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. 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 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. | ||
molecules Spatially-resolved molecules such as individual RNA molecules measured by FISH assays. | ||
cell-sets Lists or hierarchies of cell sets, used to store cell type assignments or automated clustering results. | ||
raster Multi-scale multiplexed imaging data, including OME-TIFF files and OME-NGFF stores. |
| |
expression-matrix Gene expression matrices. | ||
neighborhoods | ||
genomic-profiles Genomic profiles, such as ATAC-seq profiles. |