Data Types and File Types

Vitessce supports several data types (datasets[].files[].type in the JSON-based view config) which denote in an abstract sense the type of observations contained in a file (e.g., matrix, dataframe, image). For each data type, Vitessce may support multiple file types (datasets[].files[].fileType) which denote specific schemas and file formats that Vitessce knows how to read.

For example, a file that conforms to the cells data type may contain cell-level observations, such as cell IDs and embedding (e.g. UMAP and PCA) coordinates for each cell. But depending on which file format is more convenient, you may opt to use the cells.json or anndata-cells.zarr file type.

Data Types and File Types

Data Type	File Types	Convert from...
cells Cells, their positions (spatially and for dimensionality-reduction scatterplots), their segmentations as polygons, and other per-cell attributes.	cells.json anndata-cells.zarr	AnnData Loom Seurat SnapATAC
molecules Spatially-resolved molecules such as individual RNA molecules measured by FISH assays.	molecules.json
cell-sets Lists or hierarchies of cell sets, used to store cell type assignments or automated clustering results.	cell-sets.json anndata-cell-sets.zarr	AnnData Loom Seurat SnapATAC
raster Multi-scale multiplexed imaging data, including OME-TIFF files and OME-NGFF stores.	raster.ome-zarr (OME-NGFF) raster.json OME-TIFF Bioformats-Zarr (precursor to OME-NGFF)	Proprietary Formats
expression-matrix Gene expression matrices.	expression-matrix.zarr anndata-expression-matrix.zarr clusters.json genes.json	AnnData Loom Seurat
neighborhoods	neighborhoods.json
genomic-profiles Genomic profiles, such as ATAC-seq profiles.	genomic-profiles.zarr	SnapATAC