// Simple macro for batch counting dir = getDirectory("Choose Source Directory"); list = getFileList(dir); for (i=0; i<list.length; i++) open(dir+list[i]); run("ITCN", "width=15 min=10 threshold=20"); saveAs("Results", dir+list[i]+"_counts.csv"); close();
– If using ITCN in published work, cite: “Image-based Tool for Counting Nuclei (ITCN)” – available via ImageJ.net, and reference the ImageJ software (Schneider et al., 2012, Nat Methods). itcn imagej plugin
Every bioimage analyst should have ITCN in their toolkit. Use it as the default automated counter; switch to alternatives only when validation reveals systematic bias. Acknowledgments – Original ITCN plugin authored by Dr. Jeffrey E. Boyd and the Center for Bio-Image Informatics, UC Santa Barbara. // Simple macro for batch counting dir =