Skip to main content

Spatial data format.

Project description

SpatialData banner

SpatialData: an open and universal framework for processing spatial omics data.

Tests pre-commit.ci status codecov documentation badge DOI Downloads Release

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.

The spatialdata project uses a consensus based governance model and is fiscally sponsored by NumFOCUS. Consider making a tax-deductible donation 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.


SpatialDataOverview

  • 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 specification.

Getting started

Please refer to the documentation. In particular:

Another useful resource to get started is the source code of the spatialdata-io package, which shows example of how to read data from common technologies.

Installation

Check out the docs for more complete installation instructions. To get started with the "batteries included" installation, you can install via pip:

pip install "spatialdata[extra]"

or via conda:

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.

Finally, especially relevant for for developers that are building a library upon spatialdata, please follow this channel for:

  • Announcements on new features and important changes Zulip.

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

spatialdata-0.3.0.tar.gz (313.6 kB view details)

Uploaded Source

Built Distribution

spatialdata-0.3.0-py3-none-any.whl (179.0 kB view details)

Uploaded Python 3

File details

Details for the file spatialdata-0.3.0.tar.gz.

File metadata

  • Download URL: spatialdata-0.3.0.tar.gz
  • Upload date:
  • Size: 313.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.0.1 CPython/3.12.8

File hashes

Hashes for spatialdata-0.3.0.tar.gz
Algorithm Hash digest
SHA256 9215dd5171ac9ac0eed01a265f43092c8bdb760f0b1e994795fa274c5c638611
MD5 e6bfd45dbd09a74e8547971e5f0ed095
BLAKE2b-256 1ee1bf6cff74914efe68c1ee4c0b311dbe4fa8c48e1298d63c45409d9e4e6255

See more details on using hashes here.

File details

Details for the file spatialdata-0.3.0-py3-none-any.whl.

File metadata

  • Download URL: spatialdata-0.3.0-py3-none-any.whl
  • Upload date:
  • Size: 179.0 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.0.1 CPython/3.12.8

File hashes

Hashes for spatialdata-0.3.0-py3-none-any.whl
Algorithm Hash digest
SHA256 e060c4c93f1829771ee7a4b51c12722f658f607a2e446f981aaca54bd11a251e
MD5 3273f2e53eba20e49fc09e201ffb725d
BLAKE2b-256 e4ad63adb55dd06413e11c720917a04bd6b35092a655d5cf020b94bf9224940a

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page