ArticleeLife2024
Three-dimensional single-cell transcriptome imaging of thick tissues.
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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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.
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.
Who cites it
38 citing papers in PubMed.
- Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity.PLoS computational biology · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Article
- Cross-linked volumetric DNA microscopy for dense molecular-network phenotyping in intact tissue.bioRxiv : the preprint server for biology · 2026Article
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- From identity to function: unveiling the cellular complexity of hypothalamic feeding circuits.Reviews in endocrine & metabolic disorders · 2026Review
- Corneal Innervation Research at a Crossroads: A Tool-Driven Roadmap for the Future.Investigative ophthalmology & visual science · 2026Review
- Spatial Multiomics Reveal Insights Into ADC Efficacy.European journal of immunology · 2026Review
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Global scientific growth and thematic development of spatial transcriptomics in oncology research.Discover oncology · 2026Article
- Modern RNA Quantification Methods: From RT-qPCR to Advanced Microscopy.The journal of physical chemistry. B · 2026Review
- Physiologically Relevant Organotypic Tissue Slice Model for Evaluating Cell Responses to Ionizing Radiation.International journal of molecular sciences · 2026Review
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- From slices to deep dishes: spatial transcriptomics and translatomics of thick tissue blocks.Nature methods · 2025Article
- High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.Science (New York, N.Y.) · 2025Article
- Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.Nature methods · 2025Article
- Microglia networks within the tapestry of alzheimer's disease through spatial transcriptomics.Molecular neurodegeneration · 2025Review
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
- Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings.Nature communications · 2025Article
- Cancer-on-a-chip for precision cancer medicine.Lab on a chip · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.
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Registered trials
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.