TissUUmaps 3.1: Interactive visualization and quality assessment of large-scale spatial omics

We present TissUUmaps, browser-based tool for GPU-accelerated visualization and interactive exploration of tens of millions of 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. It is also possible to directly connect spatial markers with markers in feature space, such as UMAP plots, to interactively relate feature space with physical space. TissUUmaps was created in collaboration between BIIF and the Wählby lab. You can read more about it and test the software on its web page: https://tissuumaps.github.io/

During the seminar, we specifically showcase new features of TissUUmaps 3.1, such as:
HDF5 / AnnData files loading
Network diagram visualization
Multiple datasets displayed on a grid

00:00 Introduction to the Bio-Image Informatics Facility (https://www.scilifelab.se/units/bioim...)
03:35 History of TissUUmaps
07:11 Features of TissUUmaps 3.0
21:45 TissUUmaps 3.1
22:45 HDF5 support
31:51 AnnData support
35:23 Collection mode
38:05 Jupyter integration
42:05 Network diagrams visualization
46:06 Export to HTML
50:58 Conclusion