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CCB Seminar Series: SpatialData, an open and universal framework for processing spatial omics data

October 23 @ 10:00 am - 11:00 am

Title: CCB Seminar Series
Speaker: Luca Marconato
Topic: SpatialData, an open and universal framework for processing spatial omics data

When: Monday, October 23, 2023

Abstract: The growing abundance of spatial profiling methods comes with a heterogeneity of file formats which creates barriers in 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. To address these problems, we established a collaboration that unites research scientists from the single-cell (scverse) and imaging communities (OME, napari). Together, we developed an open, language-agnostic, cloud-ready file storage format that extends the OME-NGFF specification and is tailored for a flexible and efficient storage of spatial molecular data. We also developed a Python package, SpatialData, which provides modular, in-memory representations of the data, drawing on well-established libraries from the Python geospatial and single-cell ecosystems (Xarray, GeoPandas, AnnData, Dask). We also implemented general data manipulation operations, like coordinate transformations and spatial queries, abstracted to work interchangeably for general multi-modality spatial omics datasets. Finally, we developed a Napari plugin that enables the interactive visualization and annotation of spatial multi-omics datasets. We believe that our computational solutions for data storage, manipulation, and visualization have the potential to greatly reduce the technical overhead when dealing with spatial multi-modal datasets, and allow for easier cross-talk and repurposing of computational methods across programming languages.

Virtual: Zoom link


October 23
10:00 am - 11:00 am
Event Category: