Thread by @AaronNewmanLab

Excited to announce our new method #CytoSPACE for mapping single cells from a reference atlas to #SpatialTranscriptomics (ST) data at high resolution, out now in @NatureBiotech! 1/10

nature.com/articles/s4158…

Available assays for ST lack single-cell resolution (e.g. #Visium) or have limited gene recovery (e.g. #MERSCOPE).

CytoSPACE computationally reconstructs tissue specimens to obtain high gene coverage and spatially-resolved scRNA-seq data suitable for downstream analysis. 2/10

CytoSPACE works by constrained global optimization to yield robust mappings, outperforming existing methods across benchmarks. 3/10

We found that CytoSPACE was highly effective at recovering dense substructures in #Visium bulk ST data. For mouse kidney, which has highly granular spatial architecture, CytoSPACE reconstructed known zonal and co-localization patterns across nearly 30 epithelial states. 4/10

In the tumor microenvironment, CytoSPACE outperforms other methods to recover enrichments of cell-type-specific states with known localization, including exhausted T cells, TREM2+ and FOLR2+ macrophages, and #EcoTyper CE9 and CE10 cell states specific to 5 immune cell types. 5/10

In single-cell #MERSCOPE data, we found that CytoSPACE significantly enhances gene recovery, including the ability to interrogate spatially resolved T cell states at single-cell resolution. 6/10

CytoSPACE is quick and simple to execute. It runs in minutes even with a single CPU on a personal laptop and requires no hyperparameter tuning or gene/feature selection.

Source code is available on GitHub (github.com/digitalcytomet…). 7/10

CytoSPACE is also available as an easy-to-use online interface at cytospace.stanford.edu, requiring little or no coding! 8/10

CytoSPACE is the result of a massive team effort including co-first authors Milad R. Vahid, @erinlybrown and @ChloeBSteen; co-authors @Wubing44589261, Hyun Soo Jeon, @kang_minji_ and @askyperson; and all who tested the tool and provided feedback during development. 9/10

CytoSPACE would have not been possible without the generous support from our funding sources: @NIH, @AACR, @stiftkgj, @Kreftforeningen, @Ludwig_Cancer and the Donald E. and Delia B. Baxter Foundation. 10/10