A Letter from Vizgen CEO to Customers and Researchers

MERSCOPETM Platform for Spatial Transcriptomics

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.



Position yourself at the forefront of scientific discovery with the MERSCOPETM 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 MERSCOPETM 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 MERSCOPETM 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 500 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 VizgenTM Gene Panel Portal is a user-friendly web-based application for building custom gene panels to run on the MERSCOPETM 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

The MERSCOPE Workflow


MERSCOPETM Vizualizer Software

The MERSCOPETM  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
laptop open with MERSCOPE Vizualizer Software displaying spatial location of the detected RNA transcripts from the MERFISH Mouse Brain Receptor Map dataset.

MERSCOPE Reagents & Consumables

Explore our Reagents and Consumables
Vizgen manufactures a variety of reagents and consumables needed to run MERFISH measurements with the MERSCOPETM Platform:
Product Description
MERSCOPE Slides Sample slides for MERSCOPE Instrument that are functionalized for tissue samples to enable Vizgen sample preparation protocols.
MERSCOPE Gene Panels Custom gene panels comprised of encoding probes targeting. Currently available in three sizes; up 140 genes, up to 300 genes and up to 500 genes.
MERSCOPE Gene Imaging Kits Imaging reagent kits containing the reagents and cartridge for running a measurement on the MERSCOPE TM Platform. Currently available in three sizes; up 140 genes, up to 300 genes and up to 500 genes.
MERSCOPE Cell Boundary Staining Kit Kit containing a 3-protein staining reagent for cell segmentation in dense tissues. Compatible with Human and Mouse samples.
MERSCOPE Sample Prep Kit Kit containing sample preparation reagents for 20 samples. Compatible with fixed, fresh frozen tissue and cultured cells.
MERSCOPE Sample Verification Kit Kit containing smFISH probes and imaging reagents to do a single imaging run. Currently available for human and mouse.
MERSCOPE Protein Stain Kits MERSCOPE Anti-Mouse Protein Stain Kit, MERSCOPE Anti-Rabbit Protein Stain Kit, MERSCOPE Anti-Goat Protein Stain Kit, MERSCOPE Anti-Rat Protein Stain Kit, MERSCOPE Anti-Human Protein Stain Kit, and MERSCOPE Anti-Chicken Protein Stain Kit.
MERSCOPE Protein Stain Verification Kits MERSCOPE Protein Verification Kit (Mouse, Rabbit, Goat) and MERSCOPE Protein Verification Kit (Rat, Human, Chicken).
MERSCOPE PanNeuro Cell Type Panel MERSCOPE™ PanNeuro Cell Type 500 Gene Panel (Mouse)
MERSCOPE PanCancer Pathways Panel MERSCOPE™ PanCancer Pathways 500 Gene Panel (Human)
Explore our Reagents and Consumables

MERSCOPE Frequently Asked Questions

Still have questions? Contact us.

Popular MERSCOPE Resources


Spatio-relational inductive biases in spatial cell-type deconvolution

Ramon Viñas, Paul Scherer, Nikola Simidjievski, Mateja Jamnik, Pietro Liò
bioRxiv (2023)

Abstract Spatial transcriptomic technologies profile gene expression in-situ, facilitating the spatial characterisation of molecular phenomena within tissues, yet often at multi-cellular resolution. Computational approaches have been developed to infer fine-grained cell-type compositions across locations, but they…

Read More

WebAtlas pipeline for integrated single cell and spatial transcriptomic data

Tong Li, eDavid Horsfall, Daniela Basurto-Lozada, Kenny Roberts, Martin Prete, John E G Lawrence, Peng He, Elisabeth Tuck, Josh Moore, Shila Ghazanfar, Sarah Teichmann, Muzlifah Haniffa, Omer Ali Bayraktar
bioRxiv (2023)

Abstract Single cell and spatial transcriptomics illuminate complementary features of tissues. However, online dissemination and exploration of integrated datasets is challenging due to the heterogeneity and scale of data. We introduce the WebAtlas pipeline for…

Read More
View all resources
If you are interested in using MERSCOPE for your research, contact us today.
Request a Quote