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The MERSCOPE Platform from Vizgen is enabled by Multiplexed Error-Robust Fluorescence in-situ Hybridization (MERFISH). MERFISH is a spatial transcriptomics technology that expands the multiplexing capabilities of single molecule fluorescent in-situ hybridization (smFISH) via a combinatorial barcode coupled with sequential rounds of imaging. The technology enables detection of hundreds to thousands of single molecule targets at sub-cellular resolution. While MERFISH was designed to be compatible with fresh or fixed frozen tissues, Vizgen has demonstrated efficacy of the technology on FFPE tissue specimens.

Pros and cons


  • Commercial kit
  • Single cell resolution
  • High detection efficiency
  • Formalin fixed, paraffin embedded (FFPE) tissue compatible
  • Provides subcellular transcript localization information
  • Compatible with histological staining including DAPI
  • Protein co-detection is supported


  • A curated panel of usually a few hundred genes is required. However, Vizgen provides curated gene panels for neuroscience and oncology, as well as panel design services.
  • Data size is harder to manage for larger tissue areas and number of samples. Not all spatial analysis methods can scale to hundreds of thousands to millions of cells.

Getting Started

Several MERFISH datasets have been generated on the MERSCOPE Platform and are publicly available from Vizgen on their website. We provide examples available for processing the output of various spatial transcriptomics technologies into a SpatialFeatureExperiment(SFE) object for use with Voyager in the vignette below.

The vignette provides technology specific notes for data downloaded from Vizgen. Briefly, Vizgen provides cell metadata and the gene count matrix as CSV files which can be read in quickly with the vroom package. Cell segmentation data are provided as HDF5 files that are delineated by field of view.

Vignette Colab Notebook Description
Create a SFE object Colab Notebook Download data, create SFE object, Vizgen/MERFISH specific notes

Analysis Workflows

The vignettes below demonstrate workflows that can be implemented with Voyager using data generated with the MERFISH technology. The publicly available MERFISH datasets profile hundreds of genes in hundreds of thousands to millions of cells. Thus, the vignettes linked below can provide some context on the capabilities of Voyager for moderate to large datasets.

Vignette Colab Notebook Description
MERFISH mouse liver analysis Colab Notebook Perform basic QC, compute Moran’s I, length scales of spatial autocorrelation, binning, variogram models, PCA for large datasets
MULTISPATI PCA and negative spatial autocorrelation Colab Notebook Run MULTISPATI PCA on MERFISH mouse liver dataset, and compare the results to those from non-spatial PCA