napari-spatial-correlation-plotter 0.0.2__tar.gz → 1.0.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/LICENSE +0 -0
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/MANIFEST.in +0 -0
- {napari_spatial_correlation_plotter-0.0.2/src/napari_spatial_correlation_plotter.egg-info → napari_spatial_correlation_plotter-1.0.0}/PKG-INFO +39 -19
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/README.md +35 -10
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/pyproject.toml +0 -0
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/setup.cfg +1 -9
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter/__init__.py +1 -1
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter/_nice_colormap.py +4 -0
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter/_widget.py +20 -0
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter/napari.yaml +0 -0
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0/src/napari_spatial_correlation_plotter.egg-info}/PKG-INFO +39 -19
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter.egg-info/SOURCES.txt +1 -2
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter.egg-info/dependency_links.txt +0 -0
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter.egg-info/entry_points.txt +0 -0
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter.egg-info/requires.txt +1 -8
- {napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/src/napari_spatial_correlation_plotter.egg-info/top_level.txt +0 -0
- napari_spatial_correlation_plotter-0.0.2/src/napari_spatial_correlation_plotter/_tests/__init__.py +0 -0
{napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/LICENSE
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{napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/MANIFEST.in
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Metadata-Version: 2.
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Name: napari-spatial-correlation-plotter
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Version: 0.0
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Version: 1.0.0
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Summary: A plugin to compute and display spatial correlation histograms in Napari
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Home-page: https://github.com/jules-vanaret/napari-spatial-correlation-plotter
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Author: Jules Vanaret
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# :herb: napari-spatial-correlation-plotter
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[](https://github.com/jules-vanaret/napari-spatial-correlation-plotter/raw/main/LICENSE)
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[](https://pypi.org/project/napari-spatial-correlation-plotter)
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[](https://python.org)
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[](https://github.com/jules-vanaret/napari-spatial-correlation-plotter/actions)
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[](https://codecov.io/gh/jules-vanaret/napari-spatial-correlation-plotter)
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[](https://napari-hub.org/plugins/napari-spatial-correlation-plotter)
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<img src="https://github.com/GuignardLab/tapenade/blob/
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<img src="https://github.com/GuignardLab/tapenade/blob/main/imgs/tapenade3.png" width="100">
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A plugin to dynamically interact with the spatial correlation heatmap obtained by comparing two continuous fields of biophysical properties in 3D tissues.
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`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
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If you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).
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`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
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## Overview
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<img src="imgs/napari_correlation_demo.gif">
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While working with large and dense 3D and 3D+time gastruloid datasets, we found that being able to visualise and interact with the data dynamically greatly helped processing it.
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During the pre-processing stage, dynamical exploration and interaction led to faster tuning of the parameters by allowing direct visual feedback, and gave key biophysical insight during the analysis stage.
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11. You can click on the `Save the figure` button to save the current plot (many formats are available, including .png, .svg, .jpeg).
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12. You can interact with the plot by manually drawing a region of interest directly on the plot to automatically select and display the corresponding cells in 3D on an independant Napari Labels layer `clustered labels`. By using a left click, you can draw an arbitrary shape. By using a right click, you can draw a rectangle. If `Shift` is pressed while drawing, several groups of cells can appear on the `clustered labels` layer, each with a different color.
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13. To trigger the grid view like in the example image, you can click on the `Toggle grid mode` button. This will display all layers in a grid view. By right clicking the button, you can parametrize the grid view (e.g number of columns, number of rows, etc).
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14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
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14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
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## Demo dataset
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A demo dataset is available [here](https://amubox.univ-amu.fr/s/igYycspAiXankWF).
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### Content
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This test dataset is composed of five 3D images.
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- `bra isotropized.tif`, `dapi isotropized.tif`, and `ecad isotropized.tif` correspond to 3 biological signals images, respectively Brachyury, Dapi, and E-Cadherin.
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- `mask.tif` is a binary mask that defines the inside/outside of the sample.
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- `labels.tif` is the nuclei segmentation performed on the Dapi channel with our custom Stardist3D model.
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### How to use
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- Load the images from the folder (either drag and drop, or "File>Open file(s)").
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- Follow instructions from the plugin repository to test the plugin.
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## How to cite
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If you use this plugin for your research, please cite us using the following reference:
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- Jules Vanaret, Alice Gros, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili (2025) <b>A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales</b>. eLife 14:RP107154 ; doi:https://doi.org/10.7554/eLife.107154.2
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## Acknowledgements
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The "napari-clusters-plotter" plugin [1] heavily inspired this plugin, most notably the `SelectFromCollection`, `MplCanvas` and `FigureToolbar` classes. The `PlotterWidget` class has been modified for the specific use case of this plugin, but the core functionalites have been adapted directly.
