Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments

Y Feng; T Yang; J Zhu; M Li; M Doyle; V Ozcoban; GT Bass; A Pizzolla; L Cain; S Weng; A Pasam; N Kocovski; YK Huang; SP Keam; TP Speed; PJ Neeson; RB Pearson; S Sandhu; DL Goode; AS Trigos

Journal article

Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments

Y Feng, T Yang, J Zhu, M Li, M Doyle, V Ozcoban, GT Bass, A Pizzolla, L Cain, S Weng, A Pasam, N Kocovski, YK Huang, SP Keam, TP Speed, PJ Neeson, RB Pearson, S Sandhu, DL Goode, AS Trigos

Nature Communications | NATURE PORTFOLIO | Published : 2023

DOI: 10.1038/s41467-023-37822-0

Abstract

Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells. Ten spatial metrics of SPIAT are benchmarked using simulated data generated ..

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University of Melbourne Researchers

Angela Pizzolla Author

Tony Huang Author

Terence Speed Author

Paul Neeson Author

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Grants

Awarded by Prostate Cancer Foundation

Funding Acknowledgements

This work was supported by National Health and Medical Research Council Ideas Grants 2003887 and 2003115 awarded to A.S.T. We thank Prof. Alicia Oshlack for critical reading of the manuscript, Mr. Richard Young and Dr. George Au-Yeung for initial discussions at the start of this project, Mr. Ryan Sam for providing inspiration for spaSim, and Ms. Wei Ni Lim and Thu Ngoc Nguyen. A.S.T. is a Prostate Cancer Foundation Young Investigator. We acknowledge the Centre for Advanced Histology and Microscopy (CAHM) at the Peter MacCallum Cancer Centre for their support of this work. We thank the Research Computing Facility at the Peter MacCallum Cancer Centre for providing the infrastructure and support to carry out this project.