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High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)

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Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

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Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis

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Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

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iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging

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Clarifying Tissue Clearing

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Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

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The Central Dogma Decentralized: New Perspectives on RNA Function and Local Translation in Neurons

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In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

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Genome-wide atlas of gene expression in the adult mouse brain

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Structural and molecular interrogation of intact biological systems

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Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles

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Protein detection using proximity-dependent DNA ligation assays

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Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury

inferredcites →https://doi.org/10.1038/nmeth.1253openalex-snapshot

Imaging individual mRNA molecules using multiple singly labeled probes

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Single-cell systems biology by super-resolution imaging and combinatorial labeling

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Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

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In situ sequencing for RNA analysis in preserved tissue and cells

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Image-based transcriptomics in thousands of single human cells at single-molecule resolution

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Single-cell in situ RNA profiling by sequential hybridization

inferredcites →https://doi.org/10.1038/nmeth.3899openalex-snapshot

Nanoscale imaging of RNA with expansion microscopy

inferredcites →https://doi.org/10.1038/nmeth1036openalex-snapshot

Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain

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In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes

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Nonblinking and long-lasting single-molecule fluorescence imaging

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Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain

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Spatially resolved transcriptomics and beyond

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Triggered amplification by hybridization chain reaction

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Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification

inferredcites →https://doi.org/10.1073/pnas.1213818110openalex-snapshot

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

inferredcites →https://doi.org/10.1073/pnas.1612826113openalex-snapshot

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

inferredcites →https://doi.org/10.1088/0953-8984/22/19/194116openalex-snapshot

How deeply cells feel: methods for thin gels

inferredcites →https://doi.org/10.1093/nar/gkw784openalex-snapshot

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

inferredcites →https://doi.org/10.1093/nar/gnh056openalex-snapshot

Direct isolation of poly(A)+ RNA from 4 M guanidine thiocyanate-lysed cell extracts using locked nucleic acid-oligo(T) capture

inferredcites →https://doi.org/10.1126/science.1072241openalex-snapshot

Single-Cell Gene Expression Profiling

inferredcites →https://doi.org/10.1126/science.1190830openalex-snapshot

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain

inferredcites →https://doi.org/10.1126/science.1242975openalex-snapshot

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

inferredcites →https://doi.org/10.1126/science.1250212openalex-snapshot

Highly Multiplexed Subcellular RNA Sequencing in Situ

inferredcites →https://doi.org/10.1126/science.1260088openalex-snapshot

Expansion microscopy

inferredcites →https://doi.org/10.1126/science.280.5363.585openalex-snapshot

Visualization of Single RNA Transcripts in Situ

inferredcites →https://doi.org/10.1126/science.7522346openalex-snapshot

Padlock Probes: Circularizing Oligonucleotides for Localized DNA Detection

inferredcites →https://doi.org/10.1126/science.aaa6090openalex-snapshot

Spatially resolved, highly multiplexed RNA profiling in single cells

inferredcites →https://doi.org/10.1128/jcm.34.12.3196-3202.1996openalex-snapshot

An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma

inferredcites →https://doi.org/10.1186/2192-2853-1-6openalex-snapshot

A high-density 3D localization algorithm for stochastic optical reconstruction microscopy

inferredcites →https://doi.org/10.1242/dev.086975openalex-snapshot

A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

inferredcites →https://doi.org/10.1242/dev.138560openalex-snapshot

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1038/s41576-022-00515-3openalex-snapshot

