: Normalizing hematoxylin and eosin-stained histology images This is a medically related question...Most pathology slides are stained with hematoxylin (blue) and eosin (red). However, every lab does

@Heady304

Match colors with Gimp

Adjusting the colors of histology slides is not an easy task as we are faced with a great variation not only in staining quality but also in heterogeneous staining of different tissues, and from a great variation of color temperature from the microscope light source. This is further aggravated by poor contrasting of the raw images that come from settings of the various microscope cameras on the market.

Nevertheless we do have to normalize these images for print or for presentations to reduce the color variations as can be seen from examples below (random Google image search):




To show the effects of color normalization I deliberately did not adjust the overall image brightness and contrast. This of course should have been done before we normalize colors (see example below).

FX-foundry color match

With a default installation of Gimp we have access to FX-Foundry scripts. It is the effect "Fx-foundry - Colors - Match Color..." effect which allow to match colors to a reference image. This effect is fast, and can also be used in batch processing to give reasonably good results:

Reference image used:



Resulting color match using FX-foundry script:




We can see that there is a far better color match between the slides now. We can also see, that further adjustment of contrast enhancement for better results would be needed in addition.

Adjust contrast before color processing

Below is an automatic filter "Colors - Auto - Stretch Contrast" from Gimp I had added before color normalization on one of the images above:



If we had the time for manual adjustments we should however not use automatic processing for better results.

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