# API

## i/o

```{eval-rst}
.. module:: scispy.io
.. currentmodule:: scispy

.. autosummary::
    :toctree: generated

    io.load_merscope
    io.load_xenium
    io.load_cosmx
```

## Preprocessing

```{eval-rst}
.. module:: scispy.pp
.. currentmodule:: scispy

.. autosummary::
    :toctree: generated

    pp.run_scanpy
    pp.scvi_annotate
    pp.sync_shape
```

## Tools

```{eval-rst}
.. module:: scispy.tl
.. currentmodule:: scispy

.. autosummary::
    :toctree: generated

    tl.add_to_shapes
    tl.add_shapes_from_hdf5
    tl.add_to_points
    tl.get_sdata_polygon
    tl.run_pseudobulk
    tl.sdata_rotate
    tl.sdata_querybox
    tl.scis_prop
    tl.shapes_of_cell_type
```

## Plotting

```{eval-rst}
.. module:: scispy.pl
.. currentmodule:: scispy

.. autosummary::
    :toctree: generated

    pl.plot_qc
    pl.plot_sdata
    pl.plot_multi_sdata
    pl.plot_shapes
    pl.plot_shape_along_axis
    pl.plot_per_groups
```