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What are the general imaging system requirements for running Visium CytAssist Spatial Gene Expression assays?

Question: What are the general imaging system requirements for running Visium CytAssist Spatial Gene Expression assays?

Answer: A successful experiment is highly dependent on generating a high-quality image with which to overlay the CytAssist image and further map the Gene Expression data back to. Please refer to the Visium CytAssist Spatial Gene Expression Imaging Guidelines Technical Note for information on the following topics:

      1. General image acquisition, processing, and analysis guidelines
      2. Imaging Systems tested internally
      3. Examples of images suitable for downstream analysis with Space Ranger 
    2. Below is the recommended image formats for Space Ranger:
      1. Brightfield images for H&E stained tissue-
        • 3 x 8-bit color TIFF/bigTIFF or JPEG
        • 16-bit grayscale TIFF/bigTIFF or JPEG
        • 3 x 8-bit color pyramid TIFF and multiple 8-bit TIFF/bigTIFFs at different resolution (Space Ranger 1.2.2 or newer and Loupe Browser 5.0.1 or newer)
      2. Fluorescence images for IF stained tissue-
        • 8 or 16-bit grayscale single, multi-page TIFF/bigTIFF
        • 8 or 16-bit grayscale multiple, single-page TIFF/bigTIFF or JPEG
        • 3 x 8-bit colored image TIFF/bigTIFF or JPEG
      3. Images have a minimum size requirement of 2000 pixels in at least one direction
    3. Additional Specifications:
      • Computer with sufficient power to handle large images (0.5-5 GB)
      • Image stitching software (microscope’s native software or third-party software, such as Image J)

Products: Visium CytAssist for FFPE, Visium CytAssist for FF, Visium CytAssist for FxF