Particle analysis on only part of a complete threshold image

Hi all,

I have been using Image J for a number of years to analyse photographs of plants. The process by which I obtain the aerial visible area is as follows:

I photograph my plant and upload it into Image J and set the scale (Analyze > Set Scale):

I then adjust the colour threshold (Image > Adjust > Color Threshold …), shown below:

I then analyse particles (Analyse > Analyse Particles…). Usually all of the areas highlighted in red in the threshold image (above) will show in the Particle analysis (unless I use more stringent conditions), though now only part of the image is appearing. The part of the image that particles can be analysed from is not always the same. So in different images it is not always the bottom right hand corner that can be analysed, as shown in this example. This is the problem.

The process worked on Tuesday, however this begun to happen yesterday. I have since restarted my computer, and uninstalled to reinstall the software, but still the problem persists. Is there anyone out there who can help to get my analysis working correctly again?


Hello Kelly,

Maybe you have a ROI (selection) on that part of the image? It is hard to see in the images you posted, can you upload an example?


Hi Ignacio,

Thank you so much for your reply. Please find the upload of the image:

Threshold image:

and finally the particle analysis:


I see. What parameters you have when you click on “Analyze Particles” (size, circularity, etc)?

Also, do you have any other image open at the time you use the particle analyzer?

This looks like you have Include holes activated in the Analyze Particles dialog, so that all fields entirely enclosed by thresholded (i.e. red) area end up being a single huge object. Could this be an explanation?


Hi Ignacio,

The parameters are as follows:

Size: 10-Infinity
Circularity 0.00-1.00

Also the top four boxes are ticked: Display results, Clear results, Exclude on edges, Include holes. the remaining four are unticked.

There is definitely no additional image open when I threshold and analyse the particles of the image.

Many thanks for your help!

That’s the culprit. Uncheck Include holes and see if it gets better.



Sorry I didn’t see your earlier message.

Thank you very much for your help! My analysis is now working :smiley:


P.s. This forum is excellent!