- Script: selectAnnotations() def pathModel = 'cyto2' def cellpose = Cellpose2D.builder( pathModel ) .pixelSize( 0.3 ) // Resolution for detection in um .measureShape() // Add shape measurements .measureIntensity() // Add cell measurements (in all compartments) // Run detection for the selected objects def imageData = getCurrentImageData() def pathObjects = getSelectedObjects() if (pathObjects.isEmpty()) { Dialogs.showErrorMessage("Cellpose", "Please select a parent object!") return } cellpose.detectObjects(imageData, pathObjects) println 'Cellpose detection script done' runObjectClassifier("PAX8"); import qupath.ext.biop.cellpose.Cellpose2D ----------------------------------------------------------------------------------------- - Object classifier: { "object_classifier_type": "OpenCVMLClassifier", "featureExtractor": { "feature_extractor_type": "DefaultFeatureExtractor", "measurements": [ "Area µm^2", "Length µm", "Circularity", "Solidity", "Max diameter µm", "Min diameter µm", "Hematoxylin: Mean", "Hematoxylin: Median", "Hematoxylin: Min", "Hematoxylin: Max", "Hematoxylin: Std.Dev.", "DAB: Mean", "DAB: Median", "DAB: Min", "DAB: Max", "DAB: Std.Dev." ] }, "classifier": { "class": "RTrees", "statmodel": { "opencv_ml_rtrees": { "format": 3, "is_classifier": 1, "var_all": 17, "var_count": 16, "ord_var_count": 16, "cat_var_count": 1, "training_params": { "use_surrogates": 0, "max_categories": 10, "regression_accuracy": 0.0, "max_depth": 25, "min_sample_count": 10, "cross_validation_folds": 0, "nactive_vars": 0 }, "global_var_idx": 1, "var_idx": [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 ], "var_type": [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 ], "cat_ofs": [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ], "class_labels": [ 0, 1 ], "missing_subst": [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ], "oob_error": 0.0, "ntrees": 50, "trees": [ { "nodes": [ { 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