| Name | spatialdata JSON |
| Version |
0.5.0
JSON |
| download |
| home_page | None |
| Summary | Spatial data format. |
| upload_time | 2025-08-15 21:38:50 |
| maintainer | None |
| docs_url | None |
| author | scverse |
| requires_python | >=3.10 |
| license | BSD 3-Clause License
Copyright (c) 2022, scverse®
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# SpatialData: an open and universal framework for processing spatial omics data.
[![Tests][badge-tests]][link-tests]
[](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[](https://codecov.io/gh/scverse/spatialdata)
[](https://spatialdata.scverse.org/en/latest/)
[](https://zenodo.org/badge/latestdoi/487366481)
[](https://pepy.tech/project/spatialdata)
[](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)
[![Documentation][badge-pypi]][link-pypi]
[](https://anaconda.org/conda-forge/spatialdata)
[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-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.
[//]: # "numfocus-fiscal-sponsor-attribution"
spatialdata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
The spatialdata project also received support by the Chan Zuckerberg Initiative.
<div align="center">
<a href="https://numfocus.org/project/scverse">
<img height="60px"
src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
align="center">
</a>
</div>
<br>
- **The library is currently under review.** We expect there to be changes as the community provides feedback. We have an announcement channel for communicating these changes, please see the contact section below.
- The SpatialData storage format is built on top of the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) specification.
## Getting started
Please refer to the [documentation][link-docs]. In particular:
- [API documentation][link-api].
- [Design doc][link-design-doc] (includes the roadmap).
- [Example notebooks][link-notebooks].
Another useful resource to get started is the source code of the [`spatialdata-io`](https://github.com/scverse/spatialdata-io) package, which shows example of how to read data from common technologies.
## Installation
Check out the docs for more complete [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html). To get started with the "batteries included" installation, you can install via pip:
```bash
pip install "spatialdata[extra]"
```
~~or via conda:~~
Update Feb 2025: `spatialdata` cannot be currently be installed via `conda` because some dependencies of our dependencies are not updated in `conda-forge` and we are still waiting for an update. Please install from `pip`; the latest versions of the `spatialdata` libraries are always available via `PyPI`.
```bash
mamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spatialdata-plot
```
## Limitations
- Code only manually tested for Windows machines. Currently the framework is being developed using Linux, macOS and Windows machines, but it is automatically tested only for Linux and macOS machines.
## Contact
To get involved in the discussion, or if you need help to get started, you are welcome to use the following options.
- <ins>Chat</ins> via [`scverse` Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial) (public or 1 to 1).
- <ins>Forum post</ins> in the [scverse discourse forum](https://discourse.scverse.org/).
- <ins>Bug report/feature request</ins> via the [GitHub issue tracker][issue-tracker].
- <ins>Zoom call</ins> as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, [schedule here](https://hackmd.io/enWU826vRai-JYaL7TZaSw).
Finally, especially relevant for for developers that are building a library upon `spatialdata`, please follow this channel for:
- <ins>Announcements</ins> on new features and important changes [Zulip](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/spatialdata.20announcements).
## Citation
Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x
<!-- Links -->
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/scverse/spatialdata/issues
[design doc]: https://scverse-spatialdata.readthedocs.io/en/stable/design_doc.html
[link-docs]: https://spatialdata.scverse.org/en/stable/
[link-api]: https://spatialdata.scverse.org/en/stable/api.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[badge-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml/badge.svg
[link-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml
Raw data
{
"_id": null,
"home_page": null,
"name": "spatialdata",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.10",
"maintainer_email": "scverse <giov.pll@gmail.com>",
"keywords": null,
"author": "scverse",
"author_email": null,
"download_url": "https://files.pythonhosted.org/packages/31/29/9e7c46cf134854e27996fd4af7d27e184e57f5083b019e9757c4add6a600/spatialdata-0.5.0.tar.gz",
"platform": null,
"description": "\n\n# SpatialData: an open and universal framework for processing spatial omics data.\n\n[![Tests][badge-tests]][link-tests]\n[](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)\n[](https://codecov.io/gh/scverse/spatialdata)\n[](https://spatialdata.scverse.org/en/latest/)\n[](https://zenodo.org/badge/latestdoi/487366481)\n[](https://pepy.tech/project/spatialdata)\n[](https://github.com/scverse/spatialdata/actions/workflows/release.yaml)\n[![Documentation][badge-pypi]][link-pypi]\n[](https://anaconda.org/conda-forge/spatialdata)\n\n[badge-pypi]: https://badge.fury.io/py/spatialdata.svg\n[link-pypi]: https://pypi.org/project/spatialdata/\n\nSpatialData 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.\n\n- [spatialdata-io](https://github.com/scverse/spatialdata-io): load data from common spatial omics technologies into spatialdata.\n- [spatialdata-plot](https://github.com/scverse/spatialdata-plot): Static plotting library for spatialdata.\n- [napari-spatialdata](https://github.com/scverse/napari-spatialdata): napari plugin for interactive exploration and annotation of spatial data.\n\n[//]: # \"numfocus-fiscal-sponsor-attribution\"\n\nspatialdata is part of the scverse\u00ae project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nIf you like scverse\u00ae and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\nThe spatialdata project also received support by the Chan Zuckerberg Initiative.\n\n<div align=\"center\">\n <a href=\"https://numfocus.org/project/scverse\">\n <img height=\"60px\"\n src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n align=\"center\">\n </a>\n</div>\n<br>\n\n\n\n- **The library is currently under review.** We expect there to be changes as the community provides feedback. We have an announcement channel for communicating these changes, please see the contact section below.\n- The SpatialData storage format is built on top of the [OME-NGFF](https://ngff.openmicroscopy.org/latest/) specification.\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular:\n\n- [API documentation][link-api].\n- [Design doc][link-design-doc] (includes the roadmap).\n- [Example notebooks][link-notebooks].\n\nAnother useful resource to get started is the source code of the [`spatialdata-io`](https://github.com/scverse/spatialdata-io) package, which shows example of how to read data from common technologies.\n\n## Installation\n\nCheck out the docs for more complete [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html). To get started with the \"batteries included\" installation, you can install via pip:\n\n```bash\npip install \"spatialdata[extra]\"\n```\n\n~~or via conda:~~\nUpdate Feb 2025: `spatialdata` cannot be currently be installed via `conda` because some dependencies of our dependencies are not updated in `conda-forge` and we are still waiting for an update. Please install from `pip`; the latest versions of the `spatialdata` libraries are always available via `PyPI`.\n\n```bash\nmamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spatialdata-plot\n```\n\n## Limitations\n\n- Code only manually tested for Windows machines. Currently the framework is being developed using Linux, macOS and Windows machines, but it is automatically tested only for Linux and macOS machines.\n\n## Contact\n\nTo get involved in the discussion, or if you need help to get started, you are welcome to use the following options.\n\n- <ins>Chat</ins> via [`scverse` Zulip](https://scverse.zulipchat.com/#narrow/stream/315824-spatial) (public or 1 to 1).\n- <ins>Forum post</ins> in the [scverse discourse forum](https://discourse.scverse.org/).\n- <ins>Bug report/feature request</ins> via the [GitHub issue tracker][issue-tracker].\n- <ins>Zoom call</ins> as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, [schedule here](https://hackmd.io/enWU826vRai-JYaL7TZaSw).\n\nFinally, especially relevant for for developers that are building a library upon `spatialdata`, please follow this channel for:\n\n- <ins>Announcements</ins> on new features and important changes [Zulip](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/spatialdata.20announcements).\n\n## Citation\n\nMarconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x\n\n<!-- Links -->\n\n[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/scverse/spatialdata/issues\n[design doc]: https://scverse-spatialdata.readthedocs.io/en/stable/design_doc.html\n[link-docs]: https://spatialdata.scverse.org/en/stable/\n[link-api]: https://spatialdata.scverse.org/en/stable/api.html\n[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html\n[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html\n[badge-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml/badge.svg\n[link-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml\n",
"bugtrack_url": null,
"license": "BSD 3-Clause License\n \n Copyright (c) 2022, scverse\u00ae\n All rights reserved.\n \n Redistribution and use in source and binary forms, with or without\n modification, are permitted provided that the following conditions are met:\n \n 1. Redistributions of source code must retain the above copyright notice, this\n list of conditions and the following disclaimer.\n \n 2. Redistributions in binary form must reproduce the above copyright notice,\n this list of conditions and the following disclaimer in the documentation\n and/or other materials provided with the distribution.\n \n 3. Neither the name of the copyright holder nor the names of its\n contributors may be used to endorse or promote products derived from\n this software without specific prior written permission.\n \n THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\n FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\n DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\n SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\n CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\n OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.",
"summary": "Spatial data format.",
"version": "0.5.0",
"project_urls": {
"Documentation": "https://spatialdata.scverse.org/en/latest",
"Home-page": "https://github.com/scverse/spatialdata.git",
"Source": "https://github.com/scverse/spatialdata.git"
},
"split_keywords": [],
"urls": [
{
"comment_text": null,
"digests": {
"blake2b_256": "8b45f16a66337b05f6c4829d0e9bdc0c6f876e5a193a1cdc1c88f7dee5a3762a",
"md5": "0cf4406df559afa2f5a7ba453941498b",
"sha256": "0d513c7da63e4b05a197af70605c51bf074c3fceb81fcdda282637efef425ea6"
},
"downloads": -1,
"filename": "spatialdata-0.5.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "0cf4406df559afa2f5a7ba453941498b",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 185333,
"upload_time": "2025-08-15T21:38:49",
"upload_time_iso_8601": "2025-08-15T21:38:49.045431Z",
"url": "https://files.pythonhosted.org/packages/8b/45/f16a66337b05f6c4829d0e9bdc0c6f876e5a193a1cdc1c88f7dee5a3762a/spatialdata-0.5.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": null,
"digests": {
"blake2b_256": "31299e7c46cf134854e27996fd4af7d27e184e57f5083b019e9757c4add6a600",
"md5": "b1000f6f91aafb62420a54dc7689c4c2",
"sha256": "3c316cdebe7306e887f9383c360993a1db0a7bd1b00b5673d831d23769acf63b"
},
"downloads": -1,
"filename": "spatialdata-0.5.0.tar.gz",
"has_sig": false,
"md5_digest": "b1000f6f91aafb62420a54dc7689c4c2",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.10",
"size": 326264,
"upload_time": "2025-08-15T21:38:50",
"upload_time_iso_8601": "2025-08-15T21:38:50.213045Z",
"url": "https://files.pythonhosted.org/packages/31/29/9e7c46cf134854e27996fd4af7d27e184e57f5083b019e9757c4add6a600/spatialdata-0.5.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-08-15 21:38:50",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "scverse",
"github_project": "spatialdata",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "spatialdata"
}
