Scale-resolved correlation functions unify spatial omics across platforms and resolutions
- 1Ludwig-Maximilians-Universität München
Abstract
Spatial omics platforms populate a multidimensional parameter space and differ in resolution, panel size, sensitivity, and modality. This diversity has led to platform-specific analyses whose results are rarely comparable. Here we present SCOTE (Spatial COvariance TEnsors), a computational framework that quantifies spatial relationships of all feature pairs across all length scales, for molecule coordinates and binned counts alike. Measuring the same quantity, with statistical errors, across platforms, samples, and patients, SCOTE separates measurement effects from biology, with platform artifacts appearing as identifiable, scale-localized features. SCOTE's molecule-level functions resolved a knockout effect in mouse spleen that cell-level analyses missed, and could show that tissue area and replicates, not molecule depth, set the statistical error. To match the growth of spatial omics data sets, SCOTE runs efficiently on CPUs and GPUs, and processes a billion-molecule whole-transcriptome section at all length scales, with uncertainties, in 26 minutes on a single GPU.
Related
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- BiNVaST: niche boundary-preserving and synthetic data-guided variational autoencoders for concordant inference across high-resolution spatial transcriptomic platforms
- Octave: Scale-resolved Evaluation of Spatial Gene Expression Prediction from Histology
- Molecule-resolved inference reveals the spatial organization of transcriptional programs
- SpCAST enables scalable and interpretable integration of single-cell RNA sequencing and single-cell-resolved spatial transcriptomics
BibTeX
@misc{ilin2026scaleresolved,
title = {{Scale-resolved correlation functions unify spatial omics across platforms and resolutions}},
author = {M. Ilin and Y. Singh and S. W. Mages},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.757915},
url = {https://www.biorxiv.org/content/10.64898/2026.10.09.757915v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Scale-resolved correlation functions unify spatial omics across platforms and resolutions
AU - M. Ilin
AU - Y. Singh
AU - S. W. Mages
PY - 2026
DA - 2026/10/09
PB - bioRxiv
DO - 10.64898/2026.10.09.757915
UR - https://www.biorxiv.org/content/10.64898/2026.10.09.757915v1
AB - Spatial omics platforms populate a multidimensional parameter space and differ in resolution, panel size, sensitivity, and modality. This diversity has led to platform-specific analyses whose results are rarely comparable. Here we present SCOTE (Spatial COvariance TEnsors), a computational framework that quantifies spatial relationships of all feature pairs across all length scales, for molecule coordinates and binned counts alike. Measuring the same quantity, with statistical errors, across platforms, samples, and patients, SCOTE separates measurement effects from biology, with platform artifacts appearing as identifiable, scale-localized features. SCOTE's molecule-level functions resolved a knockout effect in mouse spleen that cell-level analyses missed, and could show that tissue area and replicates, not molecule depth, set the statistical error. To match the growth of spatial omics data sets, SCOTE runs efficiently on CPUs and GPUs, and processes a billion-molecule whole-transcriptome section at all length scales, with uncertainties, in 26 minutes on a single GPU.
ER -