TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics

February 14, 10:00 – 12:00
Registration

Organizer

Bioimage Informatics Unit
biif@scilifelab.se
View Organizer Website

Venue

Online event via Zoom

TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics

February 14, 2023 @ 10:00 12:00 CET

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 will specifically showcase new features of TissUUmaps 3.1, such as:
– HDF5 / AnnData files loading
– Network diagram visualization
– Multiple datasets displayed on a grid
– Plugin engine

The webinar will be given by Christophe Avenel and Fredrik Nysjö.

Last updated: 2023-01-18

Content Responsible: David Gotthold(david.gotthold@scilifelab.se)