Linear brightnes adjustment of a whole stack

Hello everybody,

I want to use the 3D viewer of Fiji ImageJ to take a rotation video of a rekonstructed cone like object. The problem is, that the slices have already been normalized seperatly, so that the brightness of the background is not the same for all images. At the top of the cone, the background is as bright, as the material at the bottom of the cone. So I cannot adjust a threshold to represent the object.
Is it possible to reduce the brightness linearly through the stack? Or do you have an alternative idea.


If you use Process > Enhance Contrast as @Wayne describes in this mail, is that sufficient?

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thanks for your answer!
I already tried the enhance contrast function. The problem is, that this function recalculate the contrast for each picture seperately and not for the whole stack. This leads to an even increased magnification of artifacts within the top pictures, where is no or just a little part of the sample.
It would be nice, if there is a function, that adjusts just the brightness (not the contrast) of all pictures and uses one position to set the zero value of each picture.

You’re right. The docs made it sound like it should be able to normalize on the complete stack histogram, but it doesn’t seem to be working as I expected.

Another option might be Plugins > Integral Image Filters > Normalize Local Contrast. It seems to normalize on a stack level, although I think it move to a midpoint instead of a specified zero value. Could you combine the normalization with a background subtraction to get the result you want?

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I am new and need a manuscript or paper that explains the method that performs the “Normalize Local Contrast” process in Fiji

Could you please share with me if you know such a publication

Hi @Namata,

Welcome! A good place to start with any question is to search the resources here. Searching the mailing list archives yielded this thread in which the author (Stephan Saalfeld) describes the method.

Hope this helps.


Hi @hinerm,

I tried a lot with Normalize Local Contrast, but could not suppress, that the mean brightness value of the upper pictures is set to a certain value I have no influence on.