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8 changes: 6 additions & 2 deletions README.md
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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
[![documentation badge](https://readthedocs.org/projects/scverse-spatialdata/badge/?version=latest)](https://spatialdata.scverse.org/en/latest/)
[![DOI](https://zenodo.org/badge/487366481.svg)](https://zenodo.org/badge/latestdoi/487366481)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20056407.svg)](https://doi.org/10.5281/zenodo.20056407)
[![Downloads](https://static.pepy.tech/badge/spatialdata)](https://pepy.tech/project/spatialdata)
[![Release](https://github.com/scverse/spatialdata/actions/workflows/release.yaml/badge.svg?event=release)](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)
[![Documentation][badge-pypi]][link-pypi]
Expand All@@ -15,11 +15,15 @@
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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8 changes: 7 additions & 1 deletion docs/index.md
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# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

Expand DownExpand Up@@ -119,3 +123,5 @@ references.md
[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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Update tutorials; add R and JS links by LucaMarconato · Pull Request #1133 · scverse/spatialdata · GitHub
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Update tutorials; add R and JS links#1133

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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20056407.svg)](https://doi.org/10.5281/zenodo.20056407)
[![Downloads](https://static.pepy.tech/badge/spatialdata)](https://pepy.tech/project/spatialdata)
[![Release](https://github.com/scverse/spatialdata/actions/workflows/release.yaml/badge.svg?event=release)](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)
[![Documentation][badge-pypi]][link-pypi]
Expand All@@ -15,11 +15,15 @@
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

Expand DownExpand Up@@ -119,3 +123,5 @@ references.md
[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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Update tutorials; add R and JS links by LucaMarconato · Pull Request #1133 · scverse/spatialdata · GitHub
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Update tutorials; add R and JS links#1133

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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
[![documentation badge](https://readthedocs.org/projects/scverse-spatialdata/badge/?version=latest)](https://spatialdata.scverse.org/en/latest/)
[![DOI](https://zenodo.org/badge/487366481.svg)](https://zenodo.org/badge/latestdoi/487366481)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20056407.svg)](https://doi.org/10.5281/zenodo.20056407)
[![Downloads](https://static.pepy.tech/badge/spatialdata)](https://pepy.tech/project/spatialdata)
[![Release](https://github.com/scverse/spatialdata/actions/workflows/release.yaml/badge.svg?event=release)](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)
[![Documentation][badge-pypi]][link-pypi]
Expand All@@ -15,11 +15,15 @@
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

Expand DownExpand Up@@ -119,3 +123,5 @@ references.md
[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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Update tutorials; add R and JS links by LucaMarconato · Pull Request #1133 · scverse/spatialdata · GitHub
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Update tutorials; add R and JS links#1133

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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
[![documentation badge](https://readthedocs.org/projects/scverse-spatialdata/badge/?version=latest)](https://spatialdata.scverse.org/en/latest/)
[![DOI](https://zenodo.org/badge/487366481.svg)](https://zenodo.org/badge/latestdoi/487366481)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20056407.svg)](https://doi.org/10.5281/zenodo.20056407)
[![Downloads](https://static.pepy.tech/badge/spatialdata)](https://pepy.tech/project/spatialdata)
[![Release](https://github.com/scverse/spatialdata/actions/workflows/release.yaml/badge.svg?event=release)](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)
[![Documentation][badge-pypi]][link-pypi]
Expand All@@ -15,11 +15,15 @@
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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Expand Up@@ -6,11 +6,15 @@

# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

Expand DownExpand Up@@ -119,3 +123,5 @@ references.md
[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
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[![Documentation][badge-pypi]][link-pypi]
Expand All@@ -15,11 +15,15 @@
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

Expand DownExpand Up@@ -119,3 +123,5 @@ references.md
[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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Update tutorials; add R and JS links by LucaMarconato · Pull Request #1133 · scverse/spatialdata · GitHub
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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
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[![DOI](https://zenodo.org/badge/487366481.svg)](https://zenodo.org/badge/latestdoi/487366481)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20056407.svg)](https://doi.org/10.5281/zenodo.20056407)
[![Downloads](https://static.pepy.tech/badge/spatialdata)](https://pepy.tech/project/spatialdata)
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[![Documentation][badge-pypi]][link-pypi]
Expand All@@ -15,11 +15,15 @@
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

Expand DownExpand Up@@ -119,3 +123,5 @@ references.md
[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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Update tutorials; add R and JS links by LucaMarconato · Pull Request #1133 · scverse/spatialdata · GitHub
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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
[![documentation badge](https://readthedocs.org/projects/scverse-spatialdata/badge/?version=latest)](https://spatialdata.scverse.org/en/latest/)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20056407.svg)](https://doi.org/10.5281/zenodo.20056407)
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[![Release](https://github.com/scverse/spatialdata/actions/workflows/release.yaml/badge.svg?event=release)](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)
[![Documentation][badge-pypi]][link-pypi]
Expand All@@ -15,11 +15,15 @@
[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

Expand DownExpand Up@@ -119,3 +123,5 @@ references.md
[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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LucaMarconato
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May 21, 2026

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Update tutorials; add R and JS links
#1133
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8 changes: 6 additions & 2 deletions
README.md

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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
[![documentation badge](https://readthedocs.org/projects/scverse-spatialdata/badge/?version=latest)](https://spatialdata.scverse.org/en/latest/)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20056407.svg)](https://doi.org/10.5281/zenodo.20056407)
[![Downloads](https://static.pepy.tech/badge/spatialdata)](https://pepy.tech/project/spatialdata)
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[![Documentation][badge-pypi]][link-pypi]
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[badge-pypi]: https://badge.fury.io/py/spatialdata.svg
[link-pypi]: https://pypi.org/project/spatialdata/

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.
- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.
- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.
- [SpatialData (R)](https://github.com/HelenaLC/SpatialData): R implementation of the SpatialData framework.
- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js): JavaScript/TypeScript implementation of the SpatialData framework.

[//]: # "numfocus-fiscal-sponsor-attribution"

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docs/index.md

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# An open and universal framework for processing spatial omics data.

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.
SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.

This page provides documentation on how to install, use, and extend the core `spatialdata` library. See the links below to learn more about other packages in the SpatialData ecosystem.

- `spatialdata-io`: load data from common spatial omics technologies into `spatialdata` ([repository][spatialdata-io-repo], [documentation][spatialdata-io-docs]).
- `spatialdata-plot`: Static plotting library for `spatialdata` ([repository][spatialdata-plot-repo], [documentation][spatialdata-plot-docs]).
- `napari-spatialdata-repo`: napari plugin for interactive exploration and annotation of `spatialdata` ([repository][napari-spatialdata-repo], [documentation][napari-spatialdata-docs]).
- `SpatialData` (R): R implementation of the SpatialData framework ([repository][spatialdata-r-repo]).
- `SpatialData.js`: JavaScript/TypeScript implementation of the SpatialData framework ([repository][spatialdata-js-repo]).

Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.

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[napari-spatialdata-docs]: https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html
[spatialdata-io-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
[spatialdata-plot-docs]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[spatialdata-r-repo]: https://github.com/HelenaLC/SpatialData
[spatialdata-js-repo]: https://github.com/Taylor-CCB-Group/SpatialData.js
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