# API reference

This page documents the functions used in the [tutorial notebooks](tutorials.md): the two entry points for pulling raw
Xenium data and converting it to a [SpatialData](https://spatialdata.scverse.org/en/stable/) zarr store, and the one entry
point for converting whole-slide images to pyramidal OME-TIFF. All four are importable directly off the top-level package.

## Downloading

Fetch a 10x Genomics Xenium study's raw asset bundle from a `curl -O <url>` manifest.

```{eval-rst}
.. currentmodule:: spatialrefinery

.. autosummary::
    :toctree: generated
    :nosignatures:

    download_xenium_study
```

## Converting

Convert raw vendor bundles and whole-slide images into analysis-ready formats: a
[SpatialData](https://spatialdata.scverse.org/en/stable/) zarr store for Xenium, and pyramidal OME-TIFF for microscopy images.

```{eval-rst}
.. currentmodule:: spatialrefinery

.. autosummary::
    :toctree: generated
    :nosignatures:

    xenium_to_spatialdata
    xenium_to_spatialdata_zip
    convert_to_ometiff
```

:::{note}
This reference is deliberately narrow. `spatialrefinery.core` and `spatialrefinery.io` contain additional lower-level
machinery -- the technology/converter registry, `BaseDownloader`, `XeniumConverter`, and the pseudo-spot helpers in
`core.utils` -- that other modules build on but that isn't part of the documented, stable surface yet. Expect it to change
without notice; the four functions above are the supported way to use `spatialrefinery`.
:::