The emerging landscape of spatial profiling technologies

inferred← citeshttps://doi.org/10.1038/s41586-019-1035-4openalex-snapshot

Visualizing DNA folding and RNA in embryos at single-cell resolution

inferred← citeshttps://doi.org/10.1038/s41586-019-1049-yopenalex-snapshot

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

inferred← citeshttps://doi.org/10.1038/s41586-021-03705-xopenalex-snapshot

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

inferred← citeshttps://doi.org/10.1038/s41586-023-06808-9openalex-snapshot

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

inferred← citeshttps://doi.org/10.1038/s41586-024-07806-1openalex-snapshot

Spatially clustered type I interferon responses at injury borderzones

inferred← citeshttps://doi.org/10.1038/s41587-020-00812-4openalex-snapshot

Building a high-quality Human Cell Atlas

inferred← citeshttps://doi.org/10.1038/s41587-021-01044-wopenalex-snapshot

Cell segmentation in imaging-based spatial transcriptomics

inferred← citeshttps://doi.org/10.1038/s41587-026-03328-5openalex-snapshot

Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics

inferred← citeshttps://doi.org/10.1038/s41588-020-0668-4openalex-snapshot

Characterizing the ecological and evolutionary dynamics of cancer

inferred← citeshttps://doi.org/10.1038/s41591-024-03215-zopenalex-snapshot

A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features

inferred← citeshttps://doi.org/10.1038/s41592-020-01037-8openalex-snapshot

Spatially resolved single-cell genomics and transcriptomics by imaging

inferred← citeshttps://doi.org/10.1038/s41592-020-0858-0openalex-snapshot

Highly specific multiplexed RNA imaging in tissues with split-FISH

inferred← citeshttps://doi.org/10.1038/s41592-020-0890-0openalex-snapshot

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

inferred← citeshttps://doi.org/10.1038/s41592-022-01653-6openalex-snapshot

ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

inferred← citeshttps://doi.org/10.1038/s41592-022-01673-2openalex-snapshot

Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging

inferred← citeshttps://doi.org/10.1038/s41592-023-01835-wopenalex-snapshot

IMAGE-seq and you shall find

inferred← citeshttps://doi.org/10.1038/s41592-023-01911-1openalex-snapshot

Expansion spatial transcriptomics

inferred← citeshttps://doi.org/10.1038/s41593-020-0602-1openalex-snapshot

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

inferred← citeshttps://doi.org/10.1038/s41596-019-0206-yopenalex-snapshot

Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging

inferred← citeshttps://doi.org/10.1038/s41596-019-0269-9openalex-snapshot

Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M

inferred← citeshttps://doi.org/10.1038/s41596-020-00478-xopenalex-snapshot

Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA

inferred← citeshttps://doi.org/10.1038/s41596-021-00518-0openalex-snapshot

Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue

inferred← citeshttps://doi.org/10.1038/s41596-021-00556-8openalex-snapshot

CODEX multiplexed tissue imaging with DNA-conjugated antibodies

inferred← citeshttps://doi.org/10.1038/s41598-018-22297-7openalex-snapshot

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

inferred← citeshttps://doi.org/10.1038/s41598-019-43943-8openalex-snapshot

Multiplexed detection of RNA using MERFISH and branched DNA amplification

inferred← citeshttps://doi.org/10.1038/s41598-020-70756-xopenalex-snapshot

Chromatin and transcriptome changes in human myoblasts show spatio-temporal correlations and demonstrate DPP4 inhibition in differentiated myotubes

inferred← citeshttps://doi.org/10.1038/s41598-025-17477-1openalex-snapshot

Protocol optimization improves the performance of multiplexed RNA imaging

inferred← citeshttps://doi.org/10.1038/s42003-021-02762-2openalex-snapshot

Preparation of long single-strand DNA concatemers for high-level fluorescence in situ hybridization

inferred← citeshttps://doi.org/10.1038/s42003-024-06714-4openalex-snapshot

UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples

inferred← citeshttps://doi.org/10.1038/s42003-026-09675-yopenalex-snapshot

A practical guide to targeted single-cell RNA sequencing technologies

inferred← citeshttps://doi.org/10.1038/s42003-026-09979-zopenalex-snapshot

autoFISH: a modular toolbox for sequential single-molecule RNA FISH experiments

inferred← citeshttps://doi.org/10.1038/s43586-021-00080-9openalex-snapshot

Tissue clearing

inferred← citeshttps://doi.org/10.1039/c7sc05089eopenalex-snapshot

Highly multiplexed single-cell in situ RNA and DNA analysis with bioorthogonal cleavable fluorescent oligonucleotides

