ImageJ: Analyze particles in different ROI at the same time

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

Solution

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.