For my research work i have to analyze some thousands of photos, manually it will take more time and human power but thanks to fiji I can easily carryout the analysis but for that the images should be in proper format and order. so i have to edit (cropping the image to the microscopic field and change the background to white) the batch of photospollen study. so how can i automate this for remaining thousands of photos in GIMP.

  • 1
    Why in Gimp? Can probably be done faster with ImageMagick in a shell script.
    – xenoid
    Commented May 24 at 7:54
  • can it automatically identify and crop the image to microscopic field?
    – 3ncryp70
    Commented May 24 at 10:18

1 Answer 1


With ImageMagick:

Preliminary notice, the black background is far from being uniformly back so either you make it all black (changing the black point with -levels (that also changes the blackpoint in the microscope field and makes the image a bit darker) or you use a very large -fuzz factor for the flood-fill.

In both cases we change the background to white before trimming, because before trimming all the background is connected and is easy to flood-fill, while after the trim it becomes four isolated corners.

With black point:

convert Source.jpg -level 15%,100% -fill white -fuzz 8% -floodfill +0+0 black -trim Trimmed.jpg

Trimmed with black point

Without black point:

convert Source.jpg -fill white -fuzz 20% -floodfill +0+0 black -trim Trimmed.jpg

Trimmed without black point

(using IMv6, if you use a more recent version, replace convert by magick or magick convert. There is also a mogrify command/verb that updates the image in place, when you are confident enough (or have backups).

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