Automated integration of multi-slice spatial transcriptomics data in 2D and 3D using VR-Omics
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(Published version)
Date
2025
Authors
Bienroth, D.
Charitakis, N.
Wong, D.
Zhang, Y.C.
Jaeger-Honz, S.
Ding, J.
Watt, K.I.
Stolper, J.
Chambers-Smith, H.
MacGregor, D.
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Journal article
Citation
Genome Biology, 2025; 26(1):182-1-182-29
Statement of Responsibility
Denis Bienroth, Natalie Charitakis, Dillon Wong, Yunhan C. Zhang, Sabrina Jaeger-Honz, Jialin Ding, Kevin I. Watt, Julian Stolper, Hazel Chambers-Smith, Duncan MacGregor, Bronwyn Christiansen, Celine Vivien, Adam T. Piers, Lisa N. Waylen, Lucas B. Hoffmann, Jessica Tang, Hue M. La, Mei R. M. Du, Monika Mohenska, Jose M. Polo, Sean Grimmond, Ethan Scott, Fernando J. Rossello, Enzo R. Porrello, Karsten Klein, Hieu T. Nim, David A. Elliott, Falk Schreiber, Mirana Ramialison
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Abstract
The field of spatial transcriptomics is rapidly evolving, with increasing sample complexity, resolution, and tissue size. Yet the field lacks comprehensive and intuitive solutions for automated integration and analysis of multi-slice data in either co-planar (2D) or stacked (3D) formation. To address this, we develop VR-Omics, a free, platform-agnostic software that provides end-to-end automated processing of multi-slice data through a biologist-friendly interface. Benchmarking against existing methods demonstrates VR-Omics’ unique strengths to perform comprehensive end-to-end analysis of multi-slice stacked data. Through co-planar slice analysis, VR-Omics uncovers previously undetected, dysregulated metabolic networks within rare pediatric cardiac rhabdomyomas, demonstrating its potential for biological discoveries.
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© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.