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HDF5 and Zarr store large numerical arrays in chunks (Zarr is the cloud-friendly one, and OME-Zarr its bio-imaging profile for slide tiles); Parquet stores tables column by column for fast analytical queries.
Hierarchical Data Format is a set of file formats for storing and organising large amounts of data, maintained by The HDF Group (Wikipedia); ARCHS4 distributes its million-sample expression matrix as HDF5. Zarr is an open standard for chunked multidimensional arrays designed for random access in cloud storage (Wikipedia), and OME-NGFF, or OME-Zarr, is the Open Microscopy Environment's next-generation file format for bio-imaging, including whole-slide pyramids. Apache Parquet is a column-oriented storage format for analytical queries (Wikipedia), used for clinical and metadata tables in DuckDB or Spark.
Shares Analytical databases as a data catalogue (DuckDB, PostgreSQL), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Digital pathology and whole-slide images (WSI), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Digital pathology and whole-slide images (WSI), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Digital pathology and whole-slide images (WSI), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Analytical databases as a data catalogue (DuckDB, PostgreSQL), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Digital pathology and whole-slide images (WSI), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares AnnData and h5ad files, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.