Automatically recognized objects transferred into ROIs in Imagej

Question

I am facing a challange in my field and I would need some advices.

I have an image with tree rings.

To see a photo I want to work with, you can check it from my dropbox: https://dl.dropboxusercontent.com/u/65873264/Sample.jpg

I would like to write a macro/task... in which program will recognize each ring and mark it as ROI. I was trying to make this task using some plugins: Template Matching, Feature Finder and Visual grap. But those rings could be extremely variable.

What I need is something like that: With Analyze particles function program recognize all vessels (objects) on a thresholded image. Second step is fun: for each particle, it check if there is a particle around in a range of 0.5 mm. If it is, it creates an ROI including both particles and searches for next particle in the range of 0.5 mm...

There is a smillar method [http://imagej.1557.x6.nabble.com/combine-particles-in-ROI-manager-automatically-td3692844.html] But here macro at first calculates differences between two serial particles, but I need to include all particles in range of 0.5 mm.

Answer 1

The following ImageJ macro code makes use of the Maximum and Minimum filters in ImageJ to perform a morphological closing operation on the particles in your sample image, and it then uses the Particle Analyzer to create ROIs from those:

open("https://dl.dropboxusercontent.com/u/65873264/Sample.jpg");
run("Duplicate...", "title=[Temporary Copy]");
run("8-bit");
setAutoThreshold("Default");
run("Analyze Particles...", "size=100-Infinity show=Masks clear include in_situ");
run("Maximum...", "radius=70");
run("Minimum...", "radius=70");
run("Analyze Particles...", "size=100-Infinity clear add");
selectWindow("Sample.jpg");
roiManager("Show All with labels");
roiManager("Show All");