Individual stats for images in stack

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Individual stats for images in stack

V_Skala
Hi, I have a simple problem but I can't find solution anywhere.
I have a few stacks with 50 images, every image has 6 colors. I want to know
the number of pixels of every color for individual images not for whole
stack.

I know I can find it under Analyze > Histogram > List but I have to do it
for every single image.
It is a lengthy process.

Is there some option/plugin to do this for all images at once?


Vojtech Skala, CTU in Prague



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Re: Individual stats for images in stack

Krs5
Dear Vojtech,

The macro at https://imagej.nih.gov/ij/macros/StackHistogramLister.txt will probably do what you want
imagej.nih.gov<https://imagej.nih.gov/ij/macros/StackHistogramLister.txt>
// This macro prompts for the bin count and histogram // min and max and then writes the histogram counts of // the current image or stack to the "Results" window.
imagej.nih.gov
Best wishes

Kees

________________________________


Hi, I have a simple problem but I can't find solution anywhere.
I have a few stacks with 50 images, every image has 6 colors. I want to know
the number of pixels of every color for individual images not for whole
stack.

I know I can find it under Analyze > Histogram > List but I have to do it
for every single image.
It is a lengthy process.

Is there some option/plugin to do this for all images at once?


Vojtech Skala, CTU in Prague



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Re: Individual stats for images in stack

V_Skala
That is exactly what I need, thank you very much Kees!

Best wishes,

Vojtěch



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Re: Individual stats for images in stack

Krs5
This updated code might make life a little easier

// This macro prompts for the bin count and histogram
// min and max and then writes the histogram counts of
// the current image or stack to the "Results" window.

requires("1.34m");
Dialog.create("Histogram Lister");
Dialog.addNumber("Number of Bins:", 256);
Dialog.addNumber("Histogram Min:", 0);
Dialog.addNumber("Histogram Max:", 256);
Dialog.show();
nBins = Dialog.getNumber();
hMin = Dialog.getNumber();
hMax = Dialog.getNumber();
row=0;
run("Clear Results");
setBatchMode(true);
stack = getImageID();
for(slice=1; slice<=nSlices; slice++){
row = 0;
selectImage(stack);
if (nSlices>1) run("Set Slice...", "slice=" + slice);
if (bitDepth!=32){
run("Duplicate...", "title=temp");
run("32-bit");
}
getHistogram(values,counts,nBins,hMin,hMax);
close();
for (i=0; i<nBins; i++) {
if (nSlices>1) setResult ("Bin", row, values[i]);//setResult("Slice", row, slice);
setResult("Image"+"Slice"+slice, row, counts[i]);
row++;
}
}
updateResults();

Best wishes

Kees
________________________________


That is exactly what I need, thank you very much Kees!

Best wishes,

Vojtěch



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Re: Individual stats for images in stack

V_Skala
Now it is perfect, you are the best Kees, thank you.



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Re: Individual stats for images in stack

Krs5
Can do one better; gives a results table with slice, channel and frame number in the table heading

---------------------------------------------
requires("1.34m");
if (nImages == 0) exit("This macro requires an open image.");
Dialog.create("Histogram Lister");
Dialog.addNumber("Number of Bins:", 256);
Dialog.addNumber("Histogram Min:", 0);
if (bitDepth==16) Dialog.addNumber("Histogram Max:", 65536);
else Dialog.addNumber("Histogram Max:", 256);
Dialog.show();
nBins = Dialog.getNumber();
hMin = Dialog.getNumber();
hMax = Dialog.getNumber();
run("Clear Results");
setBatchMode(true);
stack = getImageID();
for(s=1; s<=nSlices; s++){
row = 0;
selectImage(stack);
if (nSlices>1) run("Set Slice...", "slice=" + s);
Stack.getPosition(channel, slice, frame);
run("Duplicate...", "title=temp");
if (bitDepth!=32) run("32-bit");
getHistogram(values,counts,nBins,hMin,hMax);
close();
for (i=0; i<nBins; i++) {
if (nSlices>1) setResult ("Bin", row, floor(values[i]));
setResult("Slice"+slice+"-Channel"+channel+"-frame"+frame, row, counts[i]);
row++;
  }
}
updateResults();

----------------------------------------
Kees

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