RNAscope HiPlex Pipeline Example

[mattcai]

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:

• blob throws error when run with no reference_image and is_volume=False #1870
• ApplyTransform.Warp.run() alters the TransformsList such that it can't be used again #1866