QuPath extension to support opening files from a Slide Score server

This is a plugin for the image analysis software QuPath (v0.6.0+). It allows directly opening images that are stored in the digital pathology slide management software Slide Score, downloading annotations from there, uploading annotations and detections back and working with TMAs.

Installation

Just drag and drop the jar over a running QuPath instance.

Usage example

import qupath.lib.gui.QuPathGUI
import qupath.lib.scripting.QP
import qupath.lib.roi.interfaces.ROI
import qupath.lib.images.servers.slidescore.SlideScoreUploadAnnotationsCommand
import qupath.lib.images.servers.slidescore.SlideScoreImportTMAsCommand
import qupath.lib.images.servers.slidescore.SlideScoreImportAnswersCommand

//TODO: specify annotation questions to use as source and destination
def sourceQuestion = "Mark interesting area"
def destinationQuestion = "Positive_Cells"

//TODO: specify account under which the ROI annotation was made
def sourceAccount = 'demo@example.com'

qupathGUI = QuPathGUI.getInstance()
def slideScoreImportTMAsCommand = new SlideScoreImportTMAsCommand(qupathGUI)

def project = QP.getProject()

// go over all images in the project
for (projectImageEntry in project.getImageList()) { 
    def imageData = projectImageEntry.readImageData()
    def server = imageData.getServer()

    // load TMA core locations from Slide Score
    slideScoreImportTMAsCommand.run(imageData)

 
    def slideScoreImportAnswersCommand = new SlideScoreImportAnswersCommand(qupathGUI)
    slideScoreImportAnswersCommand.setQuestion(sourceQuestion)
    //optionally get only answers from a user
    slideScoreImportAnswersCommand.setEmail(sourceAccount)    
    //optionally disable automatic adding of annotations to the hierarchy
    slideScoreImportAnswersCommand.dontAddAnnotations = true;
    slideScoreImportAnswersCommand.run(imageData)
    var logger = LoggerFactory.getLogger("testscript")
    //print answers
    for (answer in slideScoreImportAnswersCommand.answers) {
         logger.info('value:' + answer.value);   
    }
    //or use
    //slideScoreImportAnswersCommand.pathObjects
    // for QuPath's PathObject shapes
    //or use 
    //slideScoreImportAnswersCommand.annotations
    // for Slide Score format:
    /*
        public class SlideScoreAnnotation {
            public class Point
            {
                public int x,y;
            }
 
            public class Label
            {
                public int x,y, fontSize;
                public String label, whenToShow;
            }
 
            public int x,y;
            public Point2 center, size, corner;
            public Point2[][] positivePolygons, negativePolygons;
            public Point2[] points;
            public String area, type, modifiedOn;
            public Label label;
        }*/

    //TODO: perform analysis, detect cells, ...

    // Send Point Annotation to Slide Score
    def hierarchy = QP.getCurrentHierarchy()
    def annotations = hierarchy.getAnnotationObjects()
    def pointAnnotation = annotations.find() {it.getROI().getRoiType() == ROI.RoiType.POINT}
    def sideScoreUploadAnnotationsCommand = new SlideScoreUploadAnnotationsCommand()
    sideScoreUploadAnnotationsCommand.submitAnnotations(imageData, [pointAnnotation], destinationQuestion)
}

Building

Clone this repo into the qupath 0.6.0 repo and add to settings.gradle.kts:

• include("qupath-extension-slidescore") below include("qupath-extension-openslide")
• mavenCentral() below maven("https://maven.scijava.org/content/groups/public/")