TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics
March 2 @ 14:00 – 15:30 CET
HDCA Seminar Series 2022 | TissUUmaps
Carolina Wählby and Christophe Avenel
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. We envision TissUUmaps to contribute to broader dissemination and flexible sharing of large-scale spatial omics data, and it is already being used for sharing of data from the Human Developmental Lung Cell Atlas, as shared via the TissUUmaps gallery: https://tissuumaps.github.io/gallery/.
Human developmental cell atlas (HDCA) is the Swedish effort within the human cell atlas (HCA), one of the largest international scientific projects. The project aim is to create a comprehensive molecular atlas of human prenatal development at the molecular resolution using state-of-the-art multi-omic technologies such as single-cell RNA-seq, Spatial Transcriptomics, in situ sequencing in order to provide deeper insight into how variations and deviations contribute to health and disease.
The HDCA Seminar Series 2022 invites you to join us on a journey of early human organogenesis of several organs at the single-cell and spatial resolution. Seminars will be held at SciLifeLab Gamma building on Wednesdays at 14:00 or 15:00 and also via Zoom. After each seminar, we will have up to 30 min round up discussions with the speaker on how you can contribute to the atlas!