Spatial data format.
Project description
SpatialData: 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 repository contains 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.
- spatialdata-plot: Static plotting library for spatialdata.
- napari-spatialdata: napari plugin for interactive exploration and annotation of spatialdata.
- The library is currently under review. We expect there to be changes as the community provides feedback.
- To get involved in the discussion, or if you need help to get started, you are welcome to join our
scverseZulip chat and our scverse discourse forum. - The SpatialData storage format is built on top of the OME-NGFF specification.
Getting started
Please refer to the documentation. In particular:
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]"
Contact
For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.
Citation
L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023. * = equal contribution
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file spatialdata-0.0.10.tar.gz.
File metadata
- Download URL: spatialdata-0.0.10.tar.gz
- Upload date:
- Size: 183.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.1 CPython/3.11.3
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | d26dfbb7fd18eec725c7e9797d7bb89475d982ab3c601ab0f090ce7660787c62 |
|
| MD5 | 155e7918c550d7d73a3e4d811919bf66 |
|
| BLAKE2b-256 | c2c87356d22356bee7f7349a70bb0480a2c716d9ef11169e6c3f66babc9b0e31 |
Provenance
File details
Details for the file spatialdata-0.0.10-py3-none-any.whl.
File metadata
- Download URL: spatialdata-0.0.10-py3-none-any.whl
- Upload date:
- Size: 98.1 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.1 CPython/3.11.3
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | f9e8467ce47b2acd70e3e49394063212ecf00d2ce119cd071ece3dad8d1bffc5 |
|
| MD5 | e9f248177c7eb66d6b014c2a2930cace |
|
| BLAKE2b-256 | 3f6c393d521da39f26d464e8601f167ada27ef94c5a4f5c3280a5f395df14017 |
