Senior Software Developer @ EMBL (Genome Biology Unit, Oliver Stegle lab), GERMANY
Addressing interoperability barriers in spatial omics
Host: S. Cacciatore
Abstract: Abstract
The growing abundance of spatial profiling methods results in a heterogeneity of file formats, creating barriers to spatial omics data analysis. Tasks such as data loading, processing, and visualization require laborious, ad-hoc manipulations and conversions. This, in turn, limits the ability to repurpose existing computational methods for new spatial technologies. Furthermore, the recent trends toward spatial multimodal profiling increase the complexity of file formats and analyses.
The talk will show how these challenges are addressed by the SpatialData framework: a Python solution developed by scverse for storing, processing, and visualizing spatial omics data. First, the main components of the framework will be introduced. After, the focus will be placed on the interoperability aspects of the framework: from interoperability across programming languages thanks to language- agnostic file formats and open specifications, to in- memory interoperability in Python thanks to the pydata, geospatial, and scverse ecosystems, enabling rich downstream analyses of spatial omics data.
International Seminar Programme
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