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napari-clusters-plotter source code is available [here](https://github.com/BiAPoL/napari-clusters-plotter/tree/main).
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## Contributing
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the coverage at least stays the same before you submit a pull request.
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[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023). napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
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## License
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[file an issue]: https://github.com/jules-vanaret/napari-spatial-correlation-plotter/issues
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[napari]: https://github.com/napari/napari
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[tox]: https://tox.readthedocs.io/en/latest/
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[pip]: https://pypi.org/project/pip/
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[PyPI]: https://pypi.org/
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{napari_spatial_correlation_plotter-0.0.2 → napari_spatial_correlation_plotter-1.0.0}/README.md
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[](https://github.com/jules-vanaret/napari-spatial-correlation-plotter/raw/main/LICENSE)
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[](https://pypi.org/project/napari-spatial-correlation-plotter)
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[](https://python.org)
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[](https://github.com/jules-vanaret/napari-spatial-correlation-plotter/actions)
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[](https://codecov.io/gh/jules-vanaret/napari-spatial-correlation-plotter)
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[](https://napari-hub.org/plugins/napari-spatial-correlation-plotter)
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A plugin to dynamically interact with the spatial correlation heatmap obtained by comparing two continuous fields of biophysical properties in 3D tissues.
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`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
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If you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).
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`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
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## Overview
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<img src="imgs/napari_correlation_demo.gif">
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While working with large and dense 3D and 3D+time gastruloid datasets, we found that being able to visualise and interact with the data dynamically greatly helped processing it.
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During the pre-processing stage, dynamical exploration and interaction led to faster tuning of the parameters by allowing direct visual feedback, and gave key biophysical insight during the analysis stage.
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11. You can click on the `Save the figure` button to save the current plot (many formats are available, including .png, .svg, .jpeg).
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12. You can interact with the plot by manually drawing a region of interest directly on the plot to automatically select and display the corresponding cells in 3D on an independant Napari Labels layer `clustered labels`. By using a left click, you can draw an arbitrary shape. By using a right click, you can draw a rectangle. If `Shift` is pressed while drawing, several groups of cells can appear on the `clustered labels` layer, each with a different color.
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13. To trigger the grid view like in the example image, you can click on the `Toggle grid mode` button. This will display all layers in a grid view. By right clicking the button, you can parametrize the grid view (e.g number of columns, number of rows, etc).
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14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
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## Demo dataset
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A demo dataset is available [here](https://amubox.univ-amu.fr/s/igYycspAiXankWF).
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### Content
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- `mask.tif` is a binary mask that defines the inside/outside of the sample.
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### How to use
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- Follow instructions from the plugin repository to test the plugin.
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## How to cite
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If you use this plugin for your research, please cite us using the following reference:
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- Jules Vanaret, Alice Gros, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili (2025) <b>A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales</b>. eLife 14:RP107154 ; doi:https://doi.org/10.7554/eLife.107154.2
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## Acknowledgements
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The "napari-clusters-plotter" plugin [1] heavily inspired this plugin, most notably the `SelectFromCollection`, `MplCanvas` and `FigureToolbar` classes. The `PlotterWidget` class has been modified for the specific use case of this plugin, but the core functionalites have been adapted directly.
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napari-clusters-plotter source code is available [here](https://github.com/BiAPoL/napari-clusters-plotter/tree/main).
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[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023). napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
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## License
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[napari]: https://github.com/napari/napari
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[PyPI]: https://pypi.org/
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"""
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Copyright (c) 2022, DFG Cluster of Excellence "Physics of Life" TU Dresden: Robert Haase, Laura Zigutyte, Marcello Zoccoler, Ryan Savill, Johannes Müller and Max Planck Institute of Molecular Physiology Dortmund: Thorsten Wagner
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"""
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def get_nice_colormap():
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"""
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Copyright (c) 2024 Jules Vanaret
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The SelectFromCollection, MplCanvas, FigureToolbar classes, and parts of
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the PlotterWidget class are licensed under
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Copyright (c) 2022, DFG Cluster of Excellence "Physics of Life" TU Dresden: Robert Haase, Laura Zigutyte, Marcello Zoccoler, Ryan Savill, Johannes Müller and Max Planck Institute of Molecular Physiology Dortmund: Thorsten Wagner
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"""
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import os
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from pathlib import Path as PathL
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from time import time
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ICON_ROOT = PathL(__file__).parent / "icons"
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"""
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This widget takes HEAVY inspiration from the napari-clusters-plotter plugin [1],
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most notably the SelectFromCollection, MplCanvas and FigureToolbar classes.
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The PlotterWidget class has been modified for the specific use case of this
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plugin, but the core functionalites have been adapted directly.
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napari-clusters-plotter source code is available at
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https://github.com/BiAPoL/napari-clusters-plotter/tree/main
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[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023).
