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Hello,
I have a question concerning the threshold image (black/white).
If I do it by hand (Image>Adjust>Threshold) I prefer the Black&White look.
(This means that areas with high intensities are black.) So I recorded a
macro in this way.
What does the macro do?
Input images are z-stacks.
1) Z-projection of Channel 1
2) Threshold this projection and convert to mask
3) Z-projection of Channel 2
4) Threshold this projection and convert to mask
5) Multiply ouput image of 2) and 4)
6) Measure output image of 5)
This works fine I guess. But there is something irritating.
I want the output images of 2) and 4) to be like this: High intensities
black.
But sometimes the output is inverted. Even of the same input image (this
means Channel 1 is inverted Channel 2 not). The ouput image of 5) always
looks okay. So it seems to be okay (but I am not sure).
Do I have to bother?
Thanks
Johannes
macro "Open Cocu" {
DIR=getDirectory("Choose Folder");
NAMES=getFileList(DIR);
for (i=0; i<NAMES.length; i++) {
open(DIR+NAMES[i]);
Aid = getImageID();
//make first projection
run("Z Project...", "start=1 stop=6 projection=[Max Intensity]");
setAutoThreshold();
//run("Threshold...");
run("Convert to Mask");
A_zproject_name = getTitle();
//This is the image of channel 1
//restore selection to the first image
selectImage(Aid);
//make second projection
run("Z Project...", "start=7 stop=12 projection=[Max Intensity]");
run("Subtract...", "value=500");
setAutoThreshold();
//run("Threshold...");
run("Convert to Mask");
B_zproject_name = getTitle();
//This is the image of channel 2
imageCalculator("Multiply create 32-bit", A_zproject_name,B_zproject_name);
//run("Image Calculator...", "image1=A_zproject_name operation=Multiply
image2=B_zproject_name create 32-bit");
run("Measure");
}
}
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