09-11, 15:45–16:45 (Europe/Berlin), Workshop room II - MW 0234
Introduction to interactive AnnData analysis with cellxgene, and interactive SpatialData analysis with Napari, vitessce and more.
Spatially resolved omics technologies are revolutionizing our understanding of biological tissues by introducing new ways to characterize tissue architectures and identify cell-cell interactions. However, handling large single-cell and spatial omics datasets poses significant challenges due to data volume and heterogeneity. AnnData and SpatialData offer innovative, robust solutions for these issues.
The workshop will provide an in-depth look at the SpatialData framework, a Python-based solution for managing spatial omics datasets, and its interlay with the AnnData Python package. Participants will learn to ingest and represent data from various commercial technologies in a unified format. The session will cover techniques for manipulating multi-sample, multi-modal datasets, including constructing common coordinate frameworks via coordinate transformations.
Attendees will discover methods for creating detailed visualizations, interactively exploring large datasets, and storing the annotations in the AnnData and SpatialData format. Additionally, the workshop will highlight data manipulation functions such as cropping, annotation transfer, and deep learning applications and discuss ensuring interoperability across different software platforms and programming languages for scalable, reproducible workflows.
No previous knowledge expected
Senior Software Developer – EMBL