VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration

Manukyan, A.; Bahry, E.; Wyler, E.; Becher, E.; Pascual-Reguant, A.; Plumbom, I.; Dikmen, H. O.; Elezkurtaj, S.; Conrad, T.; Altmüller, J.; Hauser, A. E.; Hocke, A.; Radbruch, H.; Schmidt, D.; Landthaler, M.; Akalin, A.

doi:10.1101/2023.12.15.571667

bioRxiv · 10.1101/2023.12.15.571667

VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration

Manukyan, A.·Bahry, E.·Wyler, E.·Becher, E.·Pascual-Reguant, A.·Plumbom, I.·Dikmen, H. O.·Elezkurtaj, S.·Conrad, T.·Altmüller, J.·Hauser, A. E.·Hocke, A.·Radbruch, H.·Schmidt, D.·Landthaler, M.·Akalin, A.

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Abstract

The growing number of spatial omic technologies have created a demand for computational tools capable of managing, storing, and analyzing spatial datasets with multiple modalities and spatial resolutions. Meanwhile, computer vision is becoming an integral part of processing spatial data readouts where image registration and spatial data alignment of tissue sections are essential prior to data integration. Hence, there is a need for computational platforms that analyze data across spatial datasets with diverse resolutions as well as those that manipulate and process images of microanatomical tissue structures. To this end, we have developed VoltRon, a novel R package for spatial omics analysis with a unique data structure that accommodates data readouts with many levels of spatial resolutions (i.e., multi-resolution) including regions of interest (ROIs), spots, single cells, and even subcellular entities such as molecules. To connect and integrate these spatially diverse omic profiles, VoltRon accounts for spatial organization of tissue blocks (samples), layers (sections) and assays given a multi-resolution collection of spatial data readouts. An easy-to-use computer vision toolbox, OpenCV, is fully embedded in VoltRon that allows users to both automatically and manually register spatial coordinates across adjacent layers for data transfer without the need for external software tools. VoltRon is implemented in the R programming language and is freely available at https://github.com/BIMSBbioinfo/VoltRon.

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Manukyan, A., Bahry, E., Wyler, E., Becher, E., Pascual-Reguant, A., Plumbom, I., Dikmen, H. O., Elezkurtaj, S., Conrad, T., Altmüller, J., Hauser, A. E., Hocke, A., Radbruch, H., Schmidt, D., Landthaler, M., Akalin, A.. 2023-12-15. VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration. https://doi.org/10.1101/2023.12.15.571667

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