// Assuming that this is the image youre starting with. 
// Make sure the image you want to process is the active window before hitting 'Run'

// This will only work on 2 channel composite images. 

// we only want to look at the puncta channel (2), so isolate that
run("Duplicate...", "duplicate channels=2");

// if you're only running one-channel images here, use the following command instead to duplicate. 
// run("Duplicate...", " ");

puncta = getTitle(); // Making this image a variable
//run("Brightness/Contrast...");
run("Enhance Contrast", "saturated=0.35");

// Spatial high pass filter, since our puncta are really small
run("Duplicate...", " ");
pfilter = getTitle(); // This is the image we are filtering
run("Subtract Background...", "rolling=5");

// Threshold out the bright spots based on intensity
setAutoThreshold("Otsu dark");
//run("Threshold...");
setOption("BlackBackground", false);
run("Convert to Mask");

// Circle all of the puncta with 'Analyze Particles' function
run("Analyze Particles...");

// Measure their brightness (mean) and area on the ORIGINAL RAW IMAGE
selectWindow(puncta);
run("Set Measurements...", "area mean redirect=None decimal=3");
run("Analyze Particles...", "clear add");
roiManager("Show All without labels");
roiManager("multi-measure");

// You can save the output results however you want. Usually as a CSV file. 
// Whatever you prefer to run stats in is totally up to you. 

// Here's the descriptive stats for the area and brighness distributions
run("Distribution...", "parameter=Area automatic");
run("Distribution...", "parameter=Mean automatic");