# Tutorials

Notebooks demonstrating the use of `InSituPy` for analyzing single-cell spatial transcriptomics data.

The tutorial is structured in three main topics:

```{eval-rst}
.. card:: Preprocessing of samples
    :link: preprocessing/index
    :link-type: doc
    :link-alt: Preprocessing Tutorial

    Tutorials focusing on preprocessing steps that are necessary before actually getting started with the analysis.

.. card:: Analysis of individual samples
    :link: sample_level/index
    :link-type: doc
    :link-alt: Tutorial on analysis of individual samples

    Tutorials about data loading and analysis of individual samples using the `InSituData` class.

.. card:: Multi-sample analysis
    :link: multisample_level/index
    :link-type: doc
    :link-alt: Multi-sample analysis tutorial

    This set of tutorials focuses on the analysis of multiple samples using the `InSituExperiment` class.

.. card:: Plotting
    :link: plotting_demos/index
    :link-type: doc
    :link-alt: Plotting tutorials

    Tutorials introducing different plotting functionalities.

.. card:: Manuscript-related analyses
    :link: publication/index
    :link-type: doc
    :link-alt: Publication-related analyses

    Notebooks including analyses shown in the manuscript.

```


```{toctree}
:hidden: false
:maxdepth: 2

preprocessing/index.md
sample_level/index.md
multisample_level/index.md
plotting_demos/index.md
publication/index.md
```