[Simple Life Time Measurement in ImageJ] Estimate lifetime of ROIs based on single exponential fits ( ImageJ / FIJI ) #Fiji #ROI #FLIM #BIOP

IJMeasureLifeTimeBasic.ijm

/**
 * Allows to compute in a simple manner different regions of a lifetime stack image
 *
 * REQUIREMENT : For Picoquant file reading, install PTU-Reader (https://github.com/ekatrukha/PTU_Reader)
 * 
 * How to use the script:
 * 0 open a PTU file
 * 1 make regions of interest and store them into the ROI Manager
 * 2 select the lifetime stack
 * 3 execute the script and provide the necessary parameters
 *
 * For lifetime fitting, a single exponential decay with no offset is fitted on a certain time window
 * Basic but robust
 * OUTPUT : a graph per ROI and a line (tidy data)
 * 
 * TODO : assign ROI names to data and better numbering
 *
 * @author : nicolas.chiaruttini@epfl.ch, BIOP, EPFL, 2020
 */


#@double(label = "time bin size in ps (default 8)") binSizeInPs
#@double(label = "start timepoint for exponential fit in ns") timeWindowStart
#@double(label = "end timepoint for exponentila fit in ns") timeWindowEnd

#@boolean(label = "show fit") showFit


binSizeInNs = binSizeInPs/1000.0

sliceMin = timeWindowStart/binSizeInNs
sliceMax = timeWindowEnd/binSizeInNs

//setBatchMode(true);


imgLifeTimeStack = getTitle();
run("Properties...", "channels=1 slices=1 frames="+nSlices+" unit=µm frame=["+binSizeInNs+" nsec]");

run("Z Project...", "projection=[Sum Slices]");
imgSum = getTitle();
selectWindow(imgLifeTimeStack);
run("Select None");
run("Duplicate...", "duplicate range="+sliceMin+"-"+sliceMax);
imgCropped = getTitle();

for (indexRoi = 0;indexRoi<roiManager("count");indexRoi++) {
	selectWindow(imgCropped);
	roiManager("Select", indexRoi);
	run("Plot Z-axis Profile");
	Plot.getValues(xpoints, ypoints);
	close();
	Fit.doFit("Exponential", xpoints, ypoints);
	if (showFit) {
		Fit.plot;
	}	
	selectWindow(imgSum);
	roiManager("Select", indexRoi);
	getStatistics(area, mean, min, max, std, histogram);
	print("Image \t"+imgLifeTimeStack+"\t [ \t"+sliceMin+"\t - \t"+sliceMax+"\t ] roi \t"+indexRoi+" \t fitted lifetime (ns) \t"+(-1/Fit.p(1))+"\t R^2 = "+Fit.rSquared+"\t meanValue = \t"+mean+"\t area = \t"+area);
}

selectWindow(imgCropped);
close();