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I have a collection of 142 partially overlapping images, taken on a grid with a microscope. I've had to go through some pain to patch them all together as the automated software packages seemed to have a lot of trouble doing so, but in the end it worked out. However, now I am stuck with the issue that each image was taken at slightly different lighting conditions (due to how the microscope is setup), which gives me a sort of patchwork of different brightness squares. It is illustrated by the (partial) image below:

enter image description here

As you can see, the squares have slightly different lighting. Now, of course I can manually adjust each single layer until it has the same brightness as its neighbour, this is clear. But doing this 142 times is.. time consuming at best. I feel as if there should definitely be a way to automate this, but I haven't been able to find one.

So that is my question; is there a way to automatically match the lighting on multiple layers at once? I suppose I have to pick one as a reference, that is fine.

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    Is this the entire image or is it more complex? – Ryan Jun 30 '16 at 19:36
  • There is more to it, but I can't post all of it here as it is part of unpublished research. It's mostly like the empty space with some more of the wire like structures – user129412 Jul 1 '16 at 7:47
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Do you want to remove the tint and leave only the wiring? Or there are other things that need to be visible?

This is what I get as a result when I used Level layers. levels

Of course you can play with it more with more caution to save the data you see and want to leave visible. Easy way to use levels. This is how histogram looks like before any changes. [lvl1[2] Then, point to black (wires) and white part of pictures (I've chosen the right down corner of rectangle). It create new histogram and then you can play with the settings. lvl2 If there are things that need to be preserved just copy them to another layer and move it above level layer. lvl3

  • can you explain a little bit more how to use levels to achieve this result? – Luciano Jul 1 '16 at 8:45
  • That looks quite good already. Here the parts that cover the wire (we call them airbridges) are partially taken off though, which is undesirable, but as you mention one can play with this. How exactly did you do this? With an adjustment layer? – user129412 Jul 1 '16 at 8:45
  • I added an easy tutorial, if you have any questions just ask. – SZCZERZO KŁY Jul 1 '16 at 10:33
  • My apologies, for some reason I did not receive notification about your edit. Thanks! – user129412 Jul 4 '16 at 11:49

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