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RT @RavenKwok: Derived from something I'm working on. https://t.co/HsQ1u8SxzY
About 1 day, 14 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

... so a bioimage analyst should compare all these, characterize differences, maybe also a benchmark, and write a p… https://t.co/ihRwRa5yI5
About 1 day, 21 hours ago by: Kota Miura (@cmci_)

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... and in python scipy https://t.co/onxNHF41Cb openCV https://t.co/MFQnt9hzQq skimage https://t.co/jzGvcO1fb1https://t.co/POYW6eQMzT
About 1 day, 21 hours ago by: Kota Miura (@cmci_)

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ImageJ (Michael Schmid) https://t.co/lxEwxxTdUf IJ (Filter3D, Thomas Boudier) https://t.co/sOo0UWL2jG IJ2 (Ops)… https://t.co/6eVNVPUGiU
About 1 day, 21 hours ago by: Kota Miura (@cmci_)

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Just looked around median filter implementations briefly and there are many to compare, even limiting the scope to… https://t.co/N6Z2rTOaRe
About 1 day, 21 hours ago by: Kota Miura (@cmci_)

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RT @notjustmoore: #OMENGFF joins #OMETIFF and open #HDF5 formats to more fully cover the needs of bioimaging data storage. If, e.g., you ne…
About 2 days, 9 hours ago by: Kota Miura (@cmci_)
blogtng:2010-05-04:photobleaching_correction_3d_time_series

Photobleaching Correction -3D time series

There are several IJ tools available for 2D time series bleaching correction, but seems not with 3D:

2D-t tools:

    • Phair's double normalization method. Dependent on ratio, similar to the above, but can specify reference area (if my understanding is correct).
    • proposes two ways,
      1. conceptually similar to above two: estimate the correction ratio. But this is done by fitting exponential decay curve and use decay parameter.
        1. <jsm> I_c(t) = I(t) / exp^{-\tau t}</jsm>
      2. use “enhance contrast”. framewise Histogram streching.

Among these, exponential decay method is theoretically clean (but in practice, timeseries are not teoretical…).


Anycase, there should be 3D-t bleach correction tool (and I need it NOW). I might make some quick solution using two methods, one using division of first frame and the other with exponential fitting.

By the way, bleaching corrected images cannot basically be used for intensity quantification (FRAP, on the other hands, correct bleaching after measuring the raw image). If you are analyzing shapes or positions, no problem for quantification.


here is the “ratio” version:

macro "Bleach Corection 3D-t by ratio"{
	run("Duplicate...", "title=bleach_corrected duplicate");
	getDimensions(width, height, channels, slices, frames);
	if (frames == 1) {
		uslices = getNumber("how many z slices/timepoint?", 1);
		if ((slices%uslices) !=0) exit("that slice number dows not match with the current stack");
		frames = slices / uslices;
	}
	tIntA = newArray(frames);
	setBatchMode(true);
	for(i=0; i<frames; i++){
		startf = (i*slices)+1;
		endf = (i+1)*slices;
		op ="start="+startf+" stop="+endf+" projection=[Sum Slices]";
		run("Z Project...", op);
		//print(op);
		getRawStatistics(nPixels, mean);
		if (i==0) tIntA[i] = mean;
		else tIntA[i] = mean/tIntA[0];
		close();
	}
	setBatchMode("exit and display");
	tIntA[0] =1;
	for(i=0; i<frames; i++){
		for(j=0; j<slices; j++){
			curframe = i*slices + j+1;
			setSlice(curframe);
			//print("frame"+curframe + " factor" + tIntA[i]);
			op = "value="+tIntA[i]+" slice";
			run("Divide...", op);
		}
		print("time point:"+i+1 + "  factor" + tIntA[i]);
	}	
}


Before Correction (each row is a time point, with 8 z-slices)
 Before each row is a time point Average intensity along stack slices. 5 peaks corresponds to 5 time points. Before


After Correction
After After



blogtng/2010-05-04/photobleaching_correction_3d_time_series.txt · Last modified: 2016/05/24 12:46 (external edit)