# AnnData — Annotated Data (h5ad format) ## Overview AnnData (Annotated Data) is a data format and Python object for single-cell genomics, developed by the Theislab at Helmholtz Munich (Fabian Theis group) and now co-maintained with the Broad Institute. The `.h5ad` file format (HDF5-based) is the serialised form of AnnData objects and has become a common exchange format for single-cell RNA-seq, ATAC-seq, spatial transcriptomics, and multi-omics data in the Python ecosystem. It stores a cell-by-gene count matrix together with cell metadata, gene metadata, and dimensionality reduction embeddings in a single file. ## Connections - Annotations use: [[Cell Ontology]] (cell types), [[UBERON]] (anatomy) - Upstream source: [[SAM-BAM-CRAM]] (count matrices from alignment and quantification) ## Resources - https://anndata.readthedocs.io - https://github.com/scverse/anndata