Evidence map›Paper›PMID 40598307›Full record

ArticleGenome biology2025

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

Denis Bienroth, Natalie Charitakis, Dillon Wong, Yunhan C Zhang, Sabrina Jaeger-Honz, Jialin Ding, Kevin I Watt, Julian Stolper, Hazel Chambers-Smith, Duncan MacGregor and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

29 authors.

Denis Bienroth *Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Natalie Charitakis *Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Dillon WongNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Yunhan C ZhangNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Sabrina Jaeger-HonzDepartment of Computer and Information Science, University of Konstanz, Constance, 78464, Germany.
Jialin DingNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Kevin I WattNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Julian StolperNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Hazel Chambers-SmithAnatomical Pathology, The Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
Duncan MacGregorAnatomical Pathology, The Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
Bronwyn ChristiansenAnatomical Pathology, The Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
Celine VivienNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Adam T PiersNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Lisa N WaylenNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Lucas B HoffmannDepartment of Anatomy and Physiology, University of Melbourne, Parkville, VIC, 3052, Australia.
Jessica TangNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Hue M LaCollaborative Centre for Genomic Cancer Medicine, University of Melbourne, Melbourne, Victoria, Australia.
Mei R M DuNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Monika MohenskaDepartment of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
Jose M PoloDepartment of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
Sean GrimmondCollaborative Centre for Genomic Cancer Medicine, University of Melbourne, Melbourne, Victoria, Australia.
Ethan ScottDepartment of Anatomy and Physiology, University of Melbourne, Parkville, VIC, 3052, Australia.
Fernando J RosselloNovo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Enzo R Porrello *Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
Karsten Klein *Department of Computer and Information Science, University of Konstanz, Constance, 78464, Germany.
Hieu T Nim *Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
David A Elliott *Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia. David.Elliott@mcri.edu.au.
Falk Schreiber *Department of Computer and Information Science, University of Konstanz, Constance, 78464, Germany. Falk.Schreiber@uni-konstanz.de.
Mirana Ramialison *Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia. Mirana.Ramialison@mcri.edu.au.

Funding

Heart Foundation Future Leader FellowshipNHMRC Ideas Grant APP1180905Novo Nordisk Foundation NNF21CC0073729
6 · The paper itself

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.

Indexed as

Gene Expression ProfilingSoftwareTranscriptomeHumans

Identifiers

PMID40598307
PMCPMC12219256

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.