Area changes with Threshold change in ImageJ?

Hi All

Just signed up to ask about this: I select my ROI in ImageJ and measure and I get a number for the area (say 114611.775). I then adjust the threshold to cover only the particles I’m interested in measuring, measure again and I get a different number for the area (say 91748.572). Shouldn’t the area stay the same as it’s the same ROI? IntDensity and GreyScale will change, but I don’t understand why the area changes.


Edit: On a different but related note: I am thinking of moving from ImageJ to photoshop for my analysis and doing some test images I noticed that the area doesn’t change when I make the measurements photoshop.

1 Like

Hi Danny,
Please don’t use Photoshop for image analysis! It is designed for graphics and not for quantitative image analysis of scientific data. You risk inaccurate measurements, and rejection of the data by a knowledgable reviewer.
I suggest you post your question on That is our sister image analysis forum, and many of the ImageJ developers are active members.
Best, Jennifer

Jennifer C. Waters, PhD
Director of the Nikon Imaging Center & Lecturer in Cell Biology, Harvard Medical School
Chan Zuckerberg Initiative Imaging Scientist


Hi @dschnitzler. As jennifer said, is the place to ask questions about ImageJ. Please direct future questions there.

This one is pretty straightforward though: in Analyze > Set Measurements, there is a checkbox “Limit To Threshold” that controls the behavior you’re describing. When checked, the threshold will affect area measurements, when unchecked it will not.


Sorry for using the wrong forum!

I just have a follow-up question: Do I want to limit it to threshold? Does that affect the IntDensity?


1 Like

Hey @dschnitzler,

as Jennifer and Talley just suggested: ask ImageJ and image analysis related questions at . There are maaany image analysts hanging around who may not look in this forum here so often.
To answer your question: If you increase the threshold you do that in order to exclude pixels from the area measurement. It’s absolutely reasonable that the measured area becomes smaller while intensity measurements increase.

See you at! :wink:


The comments of others are correct. But, I think what its doing is updating the area value as its calculating the area (within the roi) that satisfies the threshold values. (if that makes sense).

1 Like