scverse ecosystem update: Scanpy, Squidpy, and spatialdata

The scverse consortium — the community-maintained ecosystem for single-cell and spatial omics analysis in Python — has released updates across its core packages in early 2026. Scanpy remains the foundational toolkit for single-cell gene expression analysis, built on the anndata data structure.

Squidpy provides scalable spatial molecular data analysis and visualization, while the newer spatialdata and spatialdata-plot packages offer a unified framework for managing and visualizing complex spatial omics experiments including Visium, MERFISH, and Slide-seq data.