Posted by
Krs5 on
Oct 21, 2010; 11:09am
URL: http://imagej.273.s1.nabble.com/Different-results-from-setBatchMode-tp3686595p3686598.html
Dear list,
I seem to have the same type of problem in a macro I work on to measure dots in nuclei. I get different results when run in true and false mode. I have not been able to nail down the problem yet but one thing I noticed is that if I select a nucleus in the DAPI channel and put the ROI in the ROI manager, take the FITC channel and threshold the signal followed by adding the ROI from the manager, it does not seem to work and takes the dots from the whole FITC image. If I first put the ROI and then do the thresholding, it works (but the dots obtained in this way are too large when using the default setting for threshold). This might be all related issues?
Kees
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Pang, Zhengyu (GE Global Research)
Sent: 19 October 2010 16:31
To:
[hidden email]
Subject: Different results from setBatchMode
Dear all,
I noticed that I got different composite images when I used
setBatchMode(false) or setBatchMode(true). The macro is as follows:
setBatchMode(false)
open(");
open( "");
open("");
run("Images to Stack", "title=[]");
run("Make Composite", "display=Composite");
setSlice(1);
run("Red");
setMinAndMax(100, 1200);
setSlice(2);
run("Green");
setMinAndMax(0, 500);
setSlice(3);
run("Blue");
setMinAndMax(100, 2000);
saveAs("jpeg", ImageName);
This macro works only if I use false as a parameter for setBatchMode
function. If I use true, I noticed that setMinAndMax function does not
work at all. Is this because that you have to open images in order to
set Min and Max for displaying purpose? As the use of true parameter can
save you a lot of time, is there any way that I can use "true" and still
adjust each channel differently. Here the green channel is especially
dark.
Thanks,
Zhengyu
Dr. Zhengyu Pang
Biochemistry and Biological Engineering Laboratory
GE Global Research
Biosciences Global Technology Organization
T +1 518 387 4015
M +1 919 724 7116
F +1 518 387 7765
[hidden email]
One Research Circle
Niskayuna, NY 12309
GE imagination at work
Dr. Zhengyu Pang
Biochemistry and Biological Engineering Laboratory
GE Global Research
Biosciences Global Technology Organization
T +1 518 387 4015
M +1 919 724 7116
F +1 518 387 7765
[hidden email]
One Research Circle
Niskayuna, NY 12309
GE imagination at work