# Say hello to MuData

**MuData** is a format for annotated multimodal datasets. MuData is native to Python but provides cross-language functionality via HDF5-based `.h5mu` files.

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## MuData objects as containers

The `mudata` package introduces multimodal data objects ([MuData class](#mudata.MuData)) allowing Python users to work with increasigly complex datasets efficiently and to build new workflows and computational tools around it.

```
MuData object with n_obs × n_vars = 10110 × 110101
  2 modalities
  atac: 10110 x 100001
  rna: 10110 x 10100
```

MuData objects enable multimodal information to be stored & accessed naturally, embrace [AnnData](https://github.com/theislab/anndata) for the individual modalities, and can be serialized to `.h5mu` files. [Learn more about multimodal objects](io/mudata.md) as well as [file formats for storing & sharing them](io/output.md).

## Natural interface

MuData objects feature an AnnData-like interface and familiar concepts such as *observations* and *variables* for the two data dimensions. Get familiar with MuData in the [Quickstart tutorial](notebooks/quickstart_mudata).

## Handling MuData objects

A flagship framework for multimodal omics analysis — `muon` — has been built around the MuData format. Find more information on it [in its documentation](https://muon.readthedocs.io/en/latest/) and [on the tutorials page](https://muon-tutorials.readthedocs.io/en/latest/) as well as in the corresponding publication{cite:p}`bredikhin_2022`.

```{eval-rst}
.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Getting started

   notebooks/quickstart_mudata.ipynb
   notebooks/nuances.ipynb
   notebooks/axes.ipynb
   notebooks/annotations_management.ipynb

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Documentation

   install
   io/input
   io/mudata
   io/output
   io/spec
   api
   changelog
   contributing
   references
```