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

SpatialData Integration

Tutorials for converting between InSituPy and SpatialData formats for integration with the scverse ecosystem.

SpatialData conversion tutorials

Plotting functionalities

Tutorials introducing different plotting functionalities.

Plotting tutorials

Manuscript-related analyses

Notebooks including analyses shown in the manuscript.

Publication-related analyses