I am using QuPath Version 0.2.3.
I am trying to run a classifier with the help of a script so that I can detect the total tissue area. Since I have many files, I also want to include saving the annotations as image overlay, so that I can check all the tissue detections. Below is the script;
def viewer = getCurrentViewer() //Define the image type setImageType('FLUORESCENCE'); clearAllObjects();//Delete all objects //This function changed between 0.1.2 and 0.2.0, in 0.2.0 use viewer.getImageDisplay().availableChannels() def channels = viewer.getImageDisplay().availableChannels() // Set the range for the first two channels channels.setMinDisplay(200) channels.setMaxDisplay(5000) // Ensure the updates are visible viewer.repaintEntireImage() def minArea = 1000.0 // To change def minHoleArea = 100.0 // To change def classifierName = "DAPI_classifier" // To change // Apply pixel classifier inside them // Note: you can change this to createDetectionsFromPixelClassifier(..) if needed createAnnotationsFromPixelClassifier(classifierName, minArea, minHoleArea) print "Done!"
Below I am showing two tissue examples detected by the script. In first example, image intensity was set as described in the script.
Whereas in the the second image, intensities are not set as defined by the script and I am not able to see the image overlaid by annotations.
As this is resolved, I will work on including the script to save the image overlay.
Thanks for your help.