TMA ER analysis
Still to write... in the meantime, click image for YouTube video
There's no step-by-step guide here, although the video below shows the general process (from an older version of QuPath, so the screenshots may look a bit different).
The idea is to apply a similar workflow to that explained in detail for TMA CD3 analysis, with a few differences:
- there's no need for tissue detection; we are interested in numbers of cells but not the area of tissue to calculate our final output (an H-score)
- rather than Fast cell counts, we instead rely on Cell detection and subsequently training a classifier - the key details are in Detecting objects and Classifying objects
