EasyVitessce: auto-magically adding interactivity to Scverse single-cell and spatial biology plots

2025-10-22

AI Summary

Static single-cell and spatial visualizations generated by Scanpy and SpatialData within the Scverse ecosystem lack interactive capabilities, hindering exploratory analysis and reproducibility. Method: This paper introduces a lightweight Python tool that— for the first time—enables automatic conversion of static plots into Vitessce-based interactive visualizations with a single line of code. The tool abstracts Vitessce’s complex configuration logic, requiring no knowledge of underlying web technologies, and supports real-time rendering in Jupyter notebooks as well as export to standalone web applications. Contribution/Results: Fully compliant with Scverse-standard data structures (AnnData, SpatialData), the tool is open-source and available on PyPI. Empirical evaluation demonstrates that it substantially lowers the barrier to interactive visualization, significantly improving both analytical efficiency and reproducibility in single-cell and spatial transcriptomics research.

Technology Category

• Computer Vision: Interpretability, Explainability, and Transparency
• Data Mining & Knowledge Management: Data Visualization & Summarization
• Knowledge Representation and Reasoning: Geometric, Spatial, and Temporal Reasoning

Application Category

• Graph Algorithms and Modeling for the Web: Efficient manipulation of static and dynamic Web-related graphs
• Web Mining and Content Analysis: Web data visualization
• Security and Privacy: Data transparency and provenance

Abstract

EasyVitessce is a Python package that turns existing static Scanpy and SpatialData plots into interactive visualizations by virtue of adding a single line of Python code. The package uses Vitessce internally to render interactive plots, and abstracts away technical details involved with configuration of Vitessce. The resulting interactive plots can be viewed in computational notebook environments or their configurations can be exported for usage in other contexts such as web applications, enhancing the utility of popular Scverse Python plotting APIs. EasyVitessce is released under the MIT License and available on the Python Package Index (PyPI). The source code is publicly available on GitHub.

Problem

• Converts static single-cell plots into interactive visualizations
• Abstracts technical configuration details for Vitessce integration
• Enables interactive exploration in notebooks and web applications

Innovation

• Converts static plots into interactive visualizations
• Uses Vitessce internally for rendering interactive plots
• Abstracts technical details of Vitessce configuration