InSituPy: a framework for histology-guided, multi-sample analysis of single-cell spatial omics data

<h4>Motivation</h4>Spatial omics data provides unprecedented insights into disease biology, yet its complexity introduces significant challenges in data analysis. Comprehensive analysis requires frameworks that integrate diverse modalities and enable joint processing of multiple datasets and corresponding metadata.<h4>Results</h4>To address these challenges, we introduce InSituPy, a versatile and scalable framework for analyzing spatial omics data from the multi-sample level down to the cellular and subcellular level. Its hierarchical data structure organizes all relevant data modalities per sample and links them to their corresponding metadata, enabling scalable analysis of large patient cohorts using spatial omics technologies. Interactive visualization tools within InSituPy enable seamless integration of histopathological expertise, promoting collaborative hypothesis generation in translational research. Additionally, InSituPy includes built-in analytical algorithms and interfaces with external tools, establishing a standardized workflow for multi-sample spatial omics data analysis.<h4>Availability</h4>The Python package InSituPy is publicly available on GitHub (https://github.com/SpatialPathology/InSituPy) and PyPi (https://pypi.org/project/insitupy-spatial/), and archived on Zenodo (DOI: 10.5281/zenodo.18459471). Tutorials and documentation for InSituPy are available at https://insitupy.readthedocs.io/. All code to replicate the results shown in this manuscript can be found in the GitHub repository. Scripts to connect QuPath and InSituPy can be found at https://github.com/SpatialPathology/InSituPy-QuPath. All data required to complete the tutorials is publicly available, and functions to download the data have been implemented. A Zulip community chat for user support and discussion is accessible at https://insitupy.zulipchat.com.<h4>Contact</h4>[email protected], [email protected].