Since this question refers to the legacy classifier, I’m prepared to hear that it’s an unsolvable problem, so this is more out of curiosity than anything else… I am seeing very different classification results when taking the same image on QuPath 0.1.2 and 0.2.2 and using a classifier build with 0.1.x.
The workflows are essentially the same (via UI or script):
- load image
- set stains
- select whole image
- watershed cell detection
- load and apply classifier
The cell detection does not appear to be the problem - in both cases, it finds ~19,100 cells +/- 40 cells. It is performed with the same requestedPixelSize (0) and the same # of tiles are generated.
But the 0.1.x classifier sees them as 14,200 tumor cells and 2,700 immune cells.
The 0.2.x classifier sees them as 5,800 tumor cells and 11,600 immune cells.
This of course leads to different clusters and measurements.
I know moving forward I will move to the new classifier system but had been hoping to validate data coming out of 0.1.x… am I forgetting a step in installing this classifier? Or is this expected behavior?