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MERFISH Spatial profiling technology


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 Advantages


High Spatial Resolution

Localize RNA transcripts with subcellular resolution.


High Throughput

Profile a square centimeter of tissue in a single run.


High Sensitivity

Detect difficult-to-characterize lowly expressed genes with single-molecule sensitivity.


High Multiplexing Power

Custom multiplexing from 100s of RNAs.

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How MERFISH Technology works

Learn how Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH) spatial profiling technology works. MERFISH is a spatially resolved single-cell transcriptome profiling technology.


MERFISH technology is built upon an RNA imaging-based technique called single molecule FISH. To perform smFISH, fluorescently tagged oligo probes label RNA transcripts of interest, and by directly counting the number of fluorescent RNA targets, you can determine each gene’s expression profile. MERFISH expands on single molecule FISH by adding combinatorial labeling, sequential rounds of imaging and error robust barcoding to greatly increase the multiplexing capacity and enable spatially resolved, single-cell gene expression profiling.

MERFISH implements a novel combinatorial barcoding scheme where each targeted gene in the custom designed panel is assigned a unique binary barcode. Sequential rounds of imaging are used to generate the barcode, a sequence of zeros and ones. This combinatorial barcoding scheme dramatically increases multiplexing capacity.

Additionally, this barcoding system is further designed with error robustness. If there is a readout error, the system can assign the readout to the nearest correct barcode. This is what makes MERSCOPE’s results accurate and consistent.

With MERFISH spatial profiling technology you can spatially localize transcripts with nanometer-scale resolution, mapping gene expression across whole tissues and discovering the complex arrangement of cell types and states.

Peer-Reviewed Publications

Learn how spatially resolved transcriptomics with MERFISH technology enables the deep profiling of the expression of RNAs in single cells in their native context revealing cell type, state, organization, interactions, and function within cell culture and tissue.

Spatial and single-cell transcriptomics reveal neuron-astrocyte interplay in long-term memory

Abstract Memory encodes past experiences, thereby enabling future plans. The basolateral amygdala (BLA) is a center of salience networks that underlie emotional experience and thus plays a key role in long-term fear memory formation. Here...

InClust+: the multimodal version of inClust for multimodal data integration, imputation, and cross modal generation

Abstract With the development of single-cell technology, many cell traits (e.g. gene expression, chromatin accessibility, DNA methylation) can be measured. Furthermore, the multi-omic profiling technology could jointly measure two or more traits in a single...

STdGCN: accurate cell-type deconvolution using graph convolutional networks in spatial transcriptomic data

Abstract Spatially resolved transcriptomics performs high-throughput measurement of transcriptomes while preserving spatial information about the cellular organizations. However, many spatially resolved transcriptomic technologies can only distinguish spots consisting of a mixture of cells instead of...


What customers are saying


Using MERFISH technology, researchers at the Allen Institute were able to gather cellular-resolution spatial transcriptomic data that advanced us significantly closer toward our goal of creating a taxonomy of cell types and a description of their connectivity within brain circuits – laying the groundwork to one day understanding how brain circuits function.

In the hands of the research community, I believe that MERSCOPE will be a powerful tool for standardizing the way we characterize different cell types, not just in the brain, but also in the rest of the body, ultimately bringing a deeper level of understanding to all life science research .”

Hongkui Zeng, Ph.D.

Executive VP & Director of the Allen Institute for Brain Science


“MERSCOPE is a game changer- it’s a giant leap from customer-built microscopes that only work in a few labs to a system that’s broadly adaptable. It’s really transformative because it allows molecular labs without experience with optics to use the system and generate high quality data.”


Professor of Cellular and Molecular Medicine
Member, Ludwig Institute for Cancer Research

Data images


MERSCOPE FFPE Human Immuno-oncology

The dataset contains 16 total datasets from 8 FFPE tumor tissue types including breast, colon, lung, liver, skin, prostate, uterine and ovarian, each measuring 500 genes totaling over 4 billion transcripts and 9 million cells cumulatively.


Vizgen MERFISH Mouse Liver Map

This dataset contains a MERFISH measurement of a gene panel containing 347 total genes. The dataset includes the list of detected transcripts, gene counts per cell matrix, additional spatial cell metadata, cell boundary polygons, and DAPI images.


Vizgen MERFISH Mouse Receptor Map

This dataset contains a MERFISH measurement of a gene panel containing 483 total genes including canonical brain cell type markers, GPCRs, and RTKs measured on 3 full coronal slices across 3 biological replicates. The dataset includes the list of detected transcripts, gene counts per cell matrix, additional spatial cell metadata, cell boundary polygons, and DAPI images


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

Learn how MERFISH enables researchers to perform highly multiplexed in situ spatial gene profiling across whole tissue slices.

Learn more about MERSCOPE Platform