Posted by
Winnok H. De Vos on
Jun 04, 2008; 3:44pm
URL: http://imagej.273.s1.nabble.com/Flat-Field-Correction-for-fluorescence-tp3696040p3696041.html
Hi
You could use (quick and dirty) macro lines when both images are open:
run("Set Measurements...", " mean redirect=None decimal=2");
selectWindow("original image");
run("Measure");
meanOriginal=getResult("Mean",0);
run("Image Calculator...", "image1=[original image] operation=Divide
image2=[flat field] create 32-bit");
selectWindow("Result of original image");
run("Measure");
meanResult=getResult("Mean",1);
run("Multiply...", "value="+meanOriginal);
run("Divide...", "value="+meanResult);
I prefer normalizing the flat field image before using it for correction by
converting it to 32-bit and dividing it by its maximum intensity. I use the
normalized image for the division and don't do any math afterwards. This
doesn't result in the same mean intensity but assures your intensities
remain properly scaled to the maximum values; rationale: if there is a need
for a flat field correction, there is reason to assume the mean intensity of
the original image isn't correct.
Kind regards,
winnok
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Pang,
Zhengyu (GE, Research)
Sent: woensdag 4 juni 2008 17:10
To:
[hidden email]
Subject: Flat Field Correction for fluorescence
Dear all,
I am doing flat field correction for fluorescence image by taking a
image of a plastic colored bar (Image1). The orignal image for my target
is Image2. I applied image calculator function and used divide. The
resulting image is a 32-bit image (Image3). I then use
Process/Math/multiply. Ideally, I want image 3 has the same average
intensity as Image2 and a 16-bit image (technical my raw image is 12bit,
and the pixel value is from 0-4095). How could I do it?
In addition, I can measure the average intensity for Image2 using
Run("measure"), but how could I get that value from the Results window
and use that value in the macro?
Thanks!
Zhengyu
> g Global Research Center
>
> ______________________________________________________________________
>
> Zhengyu Pang, Ph.D.
Bioanalytics and Protein Science Laboratory
Biosciences Global Technology Organization
> One Research Circle, K1 5B37A
> Niskayuna, NY12309
> *
[hidden email]
> *(518) 387-4015
>
>
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