Formats
What adata convert reads and writes besides .h5ad and .zarr. Each page
gives the format’s mapping to AnnData, its own flags, and how it streams. The
flags every conversion takes (--output, --from, --to, --compression,
--overwrite, --force) are under convert, and
Convert formats says which to use when.
| Format | --from / --to |
Read | Write |
|---|---|---|---|
| 10x Genomics HDF5 | 10x-h5 |
Cell Ranger 2 and 3+; the matrix alone of Space Ranger and Xenium | Cell Ranger 3+ layout |
| CellBender | cellbender |
remove-background 0.2 and later, with its latents |
no |
| 10x and STARsolo MTX folders | 10x-mtx |
Cell Ranger 2 and 3+, STARsolo (velocyto too), GEO prefixes | Cell Ranger 3+ layout, gzipped |
| Visium (Space Ranger) | visium |
an outs/ folder: counts, spot or bin positions or segmented cells, tissue images, scale factors (Space Ranger 1–4; Visium HD bins need pyadata-cli[spatial]) |
no |
| Xenium | xenium |
an output bundle: counts, cells and centroids, Xenium’s clusters, UMAP and PCA | no |
| Parse Biosciences | parse |
split-pipe: a run, a sample or a DGE_* folder |
no |
| loom and SCope | loom |
loompy, velocyto, kallisto|bustools, SCope; spec 2 and 3 | spec 3.0.0; a SCope loom with --scope |
| Text tables | text |
a dense matrix in .csv, .tsv, .txt and the like, gzipped too |
no |
| HDF5 matrices | hdf5 |
one 2-D dataset of a plain HDF5 file | no |
| pycisTopic pickles | cistopic |
CistopicObject, CistopicImputedFeatures (needs pyadata-cli[pickle]) |
no |
| MuData | mudata |
each modality of an .h5mu or MuData Zarr store |
.h5mu, var split by feature type |