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README.md

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[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)
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[![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)
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This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. Here you can find the [napari-spatialdata documentation](https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
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This repository contains a napari plugin for interactively exploring and annotating
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SpatialData objects. Here you can find the [napari-spatialdata documentation]
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(https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
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## Installation
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The `all` command will install the qt bindings `PyQt5`.
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You can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/latest/installation.html).
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You can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html).
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## Using napari-spatialdata as default zarr reader
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cd napari-spatialdata
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pip install -e .
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Note: when performing an editable install of `napari-spatialdata`, `spatialdata` will be reinstalled from `pip`. So, if you previously also made an editable install of `spatialdata`, you need to re-run `pip install -e .` on the `spatialdata` repository. Please find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/latest/installation.html).
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Note: when performing an editable install of `napari-spatialdata`, `spatialdata`
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will be reinstalled from `pip`. So, if you previously also made an editable install
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of `spatialdata`, you need to re-run `pip install -e .` on the `spatialdata`
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repository. Please find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html).
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## Getting started
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To learn how to use the `napari-spatialdata` plugin, please see the [documentation](https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html). To learn how to integrate napari-spatialdata into your analysis workflows, please see the [SpatialData tutorials](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks.html). In particular:
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To learn how to use the `napari-spatialdata` plugin, please see the [documentation](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html).
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To learn how to integrate napari-spatialdata into your analysis workflows, please
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see the [SpatialData tutorials](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html). In particular:
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- [Annotating regions of interest with napari](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html)
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- [Use landmark annotations to align multiple -omics layers](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/alignment_using_landmarks.html)
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- [Annotating regions of interest with napari](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/napari_rois.html)
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- [Use landmark annotations to align multiple -omics layers](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/alignment_using_landmarks.html)
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## Contributing
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