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MERSCOPE Ultra™ Spatial Imaging

Map transcripts across 3 cm² of tissue on a single slide with MERSCOPE Ultra™, a high-resolution in situ spatial genomics platform that offers a tissue-wide view of up to 1000 custom genes at single-cell resolution.

REQUEST A QUOTE DOWNLOAD BROCHURE

Visualize the transcriptome with MERSCOPE Ultra™

Unlock new insights by mapping and quantifying RNA species in tissues at single-cell resolution with MERSCOPE Ultra™, the leading high-plex, spatial genomics solution.

MERSCOPE Ultra™ offers two flow cell sizes, which enable cost efficiency and flexible experimental setups. The larger flow chamber expands the imageable area to 3.0 cm^², efficiently accommodating larger and multiple smaller samples.

Boost your research productivity with a system that supports imaging up to 9 cm² per week with a large flow cell or 6.25 cm² per week with the standard flow cell.

SEE RESEArCH APPLICATIONS

Fresh Frozen Human Brain

1.63cm² area
98 million total transcripts
63 counts/100um²
220 transcripts/cell

Dive deeper into your samples with MERFISH 2.0 sensitivity

Coming in late 2024, get more spatial transcriptomic data out samples with degraded RNA, including archival formalin-fixed paraffin-embedded (FFPE) samples.

Launching for both the MERSCOPE Ultra™ and the MERSCOPE^® Platform MERFISH 2.0 will leverage enhanced RNA anchoring and signal enhancement to build on the original MERFISH sensitivity and reproducibility.

With MERFISH 2.0, you will be able to directly map and quantify the spatial distribution of RNA species in individual cells in a wider array of samples.

LEARN ABOUT MERFISH TECHNOLOGY

Profile more tissue than ever before with new features

MERSCOPE Ultra™ is the next generation of the MERSCOPE Platform.

All the advantages of MERSCOPE^® now with Ultra benefits:

MERSCOPE

Class-leading data quality
Effective multiplexing
Platform flexibility
Superior cell segmentation

MERSCOPE Ultra^TM

3X Larger imageable area
1.8X Faster sample imaging and analysis
Optimized cost-per-sample economics
The only system with interchangeable experiment options
Combined industry-leading sample processing and data generation

Generate beautiful images while maximizing ROI

With two flow cell options, you can now align reagent consumption with area imaged.
The larger flow cell (Image B: FCX-L) is ideal for researchers who want to study large sample types (Image D) or analyze multiple smaller samples in a single experiment (Image C).
The standard flow cell (Image A: FCX-S) is ideal for researchers studying smaller samples or who want to quickly optimize a new sample type before maximizing throughput with the large flow cell.

Explore this flexibility by accessing our spatial transcriptomics data release program and witness the beauty and comprehensiveness of MERSCOPE Ultra^TMacross several fields of study.

ACCESS DATA RELEASE

MERSCOPE Ultra™ Instrument

The MERSCOPE Ultra™ Platform includes:

MERSCOPE Ultra^™ Instrument
High-performance analysis computer & Visualization Software
Compatibility with existing MERSCOPE^® and new MERSCOPE Ultra™ Reagents & Consumables

ACCESS MERSCOPE RESOURCES

Enhance your capabilities with:

Class leading sensitivity

Sub cellular resolution paired with sample clearing reduces background ensuring highest transcript detection.

Platform Flexibility

Custom panels, scalable multiplexing, species versatility and data analysis tools that work best for your workflow.

High Quality Specificity

Error-robust barcoding and correlation to scRNA-seq provide confidence.

MERFISH Chemistry

Enables new applications with high quality results without sacrificing sensitivity or specificity. More than 170 peer-reviewed journals and pre-prints..

Superior cell segmentation

Draw biologically true cell shapes and to accurately localize transcripts to identify cell types.

High-Resolution Optics

Minimizes optical crowding and allows for accurate measurements in areas of high expression.

Configure Panel

Provide 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 ensure MERFISH compatibility.

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 application for creating custom gene panels for the MERSCOPE^® Platform.

With the Portal, you can tailor your gene panels with real-time feedback on gene suitability for MERFISH measurements. This step-by-step guidance makes it easy to design a panel tailored to your spatial imaging needs.

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 Predesigned gene panels panels that are ready for your projects.

View Predesigned Panels

MERSCOPE Vizualizer Software

Interact with, analyze, and interpret even the most complex spatial transcriptomics datasets with the MERSCOPE Vizualizer software.

Gain valuable biological insights with intuitive software that resolves spatial context at the single-cell level.

With this 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

SEE THE VISUALIZER IN ACTION

Vizgen Post-processing Tool for Cell segmentation

You can choose the sensitivity of cell segmentation detection to best fit your data and improve analysis.
The Vizgen post-processing tool (VPT) uses cell segmentation methods to draw cell boundaries and generate single-cell outputs by combining the results with Merfish data.

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 Ultra^TM frequently asked questions

MERSCOPE Ultra^TM offers enhanced flexibility with two flow cell sizes (3.0 cm^² and 1.25 cm^²), optimizing reagent use and cost while supporting interchangeable experiment options. The large flow cell is ideal for large or multiple samples, allowing up to 9.0 cm² per week, while the standard flow cell is perfect for sample optimization, handling up to 6.25 cm^² per week.

