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RNAscope HiPlex Pipeline Example #1909

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@mattcai mattcai commented Jul 30, 2020

Besides improvements to the general presentation of the example, areas that need attention are:

  • Blob detection:
    • Low-contrast regions - skip background subtraction and enhance contrast instead
    • Clustered regions - use pre-defined spot size to break up clusters and count as single spots
    • High-intensity saturated regions - use pre-defined spot size and intensity to resolve saturated regions as single spots
    • Airy disks - either remove airy disks prior to spot finding or modify spot finding algorithm to account for airy disk pattern
  • Cell Segmentation (watershed):
    • tune parameters
    • sum intensities instead of max
    • connect nuclear fragments with morphological operation

Also waiting on bug fixes:

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