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

Xie Y, Habibalahi A, Anwer AG, Wahi K, Bailey J, Lin F, Gatt C, Johansson EMV, Chtanova T, Holst J, Goldys E, Zanini F. · Genome research · 2025 · Journal publication

Original publication · Original publication · Original publication

Recorded summary

SpectralSeq combines hyperspectral autofluorescence imaging and transcriptomics from the same MCF-7 cell. The study relates optical and morphological features to gene-expression variation in this breast-cancer cell system.

Recorded limitations

The evidence concerns paired laboratory assays in individual cells. Facial imaging and gene-specific inference in people remain unvalidated extensions.

Evidence and provenance

Chapter Trust Factor uses a minimum of three distinct qualifying studies. Publication records retain their own evidence and assessment.

Study design and assessment
design
Journal publication
assessment
Not recorded
trust Factor
scope
Paper
status
unassessed
score
Not recorded
basis
Bibliographic identity checks do not establish study design, blinding or evidential strength.
jadad
status
unassessed
score
Not recorded
evidence
Not recorded
Topics and recorded topic scores
  1. key
    general:imaging-transcriptomics
    title
    Imaging, Transcriptomics and Gene Regulation
    collection
    general
    trust Score
    Not recorded
Citation snapshot and identifiers
id
hsi-6fe5f46314bf49
doi
10.1101/gr.280014.124
pmid
40628527
citation Snapshot
Not recorded
citations By Collection
general
Not recorded
Complete approved library record
id
hsi-6fe5f46314bf49
aliases
None recorded
source References
  1. ref
    NPL-9b
    record Id
    hsi-6fe5f46314bf49
    source Type
    Journal publication
    title
    Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.
    authors
    Xie Y, Habibalahi A, Anwer AG, Wahi K, Bailey J, Lin F, Gatt C, Johansson EMV, Chtanova T, Holst J, Goldys E, Zanini F.
    year
    2025
    journal
    Genome research
    doi
    10.1101/gr.280014.124
    pmid
    40628527
    pmcid
    PMC12315715
    patent Number
    Not recorded
    original Assignee
    Not recorded
    original Citation
    Xie Y, Habibalahi A, Anwer AG, Wahi K, Bailey J, Lin F, Gatt C, Johansson EMV, Chtanova T, Holst J, Goldys E, Zanini F (2025). "Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq." Genome Research 35(8):1809–1820 (PMC12315715) — Peer-reviewed published version of NPL-9; renamed from HyperSeq to SpectralSeq during peer review
    original Section
    Hyper-Seq / Transcriptomics
    metadata Status
    metadata-matched
    claim Review
    Not independently appraised
    source URL
    https://www.notion.so/3807b9c99c5680599be7d8337c817b15
    publication URL
    https://pubmed.ncbi.nlm.nih.gov/40628527/
    metadata URL
    https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID%3APMC12315715&format=json&resultType=core&pageSize=4
    corrections
    None recorded
    topic Id
    imaging-transcriptomics
    role
    Focused chapter source
source Type
Journal publication
source Verification
Bibliographic metadata matched; scientific claims await appraisal.
source Collection
Hyperspectral Imaging · patent section 2.4
related Versions
  1. ref
    NPL-9
    record Id
    hsi-7ad76f3461e8f4
  2. ref
    NPL-214
    record Id
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title
Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.
journal
Genome research
neurotransmitters
None recorded
year
2025
authors
Xie Y, Habibalahi A, Anwer AG, Wahi K, Bailey J, Lin F, Gatt C, Johansson EMV, Chtanova T, Holst J, Goldys E, Zanini F.
design
Journal publication
kind
Journal publication
identity Conflict
Not recorded
doi
10.1101/gr.280014.124
pmid
40628527
urls

https://pubmed.ncbi.nlm.nih.gov/40628527/ · https://doi.org/10.1101/gr.280014.124 · https://pmc.ncbi.nlm.nih.gov/articles/PMC12315715/

