Measure particles of a certain size and intensity

Image Analysis
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#1

Sample image and/or code

example positive-2|375x500 example positive-3

Background

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.

Challenges

  • 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!

#2

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,
Volko

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