First Platform for Massively Multiplexed Single-Cell In Situ Spatial Genomics Now Broadly Available to U.S. Market

Expanded availability coincides with Vizgen’s second public spatial genomics data set and a new web-based data visualization tool

CAMBRIDGE, Mass. January 18, 2022–(BUSINESS WIRE) —Vizgen, the life science company dedicated to improving human health by visualizing single-cell spatial genomics information, has today announced that the MERSCOPE® Platform is now broadly available across the United States.  Additionally, in a wave of innovation that has become the hallmark of the company, Vizgen has released its second, open-access data set – the MERFISH Mouse Liver Map, along with an interactive web-based data visualization platform.

Through MERSCOPE, a one-of-a-kind single-cell spatial genomics platform technology, Vizgen is ushering in a new era in genomics. Following MERSCOPE’s hugely successful limited release in August 2021, the company has continued to make this technology increasingly available and accessible, accelerating the field towards its next stage of evolution.

“At a time when the market demand for spatial genomics tools continues to grow and reach new heights, we are thrilled to make our MERSCOPE Platform available to the U.S. research community at large,” said Terry Lo, President and CEO of Vizgen. “We’ve seen great excitement surrounding our instrument, but this is just the beginning. We are working with our customers to bring new platform capabilities and applications throughout the year and continue to lead this new era of spatial genomics.”

MERSCOPE streamlines and automates MERFISH experiments, making them more accessible to a wider variety of labs, such as those led by researchers in academia, core labs, and pharmaceutical companies. The MERSCOPE Platform offers a user-friendly, full solution workflow facilitating each step of a MERFISH experiment, making it an attractive option for labs seeking to quickly and efficiently incorporate single-cell, spatial transcriptomics into their research. The instrument is accompanied by a custom gene panel design portal, reagents and consumables, an analytical computer for integrated image processing, and interactive data visualization software. The MERSCOPE Platform is also flexible and amenable to a large variety of sample or tissue types. Together these features enable the spatial profiling of hundreds of millions of individual transcripts from hundreds of genes across hundreds of thousands of cells in a single instrument run. With the highest detection efficiency available, MERSCOPE enables mapping out the spatial organization of cell types that are unresolvable with other technologies.

“We see immense potential for MERSCOPE in my lab, where we believe that this platform will soon drive countless advancements in our understanding of how gene regulatory changes alter disease risk, progression, and treatment response,” said Nicholas Banovich, Ph.D. Associate Professor at the Translational Genomics Research Institute and Director of its Center for Single Cell and Spatial Multiomics. “In carefully controlled experiments, we’ve used MERSCOPE in parallel with similar spatial genomics technologies and have found that MERSCOPE captured significantly more single-cell data than the other instruments. I’m deeply excited to see the translational impact that MERSCOPE-generated data has on human health”

MERSCOPE has broad applications in basic science, drug discovery, clinical pathology, and translational medicine in areas including oncology, immunology, infectious disease, developmental biology, and regenerative medicine. Furthermore, MERSCOPE has proven to be the premier platform for neurology studies, where spatially informed cellular data is vital to understanding how the neural network functions.

“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,” said Hongkui Zeng, Ph.D., Executive Vice President and Director of the Allen Institute for Brain Science. “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.”

Vizgen SVP Global Sales & Support Dale Levitzke adds, “Today marks the day that MERSCOPE will start earning its place as a staple in genomics and imaging labs everywhere, where we believe it will enable groundbreaking studies for years to come. We look forward to working with our US customers as well as expanding to select global markets later this year.”

About the Data Release Program at Vizgen

It is not just Vizgen customers who are mapping out biology: Vizgen continues to execute on a broader mission – to produce high-quality, open-source data sets that anyone, anywhere may access for their own research. Vizgen’s latest released data set is the MERFISH Mouse Liver Map. It is the second data release made freely available to the public through Vizgen’s ongoing Data Release Program. The map represents the exact position of transcripts from a panel of 347 genes of interest.

The Vizgen MERFISH Mouse Liver Map data set offers a single-cell, spatially informed map of the mouse liver. The liver is comprised of numerous different cell types which rely on a high degree of spatial organization to carry out key roles like taking up oxygen and nutrients, metabolizing hormones, and regulating blood glucose. By spatially profiling the expression of hundreds of genes and segmenting individual cells based on their cell boundary, the Vizgen MERFISH Mouse Liver Data Set provides a map of these tightly packed different cell types in situ and offers novel insights to the spatial heterogeneity of this organ.

One highlight of the panel is that it includes dozens of zonation-related genes that play a role in the spatial compartmentalization of metabolic pathways, a phenomenon known as liver zonation.1

This spatial division in liver metabolic function is well captured by Vizgen’s map, with differential expression profile along the liver lobular axis clearly observed among hepatocytes, which provides a unique opportunity to further explore the spatial relationships of other cell types with the hepatocytes residing in distinct zones. Vizgen’s map is meant to provide an anchor to understand changes between the cells and cell types of healthy vs. diseased tissue, and it may even indicate potential therapeutic targets to evaluate in future studies.

In addition to Vizgen’s first two publicly available data releases (mouse brain and liver), Vizgen plans to release additional data sets in 2022 from other mouse tissues as well as human tissues.


About the Interactive Web Visualizer

Vizgen has launched a free, web-based version of their complete MERSCOPE® Vizualizer software that will enable researchers to experience the advantages of MERSCOPE and catalyze engagement with the high-plex single-molecule spatial genomics data produced. Researchers everywhere will be able to conveniently interact with existing data sets and future data releases using this publicly accessible platform.

With the tool, users can interactively view the full output of a MERSCOPE experiment, including each detected transcript, the segmented cell boundaries, and underlying high-resolution images of DAPI and cell boundary stains.  As an interactive tool, users can zoom from a whole-tissue view down to subcellular resolution and visualize the expression of all or a select subset of genes across single-cells, and color cells based on their cell type annotation. The platform is easily accessible through the Vizgen website, to enable users to explore and easily draw out insight from that data.

About Vizgen

Vizgen is dedicated to pioneering the next generation of genomics, providing tools that demonstrate the possibilities of in situ single-cell spatial genomics, setting the standard for the spatial genomics field. These tools are enabling researchers to gain new insight into the biological systems that govern human health and disease with spatial context. The company’s MERSCOPE® Platform enables massively multiplexed, genome-scale nucleic acid imaging with high accuracy and unrivaled detection efficiency at subcellular resolution. MERSCOPE provides transformative insight into a wide range of tissue-scale basic research and translational medicine in oncology, immunology, neuroscience, infectious disease, developmental biology, cell and gene therapy, and is an essential tool for accelerating drug discovery and development. For more information, go to www.vizgen.com. Connect on social media TwitterLinkedIn and Facebook.


  1. Cunningham RP, Porat-Shliom N. Liver Zonation – Revisiting Old Questions with New Technologies. Front Physiol. 2021;12:732929. Published 2021 Sep 9. doi:10.3389/fphys.2021.732929