ImageJ: Analyze Particles using ROI when Calculating Area %

Question

I am a beginner using ImageJ. I have an image of a 4" diameter wafer with voiding. I 1st scale the image. I then do a Threshold Color, to highlight only the voids. I then put an ROI around wafer.

I then run the Analyze Particles routine, it surrounds the voids well and in the summary table, the Total Area column seems to come out to the correct # for Total Void Area. But the %Area column # is low, I think because it's using the Total Area\the entire Image area. I would like it to tell me the % of Voiding in the wafer, which would be Total Void Area\ROI Area(wafer area). Is there an easy way to do this, or am I doing something wrong? Another option is, I am planning to record this in a macro, since I do know the Total Wafer Area, I assume I could do some math to divide the Total void Area by the known wafer Area to get the Wafer % Voiding number I'm looking for outputted through the macro, but would need some help in how to do that. Any help with this would be greatly appreciated. thanks, Steve

Answer 1

You can use the Limit to threshold option in Analyze > Set Measurements... to measure the full area of your ROI (if the option is unchecked) and to measure only the thresholded area within the ROI (if the option is checked). Then you can calculate the percentage as the ratio of the two measurements as you suggested.

When you run Plugins > Macros > Record... before performing these steps, the macro recorder will list the commands necessary to perform the analysis, e.g.:

setAutoThreshold("Default");
run("Set Measurements...", "area limit redirect=None decimal=3");
run("Measure");
run("Set Measurements...", "area redirect=None decimal=3");
run("Measure");

Then use the getResult() macro function to get the required results and calculate your ratio, or just save the Results window as an Excel file and do the calculations in a different application.