I am trying to use starfish to automate analysis of RNAscope images (12-plex HiPlex version) that involves images from 3 imaging rounds with each round including a DAPI, FITC, Cy3, Cy5, and Cy7 channel z-stack.
My current workflow allows me to z-project, register, and filter out background on all channels at once, but I am having a hard time reliably detecting spots across all channels because the intensity of the Cy7 spots is so much lower than the other channels. A low intensity threshold that cuts out background in FITC also cuts out the real signal in the Cy7 images. I was wondering if there is a way to set different intensity threshold for each channel? I am currently detecting spots with the FindSpots.BlobDetector function and I don’t see anything in the documentation about setting different thresholds for different channels. Thanks!