# Output data

In order to save & share multimodal data, `.h5mu` file format has been designed.

```{contents}
:local:
:depth: 3
```

```{toctree}
:maxdepth: 10
:glob: *
```

## `.h5mu` files

`.h5mu` files are the default storage for MuData objects. These are HDF5 files with a standardised structure, which is similar to the one of `.h5ad` files where AnnData objects are stored. The most noticeable distinction is `.mod` group presence where individual modalities are stored — in the same way as they would be stored in the `.h5ad` files.

```python
mdata.write("mudata.h5mu")
```

Inspect the contents of the file in the terminal:

```console
$ h5ls mudata.h5mu
mod                      Group
obs                      Group
obsm                     Group
var                      Group
varm                     Group

$ h5ls data/mudata.h5mu/mod
atac                     Group
rna                      Group
```

## AnnData inside `.h5mu`

Individual modalities in the `.h5mu` file are stored in exactly the same way as AnnData objects. This, together with the hierarchical nature of HDF5 files, makes it possible to read individual modalities from `.h5mu` files as well as to save individual modalities to the `.h5mu` file:

```python
adata = mudata.read("mudata.h5mu/rna")

mudata.write("mudata.h5mu/rna", adata)
```

The function [](#mudata.read) automatically decides based on the input if [](#mudata.read_h5mu) or rather [](#mudata.read_h5ad) should be called.

Learn more about the on-disk format specification shared by MuData and AnnData [in the AnnData documentation](https://anndata.readthedocs.io/en/latest/fileformat-prose.html).

## `.zarr` files

[Zarr](https://zarr.readthedocs.io/en/stable/) is a cloud-friendly format for chunked N-dimensional arrays. Zarr is another supported serialisation format for MuData objects:

```python
mdata = mudata.read_zarr("mudata.zarr")

mdata.write_zarr("mudata.zarr")
```

Just as with `.h5mu` files, MuData objects saved in `.zarr` format resemble how AnnData objects are stored, with one additional level of abstraction:

```console
$ tree -L 1 mudata.zarr
mudata.zarr
├── mod
├── obs
├── obsm
├── obsmap
├── obsp
├── uns
├── var
├── varm
├── varmap
└── varp
```