Measure multiple ROIs in imageJ - image

Question

I'm creating a script for automated measuring fluorescence intensity. I have done some progress, the macro opens the image, split in as many channels as I have and perform some trasformation so that it is possible to execute particle analysis at image 1. Then, what I want is to measure all the created ROIs but I am stacked at this point:
here is my code
dir1 = getDirectory("Choose Source Directory ");
list = getFileList(dir1); // get the list of all filenames in the directory
subst = 3; // set the "subst" variable to 3
Dialog.create("BatchSplitStacks"); // create a dialogue to change the stack divisor
Dialog.addNumber("Number of substacks:", subst); // in the dialogue, get the number of substacks, default is "subst" (=3)
Dialog.show(); // show the above created dialogue
chan = Dialog.getNumber(); // the stack divisor is defined
setBatchMode(false); // do not show the images while processing them
for (i=0; i<list.length; i++) { // go through the files of the folder
showProgress(i+1, list.length); // the progress of the processing of the actual stack is shown in the ImageJ window
open(dir1+list[i]); // open an original stack
name = list[i]; // get the filename of the original stack
run("Stack Splitter", "number="+chan); // run the Stack Splitter plugin with the defined divisor
for (e=0; e<chan; e++) { // for each substack a saving routine is run
dotIndex = lastIndexOf(name, "."); // this line and the following line I took from another macro but I do not know
// substacks with a number below 10 are saved with a suffix and a 2 digit extension (e.g. 01 instead of the standard 1)
saveAs("tiff", dir1+"c0"+e+".tif");
close();
// closing substack
} // next saving routine
close(); // closing current original stack
open(dir1+"c02.tif");
run("Enhance Contrast", "saturated=0.35");
run("Enhance Contrast", "saturated=0.35");
run("Enhance Contrast", "saturated=0.35");
setAutoThreshold("Default");
setAutoThreshold("Default dark");
run("Make Binary");
run("Make Binary");
run("Watershed");
run("Analyze Particles...", "size=0.30-50.00 circularity=0.00-0.70 show=Masks display summarize add in_situ");
open(dir1+"c01.tif");
run("Subtract Background...", "rolling=50");
saveAs("Results", dir1+name+"c02"+ ".txt");
} // move on to next original stack in the folder
Thanks

Answer 1

You can measure all ROIs in the ROI Manager using the Measure button. In a macro, the lines are:
roiManager("Deselect");
roiManager("Measure");
You can learn more macro commands easily by using the Macro Recorder.
You can browse all the available macro functions online.
For more sophisticated per-ROI analysis, you can loop over the ROIs in the manager using the roiManager("count") and roiManager("select", i) commands. The Scale_All_ROIs macro gives an example of this; you can easily load that macro into the Script Editor by opening a new script (File > New > Script) and then choosing it from the Templates > IJ1 Macro menu of the Script Editor.