Measuring area with image J: should be simple but I can't do it!

I am trying to measure area with image J, something I have done before. I open an image, use the straight line tool to draw a line, and click on Set Scale. I then add the known distance (1cm) and and click OK (using pixel aspect ratio of 1) . When I measure straight lines I get the right lenght (1cm=1), but any area measurements are all wrong. A 1cm2 square will yeild 0.05 for area.

How could that be? Any advice?

Thanks so much!

Hello @Cargueso_Lab,

welcome to the forum!

I have tried to reproduce you issue on a recently taken TEM image with an up-to-date Fiji but was not successful. I suspect that you have used the Analyze > Measure command?

Which version of ImageJ are you running (i.e. vanilla ImageJ1, vanilla ImageJ2, Fiji, etc.)?


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Thanks so much for the reply!!

Yes, I am using Fiji

I set the scale by drawing a strainght line on a ruller I have on the picture. The lenght of the line is 1cm. I click on Analyze>Set Scale and change the known distance to 1 and the unit to cm.

Then I try to measure the area using: Analyze> Measure

Any lenghts are measured fine, but area seems wrong. As in, a 1cm line is measured 1cm, but a square with 1cm each side gives 0.05 for area.

I don’t think this is right, but I am not sure what needs to be changed.

Thanks again.

I think I got it… It had to be something simple that I was missing…
I was using the freehand line tool, when I should be using (?) the freehand selections tool…
It seems to work fine now.

Best wishes to all in the forum,


I was using the Straight Line and the Rectangular selection. For consistent results, I’d propose to use the Straight Line for selecting the scale reference.