inferred← citeshttps://doi.org/10.1039/c9sc04916aopenalex-snapshot

An intramolecular catalytic hairpin assembly on a DNA tetrahedron for mRNA imaging in living cells: improving reaction kinetics and signal stability

inferred← citeshttps://doi.org/10.1039/d2lc00067aopenalex-snapshot

Cell-based biocomposite engineering directed by polymers

inferred← citeshttps://doi.org/10.1042/ebc20180072openalex-snapshot

Application of single-cell RNA sequencing methodologies in understanding haematopoiesis and immunology

inferred← citeshttps://doi.org/10.1073/pnas.1806189115openalex-snapshot

Single-molecule analysis of endogenous β-actin mRNA trafficking reveals a mechanism for compartmentalized mRNA localization in axons

inferred← citeshttps://doi.org/10.1073/pnas.1912459116openalex-snapshot

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

inferred← citeshttps://doi.org/10.1073/pnas.2424591122openalex-snapshot

Highly spatial–temporal electrochemical profiling of molecules trafficking at a single mitochondrion in one living cell

inferred← citeshttps://doi.org/10.1080/14737159.2021.1900735openalex-snapshot

Spatial profiling technologies and applications for brain cancers

inferred← citeshttps://doi.org/10.1080/14737159.2022.2085508openalex-snapshot

Detection of SARS-CoV-2 in tissue: the comparative roles of RT-qPCR, in situ RNA hybridization, and immunohistochemistry

inferred← citeshttps://doi.org/10.1080/21541264.2023.2199669openalex-snapshot

Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies

inferred← citeshttps://doi.org/10.1088/2050-6120/abe6fbopenalex-snapshot

Navigating across multi-dimensional space of tissue clearing parameters

inferred← citeshttps://doi.org/10.1089/genbio.2023.0032openalex-snapshot

Technical Advances and Applications of Spatial Transcriptomics

inferred← citeshttps://doi.org/10.1091/mbc.e19-08-0424openalex-snapshot

From stem cell to immune effector: how adhesion, migration, and polarity shape T-cell and natural killer cell lymphocyte development in vitro and in vivo

inferred← citeshttps://doi.org/10.1093/bib/bbag190openalex-snapshot

Benchmarking cell-type-specific spatially variable gene detection methods

inferred← citeshttps://doi.org/10.1093/bioadv/vbae064openalex-snapshot

Uncover spatially informed variations for single-cell spatial transcriptomics with STew

inferred← citeshttps://doi.org/10.1093/bioinformatics/btad005openalex-snapshot

A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data

inferred← citeshttps://doi.org/10.1093/nar/gkaa312openalex-snapshot

dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues

inferred← citeshttps://doi.org/10.1093/nar/gkab120openalex-snapshot

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses

inferred← citeshttps://doi.org/10.1093/nar/gkx1206openalex-snapshot

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

inferred← citeshttps://doi.org/10.1093/nar/gkx874openalex-snapshot

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

inferred← citeshttps://doi.org/10.1093/plcell/koaf282openalex-snapshot

Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution

inferred← citeshttps://doi.org/10.1093/plcell/koaf286openalex-snapshot

Hidden gradients before form: a spatial transcriptomic atlas of wheat spike patterning

inferred← citeshttps://doi.org/10.1094/pbiomes-12-20-0090-eopenalex-snapshot

Managing Plant Microbiomes for Sustainable Biofuel Production

inferred← citeshttps://doi.org/10.1094/pbiomes-5-1openalex-snapshot

Full Issue PDF

inferred← citeshttps://doi.org/10.1097/tp.0000000000004587openalex-snapshot

Opportunities for High-plex Spatial Transcriptomics in Solid Organ Transplantation

inferred← citeshttps://doi.org/10.1101/121202openalex-snapshot

The Human Cell Atlas

inferred← citeshttps://doi.org/10.1101/2020.06.04.105700openalex-snapshot

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

inferred← citeshttps://doi.org/10.1101/2021.01.27.428247openalex-snapshot

PICASSO: Ultra-multiplexed fluorescence imaging of biomolecules through single-round imaging and blind source unmixing

