This image depicts a mouse brain tissue section where each color represents an individual cell type in the brain.

Vizgen Merscope

The Vizgen Merscope is a gene-targeted, single-cell imaging platform that profiles entire tissue regions using probe-based gene panels. This technology is based on multiplexed error robust fluorescence in situ hybridization (MERFISH) and supports custom probe designs for any species. It is compatible with formalin-fixed paraffin-embedded (FFPE) and fresh frozen samples.

This spatially resolved single-cell transcriptome profiling technology allows for the direct visualizing and counting of RNA transcripts from hundreds to more than 10,000 genes in cells or tissue slices. This is achieved by massively multiplexing single molecule fluorescence in situ hybridization (smFISH) through error robust barcoding, combinatorial labeling and sequential imaging.

Merscope is validated with human and mouse fresh frozen and FFPE tissues, but it is compatible with virtually any sample with a well-annotated transcriptome. Vizgen offers custom gene panel design through their Gene Panel Design Portal.

Custom gene panels are available in four sizes:

  • Up to 140 genes.
  • Up to 300 genes.
  • Up to 500 genes.
  • Up to 1,000 genes.

In addition to custom panels, Vizgen also provides a growing number of enabled options to be released as predesigned gene panels.

Prior to starting a project, the DV200 values of the tissue samples are measured to determine RNA integrity. Additional samples also are processed with the Merscope sample verification kit to assess the RNA quality of each sample. This will ensure that only high-quality samples are imaged.

The sample verification kit can be used to verify that the RNA quality after sample preparation will result in adequate MERFISH imaging quality. In samples where autofluorescence is prevalent, tissues are placed under the Merscope Photobleacher to remove excess background signal. Tissue samples also can be stained using the Merscope cell boundary staining kit to identify cell boundaries, enabling individual cell analysis. In addition, the Merscope platform offers investigators the opportunity to detect up to six proteins simultaneously with hundreds of RNA molecules.

Once sample quality is determined, gene panels are selected. For custom panels, Vizgen provides gene panel design software to assist with gene panel construction. Vizgen also offers bioinformatician support to aid in gene panel design and review.

Once the gene panel is received, sample processing is done by:

  • Sectioning FFPE or fresh frozen tissue sections onto round cover slides centered into a 1 cm2 imageable area.
  • Performing tissue-clearing steps to improve signal detection sensitivity.
  • Processing the tissue in the Merscope device for multiplexed, error robust florescence in situ hybridization with the gene panel of interest to generate single-cell gene expression image data.

The Merscope instrument software, in combination with the Merscope analysis computer, automatically processes the raw images to output spatial genomics measurements in a format ready for immediate downstream analysis. The output includes:

  • The list of all detected transcripts and their spatial locations in three dimensions (CSV files).
  • Mosaic images (TIFF files).
  • Output from the cell segmentation analysis: the transcripts per cell matrix (CSV files).
  • The cell metadata (CSV files).
  • The cell boundaries (HDF5 files).
  • Various logs and tasks.
  • A summary (PNG file).
  • A binary for use with the Merscope Vizualizer software to visualize and analyze the data.

The Merscope Platform includes the Merscope Vizualizer Data Visualization and Analysis software. Once analysis is complete, the output files can be analyzed using the Vizualizer software. The data outputs also are compatible with tools developed by the academic community.