This workflow performs very simple image segmentation and object feature calculation on ImageJ’s Blobs sample image. It is modeled after an equivalent ImageJ macro: // read the image data //run("Blobs (25K)"); open("blobs.tif"); // preprocessing -- image smoothing run("Duplicate...", " "); run("Median...", "radius=1"); // thresholding -- separate foreground from background setAutoThreshold("Huang"); // morphological operations -- erode x2 run("Create Mask"); setOption("BlackBackground", false); run("Erode"); run("Erode"); // define measurements run("Set Measurements...", "area mean standard redirect=None decimal=3"); // segment objects -- i.e. connected component analysis run("Analyze Particles...", "add"); // cleanup temporary images close(); close(); // measure objects on the original data selectWindow("blobs.tif"); roiManager("Measure"); // save the measurements to a CSV file saveAs("Results", "measurements.csv");