Measure particles of a certain size and intensity

Sample image and/or code

example positive-2|375x500 example positive-3


This is a cross-section of rat muscle stained with anti-desmin antibody. This is a protein that is part of the whole cell’s structure, but forms clumps/aggregates in when its mutated.

Analysis goals

I would like to find a way to measure how many desmin aggregates there are in a muscle cross section, how big their total area is and what their mean intensity is.


  • There is a lot of “background”. I don’t know how to distinguish the aggregates (which I define by being thicker than the cell membrane and their signal of a higher intensity) and summarize their measurement.
  • I have tried setting a threshold, but that only helps with signal intensity, not the size of the particles.
  • I’m sorry if this is a very basic question, my ImageJ skills are very limited.

Any help is welcome! Thank you!

If you can separate the staining of interest from the background by thresholding the image, you can then use the Particle Analyzer (Analyze → Analyze Particles) to filter particles on these binary images by size (see e.g. Particle Analysis - ImageJ for a start; there are lots of tutorials online that cover particle analysis in ImageJ).
Good luck,

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