An open and interoperable data framework for spatial omics data
☆387Aug 29, 2026Updated this week
Alternatives and similar repositories for spatialdata
Users that are interested in spatialdata are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆101Aug 11, 2026Updated 2 weeks ago
- Static plotting for spatialdata☆85Updated this week
- Interactive visualization of spatial omics data☆88Aug 1, 2026Updated 3 weeks ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆291Updated this week
- Spatial Single Cell Analysis in Python☆595Updated this week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Multimodal Data (.h5mu) implementation for Python☆132Updated this week
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆110Updated this week
- Python API and Jupyter widget for Vitessce☆67Aug 10, 2026Updated 2 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆89Nov 16, 2025Updated 9 months ago
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆394Updated this week
- ☆67Aug 18, 2026Updated last week
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆189Updated this week
- Probabilistic cell segmentation for in situ spatial transcriptomics☆187Updated this week
- Single-cell spatial omics analysis that makes you happy!☆72Updated this week
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Configure Vitessce using existing Scverse plotting APIs☆25Aug 7, 2026Updated 3 weeks ago
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆57Nov 13, 2025Updated 9 months ago
- Join subcellular Visium HD bins into cells☆143May 8, 2026Updated 3 months ago
- Vitessce is a visual integration tool for exploration of spatial single-cell experiments.☆264Updated this week
- Multiple-choice microscopy pipeline☆157Aug 3, 2026Updated 3 weeks ago
- ☆38Aug 15, 2026Updated 2 weeks ago
- BANKSY: spatial clustering☆159May 30, 2026Updated 3 months ago
- Python package to perform enrichment analysis from omics data.☆292Updated this week
- A multi-dimensional spatial image data structure for scientific Python.☆44Aug 8, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Package for the analysis of Transcripts outside segmented cells in ST data☆31Updated this week
- Spatial alignment of single cell transcriptomic data.☆371Jul 1, 2025Updated last year
- Single-cell perturbation analysis☆337Updated this week
- ☆31Aug 7, 2026Updated 3 weeks ago
- Fast array utilities☆15Updated this week
- Spatial Single-Cell Analysis Toolkit☆115Mar 11, 2026Updated 5 months ago
- Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse☆68Updated this week
- ☆20Aug 18, 2026Updated last week
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆80Aug 22, 2026Updated last week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- LIANA+: an all-in-one framework for cell-cell communication☆314Updated this week
- ☆18Updated this week
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆155Aug 21, 2026Updated last week
- Bayesian Segmentation of Spatial Transcriptomics Data☆212Jul 31, 2026Updated 3 weeks ago
- Interoperability between SpatialData and the Xenium Explorer☆26Jul 31, 2024Updated 2 years ago
- Annotated data.☆768Updated this week
- ☆236Jul 30, 2026Updated 3 weeks ago