Multiplexed Error-Robust Fluorescence in situ Hybridization

Merfish on Nikon Crest SD

MerFISH instrumental setup at DaMBIC

MerFISH – Imaging-based Spatial Transcriptomics Platform

  • Advanced platform for spatially resolved transcriptomics analysis.
  • Compatible with a wide range of cell cultures and tissue samples, including formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissues.
  • High-plex gene expression analysis, capable of profiling hundreds to thousands of RNA species simultaneously. Customizable panels to target specific genes of interest, providing flexibility for diverse research needs.
  • Flexible microscope platform allowing different levels of detail, depending on the application and need (resolution down to ~150 nm).

Explore the spatial transcriptomics capabilities with MerFISH

MerFISH combines the principles of fluorescence in situ hybridization (FISH) with multiplexed error-robust barcoding strategies. Sequential hybridization of probe sets, followed by imaging and signal decoding, allows for the precise identification of RNA species in a multiplexed manner.


The MerFISH workflow. Source: Chen, Kok Hao, et al. 2015. "Spatially resolved, highly multiplexed RNA profiling in single cells." Science.

The versatility and adaptability of MERFISH makes it a valuable tool for uncovering the complex molecular landscape of cells and tissues. See, among others, the following publications:

  • Mapping disease-related changes in gene expression: Cadinu, Paolo, et al. 2024. Cell.
  • Characterize subcellular compartmentalization of RNAs: Xia, Chenglong, et al. 2019. PNAS.

How to get access to the MerFISH technique?

For access to the MerFISH technique, under the CellX platform, please reach out to the Danish Molecular Biomedical Imaging Center (DaMBIC).


Location: V10-602a-0 (merfish)

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