collections

general

categories

Hyperspectral Imaging

targets
None recorded
priority
1
quotes
None recorded
summary
SpectralSeq combines hyperspectral autofluorescence imaging and transcriptomics from the same MCF-7 cell. The study relates optical and morphological features to gene-expression variation in this breast-cancer cell system.
limitation
The evidence concerns paired laboratory assays in individual cells. Facial imaging and gene-specific inference in people remain unvalidated extensions.
citation Count
Not recorded
paper Trust Assessment
scope
Paper
status
unassessed
score
Not recorded
basis
Bibliographic identity checks do not establish study design, blinding or evidential strength.
citations By Collection
general
Not recorded
topics
  1. key
    general:imaging-transcriptomics
    title
    Imaging, Transcriptomics and Gene Regulation
    collection
    general
    trust Score
    Not recorded
journal Key
genomeresearch
journal Label
Genome research
chapter Entries
  1. id
    general-imaging-transcriptomics-hsi-6fe5f46314bf49
    record Id
    hsi-6fe5f46314bf49
    title
    Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.
    journal
    Genome research
    year
    2025
    authors
    Xie Y, Habibalahi A, Anwer AG, Wahi K, Bailey J, Lin F, Gatt C, Johansson EMV, Chtanova T, Holst J, Goldys E, Zanini F.
    design
    Journal publication
    urls

    https://pubmed.ncbi.nlm.nih.gov/40628527/ · https://doi.org/10.1101/gr.280014.124 · https://pmc.ncbi.nlm.nih.gov/articles/PMC12315715/

    quotes
    None recorded
    summary
    SpectralSeq combines hyperspectral autofluorescence imaging and transcriptomics from the same MCF-7 cell. The study relates optical and morphological features to gene-expression variation in this breast-cancer cell system.
    related Versions
    1. ref
      NPL-9
      record Id
      hsi-7ad76f3461e8f4
    2. ref
      NPL-214
      record Id
      hsi-7ad76f3461e8f4
    limitation
    The evidence concerns paired laboratory assays in individual cells. Facial imaging and gene-specific inference in people remain unvalidated extensions.
    citation Count
    Not recorded
    source Pages
    None recorded
    doi
    10.1101/gr.280014.124
    pmid
    40628527
    targets
    None recorded
    categories

    Hyperspectral Imaging

    source References
    1. ref
      NPL-9b
      record Id
      hsi-6fe5f46314bf49
      source Type
      Journal publication
      title
      Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.
      authors
      Xie Y, Habibalahi A, Anwer AG, Wahi K, Bailey J, Lin F, Gatt C, Johansson EMV, Chtanova T, Holst J, Goldys E, Zanini F.
      year
      2025
      journal
      Genome research
      doi
      10.1101/gr.280014.124
      pmid
      40628527
      pmcid
      PMC12315715
      patent Number
      Not recorded
      original Assignee
      Not recorded
      original Citation
      Xie Y, Habibalahi A, Anwer AG, Wahi K, Bailey J, Lin F, Gatt C, Johansson EMV, Chtanova T, Holst J, Goldys E, Zanini F (2025). "Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq." Genome Research 35(8):1809–1820 (PMC12315715) — Peer-reviewed published version of NPL-9; renamed from HyperSeq to SpectralSeq during peer review
      original Section
      Hyper-Seq / Transcriptomics
      metadata Status
      metadata-matched
      claim Review
      Not independently appraised
      source URL
      https://www.notion.so/3807b9c99c5680599be7d8337c817b15
      publication URL
      https://pubmed.ncbi.nlm.nih.gov/40628527/
      metadata URL
      https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID%3APMC12315715&format=json&resultType=core&pageSize=4
      corrections
      None recorded
      topic Id
      imaging-transcriptomics
      role
      Focused chapter source
    source Type
    Journal publication
    source Verification
    Bibliographic metadata matched; scientific claims await appraisal.
    collection
    general
    chapter Number
    11
    topic Id
    imaging-transcriptomics
    topic Title
    Imaging, Transcriptomics and Gene Regulation
    trust Score
    Not recorded
    paper Trust Assessment
    scope
    Paper
    status
    unassessed
    score
    Not recorded
    basis
    Bibliographic identity checks do not establish study design, blinding or evidential strength.
jadad
status
unassessed
score
Not recorded
condition Evidence
None recorded
conditions
None recorded
topic Trust Scores
None recorded
full Text
status
not-indexed
retrieval Available
false

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