Interactive visualisation of spatial transcriptomics data

This webinar introduces approaches for visualising spatial-transcriptomics data leveraging the SpatialData framework together with open-source software tools such as napari  and Vitessce. It will demonstrate multiple examples for each tool, including datasets from both sequencing-based and imaging-based spatial-transcriptomics technologies. The session will provide a practical overview of how to configure, customise, and interact with visualisations in napari and Vitessce, and conclude with an overview of how these visualisations can be integrated in different stages of the analysis workflow from exploratory analyses to publication.

This event is part of a broader webinar series on spatial transcriptomics. For more information about the series and its webinars, please visit the following link: “Decoding spatial transcriptomics through sequences, pixels, and bioinformatics”.

You can click here to access the GitHub repo containing the materials to follow and reproduce the demo in the webinar.

Who is this course for?

Students and researchers beginning to work with spatial-transcriptomics datasets. Knowledge of spatial-transcriptomics data is required, experience with the SpatialData framework and the Python programming language would be useful but not required.
 

Outcomes

By the end of the webinar, you will be able to:

• Identify the visualisation tools best suited for your use case

• Explore spatial-transcriptomics data with napari and Vitessce

• Integrate interactive visualisations of your datasets in your analysis workflow

DOI: 10.6019/TOL.st-data-visualisation-w.2026.00001.1

This webinar took place on 11 March 2026. Please click the 'Watch video' button to view the recording.