Merfish
Higher Resolution, Greater Discovery
Reveal deeper layers of biological complexity with MERFISH 2.0, where optimized chemistry drives sharper resolution for mapping transcripts and cell types with greater precision.
- Combinatorial Labeling
- Sequential Imaging
- Error Robust Barcoding
How MERFISH 2.0 Works
Multiplexed Error-Robust Fluorescence in situ Hybridization
MERFISH is a massively multiplexed single-molecule imaging technology for spatially resolved transcriptomics capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells.
- Combinatorial Labeling
- Sequential Imaging
- Error Robust Barcoding
MERFISH technology is built on the power of single-molecule RNA Fluorescent In Situ Hybridization (smFISH), combining advanced combinatorial labeling, sequential imaging, and error-robust barcoding to achieve unparalleled multiplexing capabilities.
With MERFISH 2.0, each RNA transcript is assigned a unique binary barcode, read through sequential imaging rounds. This system dramatically increases detection capacity and ensures error correction, while producing highly accurate, reproducible data.
By localizing transcripts with nanometer-scale resolution, MERFISH 2.0 maps gene expression across entire tissue samples, enabling researchers to uncover complex patterns of tissue organization, cell states, and their interactions across length scales.
- Perfected RNA Anchoring – Maintains transcript integrity and probe accessibility
- Enhanced Probe Binding – Maximizes occupancy rates at target sites
- Amplified Readout Probes – Increases the number of readout probes to maximize fluorescent signal
MERFISH 2.0 has Built Upon MERFISH chemistry
Best-in-Class Spatial Resolution
Precisely localize RNA transcripts with subcellular detail using the MERSCOPE platforms.
High Throughput
Combine MERFISH 2.0 customizable panels with MERSCOPE® Ultra to profile 3cm or with MERSCOPE® to profile 1cm and unlock best-in-class spatial resolution.
High Sensitivity
Detect more RNA transcripts with greater sensitivity, revealing cellular heterogeneity in extraordinary detail.
Broad Sample Compatibility
Achieve high performance across diverse sample types, including archival FFPE and frozen samples.
Fully Customizable Panels
Tailor experiments to your research needs with scalable and adaptable panel sizes.
Proven Legacy
Backed by over a decade of trusted performance and 100s of peer-reviewed publications.
Why Choose MERFISH 2.0?
With MERFISH 2.0, researchers can:
- Map the spatial organization of cell types with unmatched precision.
- Detect subtle transcriptomic variations to understand cell states and their interactions.
- Compare healthy and diseased conditions to guide therapeutic research.
- Leverage archival FFPE samples for impactful discoveries in cancer and beyond.
- 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 publications. Explore groundbreaking studies that reveal the potential of spatially resolved transcriptomics to decode tissue complexity.
Spatial Single-cell Analysis Decodes Cortical Layer and Area Specification
The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas1,2. The layers and areas are distinguished both molecularly, by diverse neuronal and glial cell...
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Single-cell multi-omics, spatial transcriptomics and systematic perturbation decode circuitry of neural crest fate decisions
Cranial neural crest (NC) cells, which can migrate, adopt multiple fates, and form most of the craniofacial skeleton, are an excellent model for studying cell fate decisions. Using time-resolved single-cell multi-omics, spatial transcriptomics, and systematic...
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Control of behavioral uncertainty by divergent frontal circuits
Both ambiguous inference from current input and internal belief from prior input causes uncertainty. The uncertainty is typically manifested as a normal distribution at behavioral level when only current inference is manipulated as variable. When...
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Publications
What Researchers Are Saying
Marco Genua, Giulia Chianella, Antonella Santoro, San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET)
Marco Genua, San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET)
Raymond Yip, WEHI, Australia
University Hospital Tübingen, Germany
Explore MERFISH Data
Access comprehensive datasets from studies using MERFISH technology:
MERSCOPE FFPE Human Immuno-oncology
Includes RNA profiling of FFPE tumor tissues with over 500 genes analyzed across millions of cells.
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Vizgen MERFISH Mouse Liver Map
MERFISH gene panel profiling with spatial metadata and cell boundary data.
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Vizgen MERFISH Mouse Receptor Map
MERFISH data highlighting brain cell markers, GPCRs, and RTKs from full coronal slices.
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