napari-spatial-correlation-plotter 0.0.3__tar.gz → 1.0.1__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-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/LICENSE +0 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/MANIFEST.in +0 -0
- {napari_spatial_correlation_plotter-0.0.3/src/napari_spatial_correlation_plotter.egg-info → napari_spatial_correlation_plotter-1.0.1}/PKG-INFO +35 -20
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/README.md +28 -9
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/pyproject.toml +0 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/setup.cfg +4 -11
- napari_spatial_correlation_plotter-1.0.1/src/napari_spatial_correlation_plotter/__init__.py +4 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter/_nice_colormap.py +0 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter/_widget.py +4 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter/napari.yaml +0 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1/src/napari_spatial_correlation_plotter.egg-info}/PKG-INFO +35 -20
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter.egg-info/SOURCES.txt +1 -2
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter.egg-info/dependency_links.txt +0 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter.egg-info/entry_points.txt +0 -0
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter.egg-info/requires.txt +0 -8
- {napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/src/napari_spatial_correlation_plotter.egg-info/top_level.txt +0 -0
- napari_spatial_correlation_plotter-0.0.3/src/napari_spatial_correlation_plotter/__init__.py +0 -6
- napari_spatial_correlation_plotter-0.0.3/src/napari_spatial_correlation_plotter/_tests/__init__.py +0 -0
{napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/LICENSE
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{napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/MANIFEST.in
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Metadata-Version: 2.
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Name: napari-spatial-correlation-plotter
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Version:
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Version: 1.0.1
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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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Classifier: Programming Language :: Python
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Classifier: Topic :: Scientific/Engineering :: Image Processing
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: numpy
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Requires-Dist: napari; extra == "testing"
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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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## 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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The plugin obviously requires [napari] to run. If you don't have it yet, follow the instructions [here](https://napari.org/stable/tutorials/fundamentals/installation.html).
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Compatible with Python 3.9 to 3.13 (recommended: 3.12).
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The simplest way to install `napari-spatial-correlation-plotter` is via the [napari] plugin manager. Open Napari, go to `Plugins > Install/Uninstall Packages...` and search for `napari-spatial-correlation-plotter`. Click on the install button and you are ready to go!
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You can also install `napari-spatial-correlation-plotter` via [pip]:
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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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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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[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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## Contributing
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## License
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Distributed under the terms of the [MIT] 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-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/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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## 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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Compatible with Python 3.9 to 3.13 (recommended: 3.12).
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The simplest way to install `napari-spatial-correlation-plotter` is via the [napari] plugin manager. Open Napari, go to `Plugins > Install/Uninstall Packages...` and search for `napari-spatial-correlation-plotter`. Click on the install button and you are ready to go!
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You can also install `napari-spatial-correlation-plotter` via [pip]:
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## Demo dataset
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### Content
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### How to use
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## How to cite
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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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[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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[PyPI]: https://pypi.org/
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{napari_spatial_correlation_plotter-0.0.3 → napari_spatial_correlation_plotter-1.0.1}/pyproject.toml
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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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Name: napari-spatial-correlation-plotter
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Version:
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Version: 1.0.1
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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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Classifier: Programming Language :: Python
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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/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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## 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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The plugin obviously requires [napari] to run. If you don't have it yet, follow the instructions [here](https://napari.org/stable/tutorials/fundamentals/installation.html).
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Compatible with Python 3.9 to 3.13 (recommended: 3.12).
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The simplest way to install `napari-spatial-correlation-plotter` is via the [napari] plugin manager. Open Napari, go to `Plugins > Install/Uninstall Packages...` and search for `napari-spatial-correlation-plotter`. Click on the install button and you are ready to go!
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You can also install `napari-spatial-correlation-plotter` via [pip]:
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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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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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[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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## Contributing
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Contributions are very welcome. Tests can be run with [tox], please ensure
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## License
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Distributed under the terms of the [MIT] license,
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[file an issue]: https://github.com/jules-vanaret/napari-spatial-correlation-plotter/issues
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[PyPI]: https://pypi.org/
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