// If you use this, please acknowedge the OCS Microscopy Core at NYU Langone Medical Center. // macro written by Michael Cammer for Durga Dandamudi 20140808 // for ImageJ v 1.49e // to count colonies on 10 cm plates. // This macro could be modified to also measure distributions of sizes of colonies etc. macro "Count colonies [q]" { t = getTitle(); run("Duplicate...", "title=copy_"+t+""); setBackgroundColor(192, 192, 192); run("Clear Outside"); run("Median...", "radius=1"); run("Threshold..."); setAutoThreshold("Huang"); waitForUser("Select Threshold", "Click ok after adjusting threshold."); run("Convert to Mask"); run("Erode"); run("Erode"); run("Dilate"); run("Dilate"); run("Watershed"); run("Analyze Particles...", "size=0.02-Infinity clear include summarize"); selectWindow("Summary"); } macro "Make fixed size oval" { makeOval(338, 150, 712, 740); }