TissUUmaps is a browser-based tool for GPU-accelerated visualization and interactive exploration of 107+ datapoints overlaying tissue samples. Users can visualize markers and regions, explore spatial statistics and quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. TissUUmaps provides instant multi-resolution image viewing, can be customized, shared, and also integrated in Jupyter Notebooks. We envision TissUUmaps to contribute to broader dissemination and flexible sharing of large-scale spatial omics data.

Multimodal omics data is typically subject to two different types of investigation: unspecific high level investigation, where we visually interpret the information, see patterns, construct hypotheses and draw conclusions; and low level hypothesis testing, where we build a representation of the unknown by asking, and seeking answers to, questions that can provide statistical certainty measures to test our hypotheses. In both cases, visual exploration and inspection of data quality are crucial for constructing and validating our hypothesis. However, the complexity and scale of data often makes visual exploration fundamentally challenging. For example, a typical in situ transcriptomics (IST,[1–6]) experiment results