# API

## Core Dataclasses

```{eval-rst}
.. module:: insitupy._core
.. currentmodule:: insitupy

.. autosummary::
    :toctree: generated

    InSituData
    InSituExperiment
    MultiCellData
    CellData
    BoundariesData
    ImageData
    AnnotationsData
    RegionsData
```

## Core reading functions

```{eval-rst}
.. module:: insitupy._core
.. currentmodule:: insitupy

.. autosummary::
    :toctree: generated

    read_xenium
```

## IO

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

.. autosummary::
    :toctree: generated

    io.read_qupath_geojson
    io.write_qupath_geojson
    io.read_celldata
    io.read_multicelldata
    io.read_shapesdata
```

## Plotting

```{eval-rst}
.. module:: insitupy.plotting
.. currentmodule:: insitupy

.. autosummary::
    :toctree: generated

    plotting.plot_spatial
    plotting.plot_cellular_composition
    plotting.cell_abundance_along_axis
    plotting.cell_expression_along_axis
    plotting.volcano_plot
    plotting.plot_colorlegend
    plotting.plot_overview
```