Experimental designs grow in scale and complexity, and multiple layers of information are now profiled in individual cells. Such advances enable new data-driven insights and also pose significant challenges to handling, analysing and interpreting the data.

We designed a data standard (MuData) to address the need for a data management solution for multimodal datasets. We also built a multimodal analysis framework (muon) around it in order to handle, process, integrate and visualise complex multimodal datasets. Importantly, the data standard and the framework are integrated into a larger ecosystem of analysis tools for high-throughput omics and build the foundation for its further development and expansion.