Data Types and File Types

Vitessce supports several data types which denote in an abstract sense the type of observations contained in a file. For each data type, Vitessce may support multiple file types 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 TypeFile TypesConvert 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 pointers to OME-TIFF files and Zarr stores.
expression-matrix
Gene expression matrices.
neighborhoods
genomic-profiles
Genomic profiles, such as ATAC-seq profiles.

Constants#

We provide the DataType and FileType constants mapping from JavaScript object keys to strings. For convenience, you may specify a shorter alias such as dt or ft when the variables are imported.

Data Types#

import { DataType as dt } from 'vitessce';
KeyValue
dt.CELLScells
dt.CELL_SETScell-sets
dt.EXPRESSION_MATRIXexpression-matrix
dt.GENOMIC_PROFILESgenomic-profiles
dt.MOLECULESmolecules
dt.NEIGHBORHOODSneighborhoods
dt.RASTERraster

File Types#

import { FileType as ft } from 'vitessce';
KeyValue
ft.CELLS_JSONcells.json
ft.CELL_SETS_JSONcell-sets.json
ft.EXPRESSION_MATRIX_ZARRexpression-matrix.zarr
ft.GENOMIC_PROFILES_ZARRgenomic-profiles.zarr
ft.MOLECULES_JSONmolecules.json
ft.NEIGHBORHOODS_JSONneighborhoods.json
ft.RASTER_JSONraster.json
ft.CLUSTERS_JSONclusters.json
ft.GENES_JSONgenes.json
ft.ANNDATA_CELL_SETS_ZARRanndata-cell-sets.zarr
ft.ANNDATA_CELLS_ZARRanndata-cells.zarr
ft.ANNDATA_EXPRESSION_MATRIX_ZARRanndata-expression-matrix.zarr