Combine single-cell and spatial transcriptomics analysis with MERSCOPE spatial imaging

Explore new dimensions with MERSCOPE, the first high multiplexing, high resolution in situ platform to combine single-cell and spatial genomics analysis powered by MERFISH technology.


The MERSCOPE® Platform

Position yourself at the forefront of scientific discovery with the MERSCOPE® Platform, the industry’s first high plex, in situ single-cell spatial genomics solution. MERSCOPE uses MERFISH spatial transcriptomics technology to directly map and quantify the spatial distribution of hundreds to tens of thousands of RNA species in individual cells, without the need for downstream sequencing. MERSCOPE is incredibly versatile across applications and sample types, revolutionizing life sciences research.

A Complete Spatial Transcriptomics Solution

We integrated MERFISH spatial transcriptomics technology with high resolution spatial imaging, fluidics, image processing, and automation to deliver a complete end-to-end spatial genomics solution. The MERSCOPE® Platform comes with everything your lab needs to get started with spatial imaging. We built our expertise into every component of the system so you can easily obtain and analyze high-quality MERFISH measurements.

The MERSCOPE® Platform is comprised of:

  • MERSCOPE Instrument & Analysis Computer
  • Intuitive Instrument and Visualization Software
  • MERSCOPE Reagents & Consumables
MERSCOPE Flow Chamber (top) and MERSCOPE Imaging Cartridge (bottom). Both components get inserted into the MERSCOPE Imaging box for each MERFISH experiment.

Profile Large Tissue with Sub-cellular Resolution

Through combinatorial labeling, sequential imaging, and error-robust barcoding, MERFISH technology provides MERSCOPE with the highest detection efficiency and resolution available for spatially profiling the transcriptome, from whole tissue section to single-cell and finally sub-cellular spatial imaging across the whole tissue. We are proud to offer a Data Release Program to provide researchers with public access to MERSCOPE generated spatial genomics data.

spatially resolved transcriptome of a mouse brain slice generated by MERSCOPE. Whole tissue resolution (left). Single-Cell view (center). Sub-celluar resolution at (right).

MERSCOPE Instrument

MERSCOPE uses MERFISH technology to directly map and quantify the spatial
distribution of hundreds to tens of thousands of RNA species in individual cells, without the need for downstream sequencing. The instrument is comprised of an imaging box and a processing computer.

High Sensitivity

Detect low expressing genes that can be missed using other technologies.

High Spatial Resolution

Localize RNA transcripts at a sub-cellular level with ≤100 nm resolution.

Effective Multiplexing Capacity

High multiplexing with custom gene panel design. Current chemistry up to 1000 genes.


Measure your specified genes on many sample or tissue types.

Ease of Use

Intuitive automation and complete reagent packs allow for a walk-away system.

MERSCOPE instrument and screen
Configure Panel
Provide required information including panel name, reference organism and tissue type.
Specify Genes
Add genes to your custom MERFISH panel.
Refine Selection
Receive real-time feedback on your gene panel to resolve issues.
Request Quote
Review and finalize your gene panel to request a quote.

Vizgen® Gene Panel Design Portal

The Vizgen® Gene Panel Portal is a user-friendly web-based application for building custom gene panels to run on the MERSCOPE® Platform. With the Portal you can customize your gene panels with real-time feedback about which genes are most suitable for a MERFISH measurement. The Portal guides you through each step, making the entire process simple and easy.

From the Portal you can:

  • Build custom MERFISH gene panels
  • Request quotes for gene panels, reagents, and consumables
  • Download a panel’s Codebook
  • Access previously designed panels and quotes
  • Access Vizgen Customer resources
Explore Vizgen Gene Panel Design

Vizgen also offers Pre-Defined gene panels panels that are ready for your projects.

View Pre-Defined Panels

The MERSCOPE Workflow


MERSCOPE® Vizualizer Software

The MERSCOPE®  Vizualizer software enables users to interact, analyze, and interpret even the most complex spatial transcriptomics datasets generated by a MERFISH experiment. Our intuitive software seamlessly combines spatial context at the single-cell level to assist researchers with gaining valuable biological insights. With the tool, you can easily visualize MERFISH data including:

  • Imaged cells
  • Detected transcripts
  • Heat map- 2D cells-genes table
  • Scatterplot-displays dimensionality reduced cells and cell clusters
  • Generate high-resolution images
Learn More
laptop open with MERSCOPE Vizualizer Software displaying spatial location of the detected RNA transcripts from the MERFISH Mouse Brain Receptor Map dataset.

Vizgen Post-processing Tool for Cell segmentation

The Vizgen post-processing tool (VPT) uses cell segmentation methods to draw cell boundaries and generates single cell output by combining the results merfishdata. With VPT, users can change methods of cell segmentation to better fit the data for improved single-cell analysis.

VPT Software

Discover what customers have to say

“In my lab we are interested in biomechanical modeling of muscle, which requires a thorough understanding of the cellular and molecular organization within the tissue. By using MERSCOPE to create organ-wide atlases, we will be able to root our models in the precise physical architecture of muscles from healthy and diseased donors.”

Pallav Kosuri, PhD, Assistant Professor, Salk Institute

“I’m excited to have a MERSCOPE system installed in our Center, where we will use it to explore the molecular mechanisms of Alzheimer’s disease on a spatial transcriptome-wide level. I look forward to building on the proof-of-concept study, which cataloged the spatial distribution of 150 target genes in specific cell types and identified where early changes in gene expression occur in a mouse model of Alzheimer’s disease.”

Xiangmin Xu, PhD, Professor of Anatomy & Neurobiology and Director of the Center for Neural Circuit Mapping, School of Medicine at the University of California, Irvine

“Spatial Technologies are the new frontier in biomedical research, and we expect them to expand and potentially rewrite our understanding of human pathologies.”

Ioannis Vlachos, PhD, Director of the Spatial Technologies Unit and Co-Director of the Bioinformatics Program at BIDMC.

MERSCOPE Frequently Asked Questions

Still have questions? Contact us.

Popular MERSCOPE Resources

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If you are interested in using MERSCOPE for your research, contact us today.
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