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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.

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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 cm², 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.

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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 UltraTM

  • 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 UltraTMacross 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
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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.

MERSCOPE Ultra™ instrument specifications

Technical Specification
MERSCOPE
MERSCOPE Ultra™

Vizgen Flow Chambers Supported

Technical Specification
MERSCOPE
MERSCOPE Ultra™

1) 1.0cm2 maximum imageable area

1) FCX-S (Standard): 1.25cm2 maximum imageable area
2) FCX-L (Large): 3cm2 maximum imageable area

Throughput

Technical Specification
MERSCOPE
MERSCOPE Ultra™

Up to 3.0cm2 per week

Up to 9.0cm2 per week

Multiplex Capacity

Technical Specification
MERSCOPE
MERSCOPE Ultra™

Up to 1000 genes

Up to 1000 genes

Optical Resolution

Technical Specification
MERSCOPE
MERSCOPE Ultra™

Oil immersion; High numerical aperture objective

Oil immersion; High numerical aperture objective

Lateral Resolution

Technical Specification
MERSCOPE
MERSCOPE Ultra™

100nm pixel size

100nm pixel size

Imaging Camera

Technical Specification
MERSCOPE
MERSCOPE Ultra™

Back-thinned cooled sCMOS camera

Back-thinned cooled sCMOS camera

On-Instrument Storage Capacity

Technical Specification
MERSCOPE
MERSCOPE Ultra™

15 TB

58 TB

Analysis PC Storage Capacity

Technical Specification
MERSCOPE
MERSCOPE Ultra™

15 TB

58 TB

Illumination Source

Technical Specification
MERSCOPE
MERSCOPE Ultra™

Multi-color laser

Multi-color laser

Automated Image Processing

Technical Specification
MERSCOPE
MERSCOPE Ultra™

Transcript decoding and cell segmentation

Transcript decoding and cell segmentation

1
Configure Panel

Provide information, including panel name, reference organism, and tissue type.

2
Specify Genes

Add genes to your custom MERFISH panel.

3
REFINE SELECTION

Receive real-time feedback on your gene panel to ensure MERFISH compatibility.

4
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 UltraTM frequently asked questions

Popular MERSCOPE Resources

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