Poster Presentation Multi-Omics Conference 2024

SpatialBench: A comprehensive benchmarking study of spatial transcriptomics methods to help make informed experimental and analytical decisions (#118)

Daniela B. Amann-Zalcenstein 1 2 , Ashleigh Solano 1 2 , Raymond K. H. Yip 1 2 , Pradeep Rajasekhar 1 2 , Casey J. A. Anttila 1 2 , Ruvimbo Mishi 2 , Ling Ling 2 , Peter F. Hickey 1 2 , Charity W. Law 1 2 , Mei R. M. Du 2 , Changqing Wang 1 2 , Yang Xu 1 2 , Callum J. Sargeant 2 , Ishtar Zaman 1 2 , Yunshun Chen 1 2 , Lisa J. Ioannidis 1 2 , Kelly L. Rogers 1 2 , Diana S. Hansen 3 , Matthew E. Ritchie 1 2 , Rory Bowden 1 2
  1. Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
  2. Walter and ELiza Hall Institute, Parkville, VIC, Australia
  3. Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia

Here, we present SpatialBench, a well-controlled direct comparison of 4 spatial transcriptomics platforms (Visium, Visium HD, MERSCOPE, Xenium) paired with scRNA-seq and snRNA-seq in a single, dense and spatially complex tissue, mouse spleen. We provide a set of common quality metrics to compare and inform the selection of technologies and analysis approaches. We further evaluate the capability of different technologies to recover known biological features and uncover new insights in a mouse model of infection with a host genetic perturbation, providing a test system relevant to many real-life research questions. This project is intended to provide a continuing, open-ended resource for the evaluation and comparison of existing and new technologies for spatial analysis, which could be extended beyond spatial transcriptomics.