be convenient to float the protocol panel
| <br> **Float a panel in napari** |
------ |
3. Plot results within napari interface.
 <br> **Histogram** |  <br> **Scatterplot**|
------ | ------|
4. Customize an image analysis workflow in graphical mode (no scripting knowledge required).
|  <br> **Custom image analysis workflow** |
------ |
5. Import and Export Protocols (image analysis workflows) in graphical mode (share with the community!).
|  <br> **Import and Export of ZELDA Protocols** |
------ |
## Installation
**Option A.** The easiest option is to use the napari interface to install ZELDA (make sure napari!=0.4.11):
1. Plugins / Install/Uninstall Package(s)
2. Choose ZELDA
3. ZELDA is installed
4. Launch ZELDA
**Option B.** You can install `napari-zelda` also 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
conda install napari pyqt
pip install napari-zelda
**Option C.** Alternatively, clone the repository and install locally via [pip]:
pip install -e .
**Option D.** Get the latest code with [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) and [pip]:
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.git
## Specifications
This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
The GUI has been developed using [magicgui](https://github.com/napari/magicgui) widgets, while the image analysis and processing include functions from [scikit-image](https://scikit-image.org/), [SciPy](https://scipy.org/), and [NumPy](https://numpy.org/). Results are handled with [pandas](https://pandas.pydata.org/) and [datatable](https://datatable.readthedocs.io/en/latest/). Plots are obtained with [matplotlib](https://matplotlib.org/).
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started
and review the napari docs for plugin developers:
https://napari.org/docs/plugins/index.html
-->
## 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.
Users can add new protocol steps to their local installation using [magicgui](https://github.com/napari/magicgui) widgets.
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###
## 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.
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/RoccoDAnt/napari-zelda/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
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"description": "# napari-zelda\r\n\r\n[](https://github.com/RoccoDAnt/napari-zelda/raw/master/LICENSE)\r\n[](https://pypi.org/project/napari-zelda)\r\n[](https://python.org)\r\n[](https://github.com/RoccoDAnt/napari-zelda/actions)\r\n[](https://codecov.io/gh/RoccoDAnt/napari-zelda)\r\n\r\n## ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari\r\n#### Authors: Rocco D'Antuono, Giuseppina Pisignano\r\n\r\n###### Article: Front. Comput. Sci., 04 January 2022 | https://doi.org/10.3389/fcomp.2021.796117\r\n\r\n###### Examples of 2D and 3D data sets: [https://doi.org/10.5281/zenodo.5651284](https://zenodo.org/record/5651284#.YYgn_WDP2Ch)\r\n----------------------------------\r\n\r\n## What you can do with ZELDA plugin for napari\r\nThe plugin can be used to analyze 2D/3D image data sets. \r\nMultidimensional images (each channel corresponding to a napari layer) can be used to:\r\n\r\n1. Segment objects such as cells and organelles in 2D/3D.\r\n\r\n2. 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.\r\n\r\n Example: cell cytoplasms (parent objects) and mitochondria (child objects)\r\n  <br> **Actin** |  <br> **Mitochondria**|  <br> **Merge**\r\n ------ | ------| -----\r\n  <br> **Parent cell cytoplasms** |  <br> **Children mitochondria**|  <br> **Children labelled by Parents**\r\n\r\nThe images shown above are available in the [**docs**](https://github.com/RoccoDAnt/napari-zelda/tree/main/docs) folder of this repository and were segmented using ZELDA with the following parameters:\r\n\r\n\r\n | **Parent objects** | **GB: sigma=2.0-> Th_parents=60.0-> DistMap-> Maxima: min_dist=10** |\r\n | -----| ----|\r\n | **Children objects** | **GB: sigma=0.3-> Th_children=450.0 -> DistMap-> Maxima: min_dist=2**|\r\n\r\nFor small monitors it may be convenient to float the protocol panel\r\n\r\n | <br> **Float a panel in napari** |\r\n ------ |\r\n\r\n3. Plot results within napari interface.\r\n\r\n  <br> **Histogram** |  <br> **Scatterplot**|\r\n ------ | ------|\r\n\r\n4. Customize an image analysis workflow in graphical mode (no scripting knowledge required).\r\n\r\n |  <br> **Custom image analysis workflow** |\r\n ------ |\r\n\r\n5. Import and Export Protocols (image analysis workflows) in graphical mode (share with the community!).\r\n\r\n |  <br> **Import and Export of ZELDA Protocols** |\r\n ------ |\r\n\r\n## Installation\r\n\r\n**Option A.** The easiest option is to use the napari interface to install ZELDA (make sure napari!=0.4.11):\r\n1. Plugins / Install/Uninstall Package(s)\r\n\r\n \r\n\r\n2. Choose ZELDA\r\n\r\n\r\n3. ZELDA is installed\r\n\r\n\r\n4. Launch ZELDA\r\n\r\n\r\n\r\n**Option B.** You can install `napari-zelda` also via [pip]. For the best experience, create a conda environment and use napari!=0.4.11, using the following instructions:\r\n\r\n conda create -y -n napari-env python=3.8 \r\n conda activate napari-env\r\n conda install napari pyqt \r\n pip install napari-zelda \r\n\r\n\r\n**Option C.** Alternatively, clone the repository and install locally via [pip]:\r\n\r\n pip install -e .\r\n\r\n**Option D.** Get the latest code with [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) and [pip]:\r\n\r\n conda create -y -n napari-env python=3.8 git\r\n conda activate napari-env\r\n conda install napari pyqt\r\n pip install git+https://github.com/RoccoDAnt/napari-zelda.git\r\n\r\n\r\n## Specifications\r\n\r\nThis [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.\r\n\r\nThe GUI has been developed using [magicgui](https://github.com/napari/magicgui) widgets, while the image analysis and processing include functions from [scikit-image](https://scikit-image.org/), [SciPy](https://scipy.org/), and [NumPy](https://numpy.org/). Results are handled with [pandas](https://pandas.pydata.org/) and [datatable](https://datatable.readthedocs.io/en/latest/). Plots are obtained with [matplotlib](https://matplotlib.org/). \r\n<!--\r\nDon't miss the full getting started guide to set up your new package:\r\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\r\n\r\nand review the napari docs for plugin developers:\r\nhttps://napari.org/docs/plugins/index.html\r\n-->\r\n\r\n\r\n## Contributing\r\n\r\nContributions are welcome. Tests can be run with [tox], please ensure\r\nthe coverage at least stays the same before you submit a pull request.\r\n\r\nUsers can add new protocol steps to their local installation using [magicgui](https://github.com/napari/magicgui) widgets.\r\nCode can be added at the end of napari_zelda.py file:\r\n\r\n>###Add here new functionalities for ZELDA ###\r\n>\r\n>###@magicgui(layout=\"vertical\")\r\n>\r\n>###def new_functionality_widget(viewer: 'napari.Viewer'):\r\n>\r\n>###...\r\n>\r\n>###\r\n>\r\n>###End###\r\n\r\n\r\n\r\n## License\r\n\r\nDistributed under the terms of the [BSD-3] license,\r\n\"napari-zelda\" is free and open source software\r\n\r\n## Issues\r\n\r\nIf you encounter any problems, please [file an issue] along with a detailed description.\r\n\r\n[napari]: https://github.com/napari/napari\r\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\r\n[@napari]: https://github.com/napari\r\n[MIT]: http://opensource.org/licenses/MIT\r\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\r\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\r\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\r\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\r\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\r\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\r\n\r\n[file an issue]: https://github.com/RoccoDAnt/napari-zelda/issues\r\n\r\n[napari]: https://github.com/napari/napari\r\n[tox]: https://tox.readthedocs.io/en/latest/\r\n[pip]: https://pypi.org/project/pip/\r\n[PyPI]: https://pypi.org/\r\n",
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