Tutorials

InSituPy is built around two core classes: InSituData for analyzing individual spatial transcriptomics samples, and InSituExperiment for managing multi-sample studies. InSituData integrates multiple data modalities—cell expression matrices, transcript locations, tissue images, and spatial annotations—into a unified interface that preserves spatial context throughout your analysis. InSituExperiment extends this to collections of samples, connecting each sample to its corresponding metadata, enabling cross-sample comparisons, and coordinated workflows across entire datasets. Together, they provide a complete framework for spatial transcriptomics analysis.

Topics

To help you get started with InSituPy, you can find a collection of different tutorials here. These are divided into the following five topics:

Single-sample analysis

Step-by-step demonstration on how to perform data analysis using InSituPy and the InSituData class.

Analysis demo

Multi-sample analysis

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

Multi-sample analysis tutorials

Data import

Tutorials explaining how to import data from different technologies or tools.

Data import tutorials

Plotting functionalities

Tutorials introducing different plotting functionalities.

Plotting tutorials

Manuscript-related analyses

Notebooks including analyses shown in the manuscript.

Publication-related analyses