Script for finding max brightness and correcting B&C values

Image Analysis
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#1

Hi,

I would need a script, which would find a maximum brightness on an image stack and then correct the Brightness/Contrast settings to a minimum display value of 0 and maximum display value of e.g. 0.9-times the brightness maximum.

Currently, I am doing this manually. I have an image stack (16-bit images in grayscale), I run histogram on the stack (CTRL+h) then I look at the log scale of the histogram (so I can see the few pixels at the max values) and manually correct the Brightness/Contrast settings. I have hundreds of stacks with different max brightness. Usually, the images have only a few pixels near the maximum so I visually decide what max value to use (e.g. 0.9 of the max intensity – i.e. 10% below the max brightness).

Is there a way to automate this? The best way would probably be a script, which I would run on all open stacks and where I could manually change the max intensity factor.

Thanks,
Matjaz

#2

Welcome!

You can find an IJ macro in the link below, that emulates ImageJ automatic brightness & contrast button.

http://wiki.cmci.info/documents/120206pyip_cooking/python_imagej_cookbook#automatic_brightnesscontrast_button

Maybe modify the code for your own purpose.
HTH
Kota

2 Likes
#3

Hi Kota,

thank you for the macro. It works but only on individual image within the stack. In my stacks (i.e., videos) there are 135 images (frames) and I need to do histogram on all images in the stack. From such histogram I need to then find the max brightness and apply it to all images in the stack. Would it be possible to write such macro? Usually I have 135 images in the stack but this number changes from video to video so it should be a parameter in the macro.

Below are my modifications of the macro. My stack images are 128x64 pixel in size and 16-bit greyscale (nBins=4095).

Thank you,
Matjaz

AUTO_THRESHOLD = 128*64;
 getRawStatistics(pixcount);
 limit = pixcount/1;
 threshold = pixcount/AUTO_THRESHOLD;
 nBins = 4095;
 getHistogram(values, histA, nBins);
 i = -1;
 found = false;
 do {
         counts = histA[++i];
         if (counts > limit) counts = 0;
         found = counts > threshold;
 }while ((!found) && (i < histA.length-1))
 hmin = values[i];
 
 i = histA.length;
 do {
         counts = histA[--i];
         if (counts > limit) counts = 0; 
         found = counts > threshold;
 } while ((!found) && (i > 0))
 hmax = values[i];

 setMinAndMax(hmin, hmax);
 print(hmin, hmax);
#4

Hi again,

I did not check the code in detail, but I guess it will be easy to get the max of pixel values in the stack if you use the function

Stack.getStatistics(voxelCount, mean, min, max, stdDev)

see
https://imagej.nih.gov/ij/developer/macro/functions.html#Stack.getStatistics

#5

Great, it works! Thank you for pointing to the function.

Cheers,
Matjaz