Trying to equalize values in an image stack

I’m new to ImageJ - and am finding the number of filters and names bewildering. Is there a way to batch process a stack of images (or a folder of images) so they all fall within a pre-set value gamut.
I’m trying to do this so I can minimize banding, caused by variation in slice value ranges, on a detailed surface model.
I’m trying to go from this range in my slices-

To this more uniform range -

Thank you!

Dear @larsgw,

it sounds like you want to normalize the stack on a per-image basis. You can run the Enhance Contrast with Normalize enabled and Use Stack Histogram disabled on an image stack.

As an important side note: it is easier to verify an approach, if you provide the raw data of images instead of montages.


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Thanks Stefan -
Oddly, I opened Fiji and and it ran an auto update.
I imported a series of DICOM images and it seemed to process them as it imported. They all became quite bright - but without the variation from slice to slice I’d seen before (though I double checked in an image viewer and the variation remains in the original files.
I ran the process you mentioned, and it brought the overall contrast down to a range that wasn’t so garish…So in the end the process you mentioned did do exactly what I wanted. I’m just not sure if there was an update to Fiji that may have done something similar as well.
Either way, the banding problem appears to be resolved.
Thank you very much for the specific instructions!
I wasn’t sure whether to upload original images or not. They seemed pretty large for an online forum, but perhaps not in this case.

The issue could always be a peculiarity of your raw data, so it might make sense to upload them (no need for that now, but maybe for future requests).

There was a recent update to Bio-Formats (announced yesterday) that might have changed behavior of the import process. Another explanation might be that you have changed the preferences for import (see for details, especially the Autoscale option in the first screenshot)?