Evidence map›Paper›PMID 42608409›Full record

ArticleNature communications2026

Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT).

Felix Y Zhou, Brittany-Amber Jacobs, Adam Norton-Steele, Xiaoyue Han, Linna Zhou, Thomas M Carroll, Carlos Ruiz Puig, Joseph Chadwick, Xiao Qin, Richard Lisle and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

14 authors.

Felix Y Zhou *Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK. felix.y.zhou@vanderbilt.edu.ORCID http://orcid.org/0000-0003-4463-1165
Brittany-Amber Jacobs *Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-9741-3519
Adam Norton-Steele *Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0009-0006-1580-0117
Xiaoyue Han *Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-3905-1759
Linna ZhouNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-1938-5428
Thomas M CarrollNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-9753-2385
Carlos Ruiz PuigNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-9214-3804
Joseph ChadwickNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-5380-2125
Xiao QinNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-8738-4187
Richard LisleNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.
Lewis MarshNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.
Helen M ByrneNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-1771-5910
Heather A HarringtonMathematical Institute, University of Oxford, Oxford, UK.
Xin LuNuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK. xin.lu@ludwig.ox.ac.uk.ORCID http://orcid.org/0000-0002-6587-1152

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Live cells in tissue are plastic, phenotypically dynamic, and modify their function in response to genetic and environmental perturbations. To unleash the power of live-cell imaging to identify phenotype-genotype-function coupling over time, we report the development of a standardized Shape-Appearance-Motion (SAM) "phenome" and SAM-Phenotype-Observation-Tool (SPOT), that act as an image-"transcriptome" and image-"transcriptome analyzer" respectively, and provide an unbiased and comprehensive description of morpho-dynamic phenotypes without prior knowledge. We apply SAM-SPOT to our simulated organoids database with known ground-truth and >1.6 million mouse and human organoid instances with defined genetic and chemical perturbations. SAM-SPOT can effectively and robustly characterize 3D morpho-dynamics from 2D projection videos. Combined with single-cell RNA sequencing, SAM-SPOT reveals that altered WNT signaling, but not mutant RAS or p53, predisposes intestinal organoids to irregular morphogenesis. SAM-SPOT advances biomedical discovery by empowering live-cell imaging to identify phenotype-genotype-function relationships through large-scale and cost-effective label-free live-cell imaging.

Indexed as

Imaging, Three-DimensionalOrganoidsAnimalsGenotypeHumansMicePhenotypeSingle-Cell AnalysisTranscriptomeWnt Signaling Pathway

Identifiers

PMID42608409
PMCPMC13482367

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Registered trials

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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.