Publikation:

Automated integration of multi-slice spatial transcriptomics data in 2D and 3D using VR-Omics

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Bienroth_2-osyrk3hugh55.pdf
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Datum

2025

Autor:innen

Bienroth, Denis
Charitakis, Natalie
Wong, Dillon
Zhang, Yunhan C.
Elliott, David A.
Ramialison, Mirana
et al.

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http://nbn-resolving.de/urn:nbn:de:bsz:352-2-osyrk3hugh55
DOI (zitierfähiger Link)
https://doi.org/10.1186/s13059-025-03630-6
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CC BY-NC-ND 4.0

Angaben zur Forschungsförderung

Deutsche Forschungsgemeinschaft (DFG): EXC 2117--422037984
Deutsche Forschungsgemeinschaft (DFG): 251654672--TRR 161

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Open Access-Veröffentlichung
Open Access Gold

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Informatik und Informationswissenschaft: Publikationen
Exzellenzcluster "Centre for the Advanced Study of Collective Behaviour": Publikationen
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Published

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Genome Biology. Springer Science and Business Media LLC. 2025, 26(1), 182. eISSN 1474-760X. Verfügbar unter: doi: 10.1186/s13059-025-03630-6

Zusammenfassung

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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ISO 690BIENROTH, Denis, Natalie CHARITAKIS, Dillon WONG, Yunhan C. ZHANG, Sabrina JAEGER-HONZ, Karsten KLEIN, Hieu T. NIM, David A. ELLIOTT, Falk SCHREIBER, Mirana RAMIALISON, 2025. Automated integration of multi-slice spatial transcriptomics data in 2D and 3D using VR-Omics. In: Genome Biology. Springer Science and Business Media LLC. 2025, 26(1), 182. eISSN 1474-760X. Verfügbar unter: doi: 10.1186/s13059-025-03630-6
BibTex
@article{Bienroth2025-07-02Autom-73837,
  title={Automated integration of multi-slice spatial transcriptomics data in 2D and 3D using VR-Omics},
  year={2025},
  doi={10.1186/s13059-025-03630-6},
  number={1},
  volume={26},
  journal={Genome Biology},
  author={Bienroth, Denis and Charitakis, Natalie and Wong, Dillon and Zhang, Yunhan C. and Jaeger-Honz, Sabrina and Klein, Karsten and Nim, Hieu T. and Elliott, David A. and Schreiber, Falk and Ramialison, Mirana},
  note={Article Number: 182}
}
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Interner Vermerk

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