I was thinking of ImageMagick …
I came across phatch, I read of it here. It's a GUI, that helps running ImageMagick with certain operations in a batch. It came with a lot of dependencies on other packages. I tried to fullfil some of of them, eventually I gave up. If I very sure, that phatch was the way to go, that dependency hell wouldn't be a dead end. Spending time on getting phatch to run was a dead end for me.
There is a book on ImageMagick at PackPub, there is also one at Apress. I bought both of them as PDFs. That was the key to the success. I found nice examples, and I was able to apply some easy recipe to my task.
$ convert orig.png -crop geometry new.png
Actually the recommendation says to use "+repage", in order to not confuse certain software:
$ convert orig.png -crop geometry +repage new.png
Without "+repage" the file stores the displacement of the segment wrt. the original image, which comes in quite handy, but … certain software gets confused, eg. when I loaded one such new image into GIMP, GIMP displayed the displacement and presented me rubbish.
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