Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
☆277May 7, 2026Updated last week
Alternatives and similar repositories for sopa
Users that are interested in sopa are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An open and interoperable data framework for spatial omics data☆370Updated this week
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆130Updated this week
- BANKSY: spatial clustering☆147May 2, 2026Updated 2 weeks ago
- ☆95May 11, 2026Updated last week
- Join subcellular Visium HD bins into cells☆142May 8, 2026Updated last week
- 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.
- Automatically annotate cell types, consistently across samples.☆21Updated this week
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Apr 25, 2026Updated 3 weeks ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆171Updated this week
- From geospatial to spatial -omics☆103May 8, 2026Updated last week
- Interoperability between SpatialData and the Xenium Explorer☆26Jul 31, 2024Updated last year
- Bayesian Segmentation of Spatial Transcriptomics Data☆205Apr 30, 2026Updated 2 weeks ago
- Static plotting for spatialdata☆80Updated this week
- comseg☆24Feb 6, 2025Updated last year
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆173May 8, 2026Updated last week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Analyzing cellular niches in spatial transcriptomics data☆35Nov 18, 2024Updated last year
- Interactive visualization of spatial omics data☆85May 12, 2026Updated last week
- Vitessce is a visual integration tool for exploration of spatial single-cell experiments.☆248May 6, 2026Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Nov 16, 2025Updated 6 months ago
- Code used to benchmark Xenium☆81Apr 10, 2026Updated last month
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆370Updated this week
- Spatial Single-Cell Analysis Toolkit☆111Mar 11, 2026Updated 2 months ago
- Python API and Jupyter widget for Vitessce☆66Apr 17, 2026Updated last month
- GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems☆39Jul 11, 2025Updated 10 months ago
- 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.
- Spatial Single Cell Analysis in Python☆568May 12, 2026Updated last week
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆109May 11, 2026Updated last week
- ☆38Dec 13, 2023Updated 2 years ago
- A multi-dimensional spatial image data structure for scientific Python.☆44Aug 8, 2025Updated 9 months ago
- ☆71Jan 18, 2023Updated 3 years ago
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆55Nov 13, 2025Updated 6 months ago
- ☆46Feb 13, 2026Updated 3 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆90Mar 16, 2026Updated 2 months ago
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆105Updated 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.
- An R package for performing cell typing in SMI and other single cell data☆49May 1, 2026Updated 2 weeks ago
- An introduction to OME-Zarr for big bioimaging data☆26Updated this week
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆49Jul 16, 2024Updated last year
- ☆66May 5, 2026Updated 2 weeks ago
- Python package for Probe set selection for targeted spatial transcriptomics.☆49Nov 8, 2025Updated 6 months ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆79Nov 13, 2025Updated 6 months ago
- Extension of SpatialExperiment with sf☆57May 6, 2026Updated last week