ImageJ: Analyze particles in different ROI at the same time

Question

I am measuring vessel area in different annual rings (trees; dendrochronology). I captured high quality pictures with approximatelly 20 annual rings. Each annual ring is my ROI.

I croped my image into 20 smaller images, each annual ring is one image. I open each image, I treshold it and use function: analyze particles.

However, it would be much less time consuming, if I could use my original image with 20 rings; I would separate each annual ring by defining ROI and I would label each ROI by 2012, 2011, 2010... After I would treshold the image and use function analyze particles. In my result table I would get area of vessel lumen for each vessel, separately for each annual ring.

The question is: is it possible to use ROI Manager and to set more ROIs and to analyze particles in them.

Thank you very much for your time.

Jernej

Answer 1

Use the ROI Manager to store your ROIs. Then use the ImageJ macro language and its built-in roiManager functions to loop over all ROIs. Record your analysis via Plugins > Macros > Record... to get the relevant macro commands.

Here's an example:

id = getImageID();
setAutoThreshold("Default");
for (i=0 ; i<roiManager("count"); i++) {
    selectImage(id);
    roiManager("select", i);
    run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Masks clear");
}

To answer the additional questions you posted in another answer:

• You get the name of the current ROI using Roi.getName() that you can use to name the results file:

  current = Roi.getName();
  saveAs("Results", "/path/to/results/Results_" + current + ".txt");
  

• Alternatively, you can include the current ROI name in each line of your results by checking Display label in the Analyze > Set Measurements... dialog, resulting in a macro command similar to this:

  run("Set Measurements...", "area display redirect=None decimal=3");
  

Please see the macro language documentation and the ImageJ mailing list archives before posting any new questions related to ImageJ macros.