SCOPE: A Spatial Co-registration and Omics Pipeline for Comparative Mass Spectrometry Imaging Data Analysis
- 1Department of Physiology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand .
- 2La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Melbourne, Victoria, Australia .
Abstract
Spatially resolved omics technologies have transformed our ability to map molecular organization within tissues. However, the absence of anatomically consistent spatial units across biological replicates fundamentally limits cross-sample comparison and rigorous population-level inference at high spatial fidelity. Current approaches rely either on segmentation-dependent region definitions, which risk obscuring fine-scale molecular heterogeneity, or on analyses confined to individual specimens without cross-replicate spatial correspondence. Here, we introduce SCOPE, a spatial co-registration and omics pipeline that integrates deformable image co-registration with a shared spatial reference, HexBin, to establish anatomically homologous spatial units across samples. By enabling segmentation-free comparison while preserving high spatial fidelity, SCOPE maintains intrinsic molecular heterogeneity and supports statistically robust cross-replicate comparison. Application of SCOPE to an ex vivo bovine lens model of oxidative stress reveals region- and microdomain-specific remodeling of glutathione metabolism that is obscured by whole-tissue averaging or coarse segmentation. High-spatial-fidelity mapping identifies anterior–posterior asymmetries and localized vulnerabilities within lens fiber cell populations and enables relative quantitative evaluation of the thiol-based antioxidant therapeutic N-acetylcysteine amide. SCOPE advances spatial omics beyond segmentation-dependent and single-section descriptive analyses toward reproducible cross-sample quantitative inference, providing a scalable foundation for high-spatial-fidelity analysis across biological tissues.
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BibTeX
@article{shi2026scope,
title = {{SCOPE: A Spatial Co-registration and Omics Pipeline for Comparative Mass Spectrometry Imaging Data Analysis}},
author = {Dingchang Shi and Emily MacFarlane and Berin A. Boughton and Paul J. Donaldson and George Guo and Angus C. Grey},
journal = {Computational and Structural Biotechnology Journal},
year = {2026},
month = oct,
doi = {10.34133/csbj.0237},
url = {https://doi.org/10.34133/csbj.0237},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - SCOPE: A Spatial Co-registration and Omics Pipeline for Comparative Mass Spectrometry Imaging Data Analysis
AU - Dingchang Shi
AU - Emily MacFarlane
AU - Berin A. Boughton
AU - Paul J. Donaldson
AU - George Guo
AU - Angus C. Grey
PY - 2026
DA - 2026/10/26
JO - Computational and Structural Biotechnology Journal
DO - 10.34133/csbj.0237
UR - https://doi.org/10.34133/csbj.0237
AB - Spatially resolved omics technologies have transformed our ability to map molecular organization within tissues. However, the absence of anatomically consistent spatial units across biological replicates fundamentally limits cross-sample comparison and rigorous population-level inference at high spatial fidelity. Current approaches rely either on segmentation-dependent region definitions, which risk obscuring fine-scale molecular heterogeneity, or on analyses confined to individual specimens without cross-replicate spatial correspondence. Here, we introduce SCOPE, a spatial co-registration and omics pipeline that integrates deformable image co-registration with a shared spatial reference, HexBin, to establish anatomically homologous spatial units across samples. By enabling segmentation-free comparison while preserving high spatial fidelity, SCOPE maintains intrinsic molecular heterogeneity and supports statistically robust cross-replicate comparison. Application of SCOPE to an ex vivo bovine lens model of oxidative stress reveals region- and microdomain-specific remodeling of glutathione metabolism that is obscured by whole-tissue averaging or coarse segmentation. High-spatial-fidelity mapping identifies anterior–posterior asymmetries and localized vulnerabilities within lens fiber cell populations and enables relative quantitative evaluation of the thiol-based antioxidant therapeutic N-acetylcysteine amide. SCOPE advances spatial omics beyond segmentation-dependent and single-section descriptive analyses toward reproducible cross-sample quantitative inference, providing a scalable foundation for high-spatial-fidelity analysis across biological tissues.
SN - 2001-0370
ER -