MERSCOPE Ultra^TM Spatial Imaging

MERSCOPE Ultra^TM frequently asked questions

• What’s new in MERSCOPE Ultra^TM?

  MERSCOPE Ultra^TM offers enhanced flexibility with two flow cell sizes (3.0 cm^² and 1.25 cm^²), optimizing reagent use and cost while supporting interchangeable experiment options. The large flow cell is ideal for large or multiple samples, allowing up to 9.0 cm² per week, while the standard flow cell is perfect for sample optimization, handling up to 6.25 cm^² per week.

  Spatial imaging and analysis speeds are up to 2.0 times faster, with an optimized optical design and modernized APC for efficient processing. Compared to MERSCOPE, MERSCOPE Ultra^TM reduces imaging time for 1.0 cm^² from ~35 hours to ~18 hours, and can image 3.0 cm^² in ~36 hours.

• What types of samples are compatible?
  • Fresh or fixed frozen,
  • Adherent or suspended cells
  • Formalin-fixed paraffin-embedded (FFPE) enabled by our FFPE Sample Preparation Kit.
• What is a standard number of target genes?

  We offer four different target sizes of our Gene Panels and Imaging Kits at this time:

  • Up to 140 genes
  • Up to 300 genes
  • Up to 500 genes
  • Up to 1000 genes
• Are MERSCOPE Ultra^TM reads being sequenced?

  No. MERFISH is not a sequencing technology but leverages single-molecule FISH, the gold standard for quantifying gene expression. It uses multiple fluorescent probes to bind specifically to RNA targets, allowing direct counting of fluorescent RNA molecules.

  This method ensures high detection efficiency, accurately quantifying RNA expression, including low-expressing genes that traditional single-cell sequencing struggles to detect.

• What is the imagable area of a MERSCOPE Ultra^TM run?

  MERSCOPE Ultra^TM offers two different flow cell sizes: FCX-L (3.0 cm^²) and FCX-S (1.25 cm^²). The imagable area for the legacy MERSCOPE system is 1.0 cm^².

  The interchangeable flow cell options within MERSCOPE Ultra allow you to customize your experiments better and run them efficiently, either by studying large tissues or multiple samples for maximum reagent efficiency or testing smaller samples prior to scale-up with FCX-L.

• What does the data output from a MERSCOPE measurement look like?

  The data output from a MERSCOPE measurement includes:

  • The list of all detected transcripts and their spatial locations in three dimensions (.CSV)
  • The mosaic images (.TIFF)
  • Output from the cell segmentation analysis:
    • The transcripts per cell matrix (.CSV)
    • The cell metadata (.CSV)
    • The cell boundaries (.HDF5)