Luca Marconato: "Bridging the imaging and sequencing world: OME-NGFF-based solution for dealing..."
Luca Marconato (EMBL) presents "Bridging the imaging and sequencing world: OME-NGFF-based solution for dealing with multi-modal spatial molecular profiles."
Abstract. The appreciated abundance of technologies for detecting spatially-resolved molecular profiles unfortunately comes along with an heterogeneity of file formats and in-memory data representations, which create time-consuming barriers in everyday analyses: from simple visualization tasks to the repurposing of existing computational methods. Furthermore, the recent emergence of multi-omics spatial molecular data combinatorically increases the complexity of file formats and analyses. To address these challenges, we propose an abstraction in the data storage which is not technology-centered but instead provides a small set of spatial "building blocks" that can be arbitrarily combined to represent standard spatial -omics datasets, and possibly complex, yet-to-be-released spatial multi-modal datasets. We propose an extension to the OME-NGFF open format to implement this abstraction so we can rely upon a robust and established ground and at the same time create a bridge with the imaging world. We are also developing three Python packages, one for the in-memory data representation and basic preprocessing operations, relying on the OME-ZARR implementation of OME-NGFF, one for complex analyses, with a particular focus on multi-modality datasets, and one Napari extension to provide interactive visualization capabilities. I am Luca Marconato, Ph.D. Student in the Oliver Stegle group, EMBL Heidelberg and I am working together with Danila Bredikhin, Giovanni Palla, Haimasree Bhattacharya, Ilia Kats, Isaac Virshup, Kevin Yamauchi, Tim Treis, from the Oliver Stegle Lab, Fabian Theis Lab, Dagmar Iber Lab.
More information about Janelia’s Optical Interest Group can be found here: https://www.janelia.org/OIG
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