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napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
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"""
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# TODO:
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# - add log scale to heatmap colors
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Metadata-Version: 2.
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Metadata-Version: 2.4
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Name: napari-spatial-correlation-plotter
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Version: 0.0
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Version: 1.0.0
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Summary: A plugin to compute and display spatial correlation histograms in Napari
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Home-page: https://github.com/jules-vanaret/napari-spatial-correlation-plotter
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Author: Jules Vanaret
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Requires-Dist: scikit-image
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Requires-Dist: pytest; extra == "testing"
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Requires-Dist: napari; extra == "testing"
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Requires-Dist: pyqt5; extra == "testing"
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Requires-Dist: tapenade
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Dynamic: license-file
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# :herb: napari-spatial-correlation-plotter
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[](https://github.com/jules-vanaret/napari-spatial-correlation-plotter/raw/main/LICENSE)
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[](https://pypi.org/project/napari-spatial-correlation-plotter)
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[](https://python.org)
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[](https://github.com/jules-vanaret/napari-spatial-correlation-plotter/actions)
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[](https://codecov.io/gh/jules-vanaret/napari-spatial-correlation-plotter)
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[](https://napari-hub.org/plugins/napari-spatial-correlation-plotter)
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<img src="https://github.com/GuignardLab/tapenade/blob/
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<img src="https://github.com/GuignardLab/tapenade/blob/main/imgs/tapenade3.png" width="100">
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A plugin to dynamically interact with the spatial correlation heatmap obtained by comparing two continuous fields of biophysical properties in 3D tissues.
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`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
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If you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).
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`napari-spatial-correlation-plotter` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.
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## Overview
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<img src="imgs/napari_correlation_demo.gif">
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While working with large and dense 3D and 3D+time gastruloid datasets, we found that being able to visualise and interact with the data dynamically greatly helped processing it.
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During the pre-processing stage, dynamical exploration and interaction led to faster tuning of the parameters by allowing direct visual feedback, and gave key biophysical insight during the analysis stage.
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11. You can click on the `Save the figure` button to save the current plot (many formats are available, including .png, .svg, .jpeg).
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12. You can interact with the plot by manually drawing a region of interest directly on the plot to automatically select and display the corresponding cells in 3D on an independant Napari Labels layer `clustered labels`. By using a left click, you can draw an arbitrary shape. By using a right click, you can draw a rectangle. If `Shift` is pressed while drawing, several groups of cells can appear on the `clustered labels` layer, each with a different color.
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13. To trigger the grid view like in the example image, you can click on the `Toggle grid mode` button. This will display all layers in a grid view. By right clicking the button, you can parametrize the grid view (e.g number of columns, number of rows, etc).
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14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
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14. You can switch between 2D and 3D view at all time by clicking on the `Toggle 2D/3D view` button (it resembles a square when in 2D mode, or a cube when in 3D mode).
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## Demo dataset
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A demo dataset is available [here](https://amubox.univ-amu.fr/s/igYycspAiXankWF).
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### Content
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This test dataset is composed of five 3D images.
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- `bra isotropized.tif`, `dapi isotropized.tif`, and `ecad isotropized.tif` correspond to 3 biological signals images, respectively Brachyury, Dapi, and E-Cadherin.
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- `mask.tif` is a binary mask that defines the inside/outside of the sample.
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- `labels.tif` is the nuclei segmentation performed on the Dapi channel with our custom Stardist3D model.
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### How to use
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- Load the images from the folder (either drag and drop, or "File>Open file(s)").
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- Follow instructions from the plugin repository to test the plugin.
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## How to cite
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If you use this plugin for your research, please cite us using the following reference:
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- Jules Vanaret, Alice Gros, Valentin Dunsing-Eichenauer, Agathe Rostan, Philippe Roudot, Pierre-François Lenne, Léo Guignard, Sham Tlili (2025) <b>A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales</b>. eLife 14:RP107154 ; doi:https://doi.org/10.7554/eLife.107154.2
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## Acknowledgements
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The "napari-clusters-plotter" plugin [1] heavily inspired this plugin, most notably the `SelectFromCollection`, `MplCanvas` and `FigureToolbar` classes. The `PlotterWidget` class has been modified for the specific use case of this plugin, but the core functionalites have been adapted directly.
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napari-clusters-plotter source code is available [here](https://github.com/BiAPoL/napari-clusters-plotter/tree/main).
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## Contributing
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the coverage at least stays the same before you submit a pull request.
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[1] Zigutyte, L., Savill, R., Müller, J., Zoccoler, M., Wagner, T., & Haase, R. (2023). napari-clusters-plotter. Zenodo. https://doi.org/10.5281/zenodo.5884657
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## License
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[file an issue]: https://github.com/jules-vanaret/napari-spatial-correlation-plotter/issues
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[napari]: https://github.com/napari/napari
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[PyPI]: https://pypi.org/
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