MERSCOPE® VIZUALIZER SOFTWARE for Single Cell Gene Expression Analysis

MERSCOPE® VIZUALIZER SOFTWARE for Single Cell Gene Expression Analysis

The MERSCOPE® Vizualizer software enables interactive visualization of MERFISH spatial genomics data generated by the MERSCOPE­® Platform. Explore detected transcripts, segmented cell boundaries, high-resolution images and integrate single-cell gene expression analysis results.


Simple Installation

Software is easily downloaded and installed from our Vizgen Portal. It’s included with instrument purchase or Vizgen Lab Services Projects as part of the full MERSCOPE Platform solution.


Flexible Formats

The MERSCOPE Vizualizer loads MERFISH data using the .VZG file generated by each MERSCOPE instrument run, and integrates with multiple open file formats such as .CSV, .Parquet, and .HDF5.


Seamless Interactive Visualization

Users can zoom from a whole-tissue view down to sub-cellular resolution, visualize the expression of all or a select subset of genes across single cells, and color cells based on their cell type annotation.

See the software in action

See the Vizualizer in Action

The MERSCOPE Vizualizer software is available for all MERSCOPE users. Simply load MERFISH data generated from your MERSCOPE experiment into the Vizualizer to begin your single-cell gene expression analysis. Then start exploring the spatial distribution of transcripts and proteins across whole large tissue sections, down to the subcellular level. Turn transcripts on and off from the genes interface to focus on your genes of interest and uncover biological insights. Export your configured data images to use in scientific posters and manuscripts.

The FFPE Human Immuno-oncology Data Release spatially profiled eight different malignant human tumor types using a 500 gene panel, MERSCOPE FFPE Sample Prep Solution, and the MERSCOPE Cell Boundary Stain Kit. Above shows the MERFISH data generated by MERSCOPE from a human ovarian tumor tissue section featured in the data release displayed in the MERSCOPE Vizualizer. The richness of MERSCOPE data reveals the intricate spatial distribution of transcripts across the large tumor tissue section, down to the single-cell level, mapping the tumor microenvironment. Individual stromal cells are distributed across the tumor with 100s of transcripts detected per single cell. MERSCOPE detected 174 million individual transcripts from 500 genes across the tumor tissue section.


Spatial genomics information is only useful if you also have the right tools to make sense of it. The MERSCOPE Vizualizer software enables users to interact, analyze, and interpret even the most complex spatial genomics datasets generated by a MERFISH experiment. Our intuitive software seamlessly combines spatial context at the single-cell level to assist researchers with gaining a deeper understanding of biological complexity. With the tool, you can easily visualize MERFISH gene expression data from single cells to large areas of interest:

  • Explore detected transcripts, imaged proteins, and segmented cell boundaries
  • Import single-cell clustering/annotation and dimensionality reduction results from external analysis
  • Interact with UMAP/t-SNE scatter plots and heatmaps
  • Select genes and create custom gene groups with the genes interface
  • Select regions of interest for downstream analysis of your MERFISH data

Stained Images

Images of the image channels, if checked (e.g., DAPI, PolyT, or other co-detected proteins). The Images slider is used to set the overall transparency for the images. Individual channel sliders are used to set minimum and maximum contrast thresholds for each channel.



Shows the polygons representing cells, identified during data processing. The slider controls the transparency.



Visualize all or a subset of genes as dots, control color opacity, and size.


Regions of Interest (ROI)

Shows the ROIs in the set. The slider controls the transparency. ROIs span all z-planes and an ROI has the same boundary for all z-planes.


Cell Clustering

Cells can be clustered and exported to perform additional 3rd party analysis before being reimported.



Normalized and z-scored Leiden gene expression heatmaps

MERFISH Data Analysis

Use open source tools to perform single cell analysis such as Scanpy/Squidpy Seurat, or the Vizgen MERSCOPE Vizualizer Clustering Template, to create UMAP/tSNE plots and Leiden Clustering to interpret MERFISH spatial data.

  • Group and analyze cells by gene expression
  • Annotate and compare regions of interests
  • Identify and map cells to the spatial coordinates within the tissue
  • Visualize two data-sets side by side
  • Export high-resolution data images
Explore MERFISH Datasets

Gain Valuable Biological Insights with Your Spatial Data

Bulk and single-cell sequencing can simultaneously profile a multitude of cells on a genomics level, but these methods require the destruction of the native cellular structure. In contrast, in situ spatial genomics approaches like MERFISH with the MERSCOPE Platform can quantify hundreds of genes at single-cell resolution while retaining spatial context. MERFISH offers an unprecedented view into the cellular heterogeneity of tissues. The MERSCOPE Vizualizer gives researchers a way to easily access their MERFISH spatial data and uncover biological insights with single-cell gene expression analysis.

  • Discover and map novel cell types and cell states
  • Spatially profile gene expression in situ and directly visualize protein markers simultaneously within the same tissue sample
  • Resolve individual transcripts with nanometer-scale resolution
Learn more about MERSCOPE applications

System Requirements

For optimal performance, the MERSCOPE® Vizualizer software should be run on a system with the following recommended criteria:

  • Processor: Intel Core i9
  • RAM: 32 GB
  • Graphics: NVIDIA GeForce RTX 3080-10 Gb
  • SSD Capacity: 1 TB
Note: The MERSCOPE® Vizualizer software can be run on a system with lower capability, but may result in suboptimal performance, especially for large datasets. In the absence of an optimal graphics card, the MERSCOPE® Vizualizer software can be run on a GPU-enabled AWS EC2 instance. Install NVIDIA drivers following the instructions under Option 4: NVIDIA gaming drivers (G5 and G4dn instances)

File Formats Accepted

The MERSCOPE® Vizualizer software supports the import of data to feature sets via:

  • Annotated data, AnnData, saved using the .HDF5 format
  • Cell metadata as .CSV or .Parquet files
  • Region of Interest (ROI) geometries .CSV files

Frequently Asked Questions