Evidence map›Paper›PMID 40628527›Full record

ArticleGenome research2025

Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.

Yike Xie, Abbas Habibalahi, Ayad G Anwer, Kanu Wahi, Jacqueline Bailey, Francis Lin, Catherine Gatt, Emma M V Johansson, Tatyana Chtanova, Jeff Holst and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome research, 2025. 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. Visualizing Epigenetics: A Review of Microscopy Techniques for Investigating DNA Methylation Patterns, Chromatin Structure, and Gene Expression.Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada · 2025
    Review
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

12 authors.

Yike XieSchool of Clinical Medicine, UNSW Sydney, Sydney, New South Wales 2052, Australia.ORCID 0000-0001-6980-761X
Abbas HabibalahiSchool of Biomedical Engineering, UNSW Sydney, Sydney, New South Wales 2033, Australia.ORCID 0000-0001-7833-1705
Ayad G AnwerSchool of Biomedical Engineering, UNSW Sydney, Sydney, New South Wales 2033, Australia.
Kanu WahiSchool of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia.ORCID 0000-0003-1114-6075
Jacqueline BaileySchool of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, New South Wales 2052, Australia.
Francis LinSchool of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, New South Wales 2052, Australia.
Catherine GattSchool of Clinical Medicine, UNSW Sydney, Sydney, New South Wales 2052, Australia.ORCID 0009-0000-8682-2512
Emma M V JohanssonFlow Cytometry Unit, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales 2033, Australia.ORCID 0000-0002-1863-3020
Tatyana ChtanovaSchool of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, New South Wales 2052, Australia.ORCID 0000-0003-3419-4483
Jeff HolstSchool of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia.ORCID 0000-0002-0377-9318
Ewa Goldys *School of Biomedical Engineering, UNSW Sydney, Sydney, New South Wales 2033, Australia; fabio.zanini@unsw.edu.au e.goldys@unsw.edu.au.ORCID 0000-0003-2470-7118
Fabio Zanini *School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales 2052, Australia; fabio.zanini@unsw.edu.au e.goldys@unsw.edu.au.ORCID 0000-0001-7097-8539

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Microscopy and omics are complementary approaches to probe cellular molecular states in health and disease, combining granularity with scalability. However, integrating both imaging- and sequencing-based assays on the same cell has proven challenging. This study demonstrates a new approach called SpectralSeq that combines hyperspectral autofluorescence imaging with transcriptomics on the same cell. SpectralSeq is applied to Michigan Cancer Foundation-7 (MCF-7) breast cancer cells and identifies a subpopulation of cells exhibiting bright autofluorescence rings at the plasma membrane in optical channel 13 (λ

Indexed as

Gene Expression ProfilingHyperspectral ImagingOptical ImagingSingle-Cell AnalysisTranscriptomeBreast NeoplasmsFemaleHumansMCF-7 Cells

Identifiers

PMID40628527
PMCPMC12315715

What OpenQuestion holds

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LicenceCC BY
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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.