inferred← citeshttps://doi.org/10.1101/2022.02.28.482278openalex-snapshot

Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas

inferred← citeshttps://doi.org/10.1101/2022.04.17.488596openalex-snapshot

SOAR elucidates disease mechanisms and empowers drug discovery through spatial transcriptomics

inferred← citeshttps://doi.org/10.1101/2022.06.27.497769openalex-snapshot

Three-dimensional Interrogation of Cell Types and Instinctive Behavior in the Periaqueductal Gray

inferred← citeshttps://doi.org/10.1101/2022.09.14.507902openalex-snapshot

ARTseq-FISH reveals position-dependent fate decisions driven by cell cycle changes

inferred← citeshttps://doi.org/10.1101/2022.09.14.508048openalex-snapshot

Mapping the cellular and molecular organization of mouse cerebral aging by single-cell transcriptome imaging

inferred← citeshttps://doi.org/10.1101/2023.01.07.523058openalex-snapshot

Development of Multiomics in situ Pairwise Sequencing (MiP-Seq) for Single-cell Resolution Multidimensional Spatial Omics

inferred← citeshttps://doi.org/10.1101/2023.07.23.550157openalex-snapshot

Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery

inferred← citeshttps://doi.org/10.1101/2023.10.10.561789openalex-snapshot

Uncover spatially informed shared variations for single-cell spatial transcriptomics with STew

inferred← citeshttps://doi.org/10.1101/2023.12.17.572084openalex-snapshot

STIE: Single-cell level deconvolution, convolution, and clustering in spatial transcriptomics by aligning spot level transcriptome to nuclear morphology

inferred← citeshttps://doi.org/10.1101/2024.07.03.601914openalex-snapshot

A DIY guide for image-based spatial transcriptomic: TLS as a case example

inferred← citeshttps://doi.org/10.1101/2024.11.14.623566openalex-snapshot

autoFISH - a modular toolbox for sequential smFISH experiments

inferred← citeshttps://doi.org/10.1101/2024.11.18.624217openalex-snapshot

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

inferred← citeshttps://doi.org/10.1101/2024.12.06.627193openalex-snapshot

A spatial mRNA profiling workflow using Rapid Amplified Multiplex FISH (RAMFISH)

inferred← citeshttps://doi.org/10.1101/2025.04.08.645087openalex-snapshot

Self-contrastive learning enables interference-resilient and generalizable fluorescence microscopy signal detection without interference modeling

inferred← citeshttps://doi.org/10.1101/2025.05.09.653118openalex-snapshot

In situ profiling of plasma cell clonality with image-based single-cell transcriptomics

inferred← citeshttps://doi.org/10.1101/2025.06.13.659535openalex-snapshot

Non-disruptive 3D profiling of combinations of epigenetic marks in single cells

inferred← citeshttps://doi.org/10.1101/2025.10.01.679703openalex-snapshot

Photolabile oligonucleotides combined with topologically imposed light gradients enable spatially resolved single-cell transcriptomics and epigenomics

inferred← citeshttps://doi.org/10.1101/2025.11.02.686137openalex-snapshot

MERFISH+, a Large-Scale, Multi-Omics Spatial Technology Resolves the Molecular Holograms of the 3D Human Developing Heart

inferred← citeshttps://doi.org/10.1101/208355openalex-snapshot

The Transcriptional Logic of Mammalian Neuronal Diversity

inferred← citeshttps://doi.org/10.1101/432104openalex-snapshot

Single-cell in situ transcriptomic map of astrocyte cortical layer diversity

inferred← citeshttps://doi.org/10.1101/456855openalex-snapshot

Resolving Tumour Clonal Heterogeneity and Spatial Complexity using Nuclear Tandem Epitope Protein (nTEP) Barcoding

inferred← citeshttps://doi.org/10.1101/cshperspect.a034124openalex-snapshot

Proteome-Scale Mapping of Perturbed Proteostasis in Living Cells

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