What is multiplexing in situ hybridization?

Multiplexing in situ hybridization (MISH) is a technique that allows the simultaneous detection of multiple RNA targets within a single sample. By using unique probes labeled with different fluorophores or barcodes, researchers can visualize and analyze gene expression patterns with spatial context.

What are the limitations of fluorescence in situ hybridization?

FISH has limited multiplexing capacity compared to newer techniques, lower sensitivity for detecting low-abundance targets, and can be affected by autofluorescence in tissues. It also requires careful probe design and optimization to ensure specificity and signal clarity.

What is the difference between MERFISH and seqFISH?

Both are multiplexed in situ hybridization techniques, but they differ in encoding and readout strategies. MERFISH (Multiplexed Error-Robust FISH) uses barcoded probes with error-correction to improve accuracy, while seqFISH (Sequential FISH) relies on iterative hybridization and imaging cycles to detect transcripts. MERFISH prioritizes high detection efficiency, while seqFISH offers flexibility in multiplexing.

Technology > MERFISH

MERFISH 2.0

Higher Resolution, Greater Discovery

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How MERFISH 2.0 Works

Multiplexed Error-Robust Fluorescence in situ Hybridization

Reveal deeper layers of biological complexity with MERFISH 2.0, a single-molecule FISH-based imaging technology for spatially resolved transcriptomics, where optimized chemistry drives sharper resolution for mapping transcripts and cell types with greater precision.

MERFISH achieves unmatched multiplexing and subcellular resolution by assigning each RNA transcript a unique binary barcode decoded through iterative imaging rounds for accurate, reproducible results. Optimized probe chemistry and enhanced readout design boost sensitivity and specificity, even in degraded or archival FFPE samples, expanding transcript detection across diverse tissue types.

By localizing transcripts with nanometer precision, MERFISH 2.0 reveals the spatial organization of genes, cell states, and interactions, creating molecular maps that link expression to function.

Combinatorial Labeling
Sequential Imaging
Error Robust Barcoding

Perfected RNA Anchoring – Maintains transcript integrity and probe accessibility.
Enhanced Probe Binding – Maximizes occupancy at target sites for improved coverage.
Amplified Readout Probes – Boosts fluorescent signal for higher sensitivity and accuracy.

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MERFISH 2.0 is Built Upon MERFISH Chemistry

Map Challenging Tissues

Acquire high-quality, reproducible spatial data from even the most difficult samples, including archival FFPE and fresh-frozen tissues.

High Dynamic Range Transcript Capture

Improved sensitivity detects more RNA molecules with uncompromised specificity and subcellular resolution, revealing subtle expression gradients.

More Cells, More Insights

Generate richer datasets with more cells passing quality filters, enabling higher transcript detection and deeper biological context per sample.

Identify Cell Types and States

Distinguish rare and abundant cell populations across complex tissues to illuminate the mechanisms that drive health and disease.

Uncover More Spatial Interactions

Explore molecular and cellular crosstalk within intact tissue architecture to inform disease models and therapeutic discovery.

Proven, Scalable MERFISH Chemistry

Built on decades of MERFISH spatially resolved transcriptomics innovation, MERFISH 2.0 delivers scalable, high-confidence results.

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Why Choose MERFISH 2.0?

With MERFISH 2.0, researchers can:

Map cell types and spatial relationships with unmatched precision
Detect transcriptomic variations to study cell states and disease mechanisms
Leverage archival FFPE samples for high-quality data and impactful discoveries
Customize experiments to fit evolving research questions

More transcripts. More cells. More insights.

Peer-Reviewed Publications

Trusted by researchers worldwide, MERFISH is supported by 100s of peer-reviewed studies showcasing spatially resolved transcriptomics to decode tissue complexity and cellular organization.

Publications & Posters

Spatial Single-cell Analysis Decodes Cortical Layer and Area Specification

Publications & Posters

Single-cell multi-omics, spatial transcriptomics, and systematic perturbation decode circuitry of neural crest fate decisions

Publications & Posters

Control of behavioral uncertainty by divergent frontal circuits

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What Customers Are Saying

"Sectioning Bone Marrow for Spatial Transcriptomics required extensive optimization to preserve tissue quality and concomitantly maintain RNA integrity. Thanks to MERFISH 2.0, we were able to quantify millions of transcripts in this complex tissue. This will unleash a more comprehensive understanding of the bone-marrow microenvironment where cells of different lineage and commitment coexist within tight spatial confines."

Marco Genua, Giulia Chianella, Antonella Santoro, San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET)

"MERFISH and MERSCOPE are the perfect companion to achieve high quality spatial transcriptomic data which are extremely important to dissect the complexity of the tumor microenvironment. Thanks to MERFISH 2.0 we obtained incredible data also with pancreatic ductal adenocarcinoma (PDAC) tissue for which suboptimal RNA quality - given by the high RNase tissue content - will be not a technical constraint anymore."

Marco Genua, San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET)

“The data really amazed us with the extraordinary number of transcripts we could detect in sub-optimal samples—almost 10-fold higher than MERFISH 1.0!”

Raymond Yip, WEHI, Australia

"We decided on MERFISH due to the high sensitivity and the relatively low requirements for tissue samples. Our expectations were greatly surpassed by the astonishing (subcellular) resolution of MERFISH 2.0, especially when compared to MERFISH 1.0. This will allow us to mechanistically test the main hypothesis of the project using this data alone, Thank you very much!!!"

University Hospital Tübingen, Germany

Explore MERFISH Data

Access datasets from MERFISH 2.0 spatially resolved transcriptomics experiments and legacy MERFISH chemistry, showcasing the system’s sensitivity across diverse tissues.

MERFISH 2.0

From Breast and Colon Cancer to Human and Mouse Brain, this data release showcases how MERFISH 2.0 pushes the boundaries of spatial transcriptomics.

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MERSCOPE Ultra Data Release

Explore the spatial transcriptome with the latest generation of the MERSCOPE platform.

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Vizgen MERFISH (1.0) Mouse Receptor Map

Full coronal brain slices highlighting GPCR and RTK expression using legacy MERFISH chemistry.

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If you are interested in applying MERFISH 2.0 to your research, click here to learn more about Vizgen’s early engagement programs.

Learn More About Merscope Ultra Platform

Whether uncovering subtle transcriptomic variations or mapping complex cellular interactions, MERFISH 2.0 and MERSCOPE Ultra empower you to explore further and accelerate discoveries in spatial biology.

FAQ

Both are multiplexed in situ hybridization techniques, but they differ in encoding and readout strategies. MERFISH (Multiplexed Error-Robust FISH) uses barcoded probes with error-correction to improve accuracy, while seqFISH (Sequential FISH) relies on iterative hybridization and imaging cycles to detect transcripts. MERFISH prioritizes high detection efficiency, while seqFISH offers flexibility in multiplexing.