The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.

## Package options

SeuratDisk uses the following options to control behaviour, users can configure these with options:

SeuratDisk.dtypes.logical_to_int

When writing logical vectors, coerce to integer types to ensure compatibility across languages (see BoolToInt for more details)

SeuratDisk.dtypes.dataframe_as_group

When writing data.frames, always write out as a group regardless of factor presence

SeuratDisk.chunking.MARGIN

Default direction for chunking datasets; choose from:

largest

Chunk along the largest dimension of a dataset

smallest

Chunk along the smallest dimension

first

Chunk along the first dimension

last

Chunk along the last dimension