Do the analysis in several selected parts of an image

Good afternoon,

I am a beginner with ImageJ, and I need your help.

My aim is to quantify amyloid plaques in brain slices. I have done a macro that works and give me the good results (yeah !!). But, I would like to be able to select an area, and get a table with only the infos of the plaques inside this area.
For example I would like a table with all the numbers in the cortex (yellow area) and another with all the numbers in the hippocampus (green area). If the summary of those tables could appear in the summary window too, it would even be better !

I tried to play with Roi (the 2 area are added to it), but I didn’t succeed to find the right tools

I tried to do the areas before doing the analysis (one after the other), but the lines are counted as plaques, so it doesn’t really work. (Did I mess something up at some point ?)

Please help me !

Thank you,

Hi Julia,

In ImageJ, all operators are applied inside a ROI. Default ROI is the entire image. If you want to make some measurements in a defined area, you first have to define a restricted ROI.
In your case, you have 2 solutions

  1. play with the ROI manager. Draw a ROI, (eventually add it to the manager, and select it) and perform your analysis. Be careful that if you do Particle Analysis with clear option, your ROI manager won’t keep your ROI.
  2. create a mask of your areas of interest. Cross your mask(s) and your image with Process>Image Calculator so that only the areas of interest are processed.

Solution 1 needs less memory, solution 2 needs less programing.


Thanks you so much for your answer !
I succeed to make it work using kind of your 1st option.
I discovered the waitForUser("…") function which was really helpful to trace the area in the middle of the run ! (before the thresholding, so I could still see the background)
Also, I was transforming my “image to mask” after the thresholding, but then my area disappeared, and I realized that i actually didn’t need to do this transformation for it to work ^^

Thanks again !