Tidying up photomicrographs using GIMP

I will take you though some steps that will help get better looking micrographs.

GIMP (GNU Image Manipulation Program ) is a powerful and comprehensive package for image processing, but it comes with a steep learning curve. It does most of the things that Photoshop does (also a steep learning curve) and all for the measly sum of FREE! What a bargain. Grab a copy from https://www.gimp.org.

Open your micrograph using GIMP. The example I am using is a micrograph from Wilson Staples of tammar developing testis stained with Haematoxylin and Eosin. Note the background (outside the tissue section area) is rather yellowish – an issue of the colour balance that will distort your perception of the tissue sample’s staining. But a few quick steps this can be fixed.

On the menu choose Colours>>Levels.

This brings up the levels dialog. Select the WHITE eyedropper tool in the lower right.

Now click on an area of the background outside the tissue section, an area that should appear white.

The click should immediately adjust the image so the background is white, and shift the red, green and blue channels so that the whole image now looks to have better colour balance. Click the OK button to save the change.

Now zoom your image to 100% (menu View>>Zoom). Is the image sharp enough. Would a bit of Image sharpening help?

GIMP provides a variety of ways to sharpen, but the simplest is to use the menu Filters>>Enhance>>Sharpen (Unsharp mask).

This brings up a dialog where you can adjust some parameters (make sure the preview check box is ticked so you can see the effect; if needed adjust radius, amount, threshold to tweak the sharpening effect). Search the documentation for full details, but the default settings will probably work OK. Don’t overdo it. You are trying to fix unsharpness caused by poor focus, vibration of the microscope during exposure, lens defects etc. If you overdo it you are just introducing artifacts so that the resulting image may not accurately reflect the reality of your specimen. Toggle the preview checkbox to compare the before/after.

Once you are happy with the sharpening effect click OK to apply the filter to the image.

Save your edited image.

Note that in this example there is a large area outside the tissue area to click on to adjust the background colour balance. If you don’t have such an area, zoom in on the specimen and look for a clear space between cells – there are usually such areas where you can click.

Hope that helps.