I am putting together fluorescent images taken on a microscope. I have taken sequential images that overlap for anywhere between 20 - 50 pixels at the edges. I have set up grids so that I have perfect overlap between them. These images are taken at different focus depths because our slide holder is slightly bent (cannot get it fixed just yet) so the overlapping colors are slightly different.

I was wondering if there is a method in GIMP to take a single pixel (or several) in the overlapping region from one layer and match it in the same pixel to an adjacent layer so that the entire color level of the adjacent layer matches the first layer based on that pixel selection?

First image is my whole image with guides removed. You can see the change in color between the various overlapping layers.

Second image are two overlapping layers I separated. The thing rectangle on the right side of the left image, and the thin rectangle on the left side of the right image will overlap when put together. I would like to take one bright spot in one of these rectangular regions to alter my colors in the other layer using the same spot.

I only recently started using GIMP and I am poorly experienced in image editing in general.

Whole image, guides removed

Overlapping layers separated

  • \$\begingroup\$ This might be better addressed at graphic design SE. It's on subject here, but you might find more expertise with your particular issue there. \$\endgroup\$
    – Michael C
    Commented Feb 22, 2021 at 15:30
  • \$\begingroup\$ I will post over there as well, thanks! \$\endgroup\$
    – David
    Commented Feb 22, 2021 at 18:01
  • 1
    \$\begingroup\$ It might be that you actually need a different tool. Consider looking at Hugin, which is a GUI program to drive tools to align, adjust and seamlessly blend overlapping images such as these. \$\endgroup\$ Commented Feb 22, 2021 at 20:55

1 Answer 1


IMHO copying colors from one to the other isn't going to work. What you want is a smooth transition, if the layers overlap you just add a layer mask to the top one with a black to white gradient along the edge to make it fade:

enter image description here

If you want to tweak the colors you try this.

But I agree with the comments that a panorama stitching app such as Hugin is likely to do a better job (alignment and color matching).


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