User Tools

Site Tools


Sidebar

Top
Seminar
Courses
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @biomicugm: Topics: Biostatistics, computational evolutionary biology, computational genomics and proteomics, graph models, image analys…
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @JustinMCrocker: We are looking for an interdisciplinary EIPOD postdoc to join our group @EMBL! Potential projects with @Eileen_Furlong,…
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BioImagingUK: This maybe of interest to the @NEUBIAS_COST @openmicroscopy communities #imageAnalysis #imagingScientist https://t.co/I5
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BioImagingUK: Software developer position on large image data analysis - working closely with the lab of @bayraktar_lab @sangerinstitut…
About 6 days, 1 hour ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @AssafZaritsky: Modeling the interplay of lamellipodial motion and the intercellular actomyosin cable during epithelial wound healing h…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jytinevez: @florianjug says be careful when using #CARE for intensity based quantification; CARE restoration is like a non linear trans…
About 1 week, 1 day 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 05:46 (external edit)