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 thin 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 with guides removed

Overlapping layers separated

  • There's nothing in GIMP that can do this automatically unfortunately. Manual curves adjustments for each image might be possible. Maybe concentrate on getting the slide holder fixed. Also make sure the images are taken using the exact same exposure (not auto exposure). Different exposures will always make any kind of image stitching look terrible. – Billy Kerr Feb 22 at 18:33
  • I was afraid of that. Figured it would be worth trying to do while we wait for the repair. Thanks! – David Feb 22 at 20:10

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