// SetROIs_iso.ijm function SetROIs_iso(savedir, stk) { n_avg = 50; run("Z Project...", "stop=&n_avg projection=[Average Intensity]"); avgip = getTitle(); run("Enhance Contrast", "saturated=0.35"); save(savedir+stk+"_avgip.tif"); // Step 2: Prompt user for ROIs setTool("ellipse"); waitForUser("Draw ROIs on image. Press 'T' to add them to the ROI manager"); roiManager("show all with labels"); roiManager("save", savedir+"\\"+stk+"_roi.zip"); // Close out of window //close("*"); }