Spatial imaging and analysis speeds are up to 2.0 times faster, with an optimized optical design and modernized APC for efficient processing. Compared to MERSCOPE, MERSCOPE Ultra^TM reduces imaging time for 1.0 cm^² from ~35 hours to ~18 hours, and can image 3.0 cm^² in ~36 hours.
- Fresh or fixed frozen,
- Adherent or suspended cells
- Formalin-fixed paraffin-embedded (FFPE) enabled by our FFPE Sample Preparation Kit.
We offer four different target sizes of our Gene Panels and Imaging Kits at this time:
- Up to 140 genes
- Up to 300 genes
- Up to 500 genes
- Up to 1000 genes
No. MERFISH is not a sequencing technology but leverages single-molecule FISH, the gold standard for quantifying gene expression. It uses multiple fluorescent probes to bind specifically to RNA targets, allowing direct counting of fluorescent RNA molecules.

This method ensures high detection efficiency, accurately quantifying RNA expression, including low-expressing genes that traditional single-cell sequencing struggles to detect.
MERSCOPE Ultra^TM offers two different flow cell sizes: FCX-L (3.0 cm^²) and FCX-S (1.25 cm^²). The imagable area for the legacy MERSCOPE system is 1.0 cm^².

The interchangeable flow cell options within MERSCOPE Ultra allow you to customize your experiments better and run them efficiently, either by studying large tissues or multiple samples for maximum reagent efficiency or testing smaller samples prior to scale-up with FCX-L.
The data output from a MERSCOPE measurement includes:
- The list of all detected transcripts and their spatial locations in three dimensions (.CSV)
- The mosaic images (.TIFF)
- Output from the cell segmentation analysis:
  - The transcripts per cell matrix (.CSV)
  - The cell metadata (.CSV)
  - The cell boundaries (.HDF5)

Popular MERSCOPE Resources

Application & Technical Notes

Vizgen 1000 Plex Gene Panel Lists

Vizgen 1000 Plex Gene Panel Lists for Human Brain and Mouse Brain.

Safety Data Sheets

MERSCOPE gene Imaging Cartridge 1000 SDS

VIEW ALL RESOURCES

Ready to unlock new dimensions in your research with MERSCOPE spatial transcriptomics?

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MERSCOPE Ultra™ Spatial Imaging

Visualize the transcriptome with MERSCOPE Ultra™

Dive deeper into your samples with MERFISH 2.0 sensitivity

Profile more tissue than ever before with new features

All the advantages of MERSCOPE^® now with Ultra benefits:

MERSCOPE

MERSCOPE Ultra^TM

Generate beautiful images while maximizing ROI

MERSCOPE Ultra™ Instrument

Enhance your capabilities with:

Class leading sensitivity

Platform Flexibility

High Quality Specificity

MERFISH Chemistry

Superior cell segmentation

High-Resolution Optics

MERSCOPE Ultra™ instrument specifications

Vizgen Flow Chambers Supported

Throughput

Multiplex Capacity

Optical Resolution

Lateral Resolution

Imaging Camera

On-Instrument Storage Capacity

Analysis PC Storage Capacity

Illumination Source

Automated Image Processing

Vizgen^® Gene Panel Design Portal

MERSCOPE Vizualizer Software

Vizgen Post-processing Tool for Cell segmentation

Discover what customers have to say

MERSCOPE Ultra^TM frequently asked questions

Popular MERSCOPE Resources

Vizgen 1000 Plex Gene Panel Lists

MERSCOPE gene Imaging Cartridge 1000 SDS

MERSCOPE Ultra™ Spatial Imaging

Visualize the transcriptome with MERSCOPE Ultra™

Dive deeper into your samples with MERFISH 2.0 sensitivity

Profile more tissue than ever before with new features

All the advantages of MERSCOPE® now with Ultra benefits:

MERSCOPE

MERSCOPE UltraTM

Generate beautiful images while maximizing ROI

MERSCOPE Ultra™ Instrument

Enhance your capabilities with:

Class leading sensitivity

Platform Flexibility

High Quality Specificity

MERFISH Chemistry

Superior cell segmentation

High-Resolution Optics

MERSCOPE Ultra™ instrument specifications

Vizgen Flow Chambers Supported

Throughput

Multiplex Capacity

Optical Resolution

Lateral Resolution

Imaging Camera

On-Instrument Storage Capacity

Analysis PC Storage Capacity

Illumination Source

Automated Image Processing

Vizgen® Gene Panel Design Portal

MERSCOPE Vizualizer Software

Vizgen Post-processing Tool for Cell segmentation

Discover what customers have to say

MERSCOPE UltraTM frequently asked questions

Popular MERSCOPE Resources

Vizgen 1000 Plex Gene Panel Lists

MERSCOPE gene Imaging Cartridge 1000 SDS

All the advantages of MERSCOPE^® now with Ultra benefits:

MERSCOPE Ultra^TM

Vizgen^® Gene Panel Design Portal

MERSCOPE Ultra^TM frequently asked questions