So the complete summary now, hihi 
1. remove the "border" around the squares
2. I also need to remove the black background of all the squares (and add alpha layer for transparency). I did this with the "select by color" tool. This works great.
3. But then gmic doesn't detect the objects anymore (if the background is transparent) and it doesn't extract them.
So I'm stuck at doing 3. after 2., which doesn't work anymore
(3. however works without removing the background, but this is not what I want)
How do I combine the removal of the black background and the "extract objects" of gmic so I can do both after each other? I don't want to use the "select by color" on all created layers by gmic one by one.
1. remove the "border" around the squares
2. I also need to remove the black background of all the squares (and add alpha layer for transparency). I did this with the "select by color" tool. This works great.
3. But then gmic doesn't detect the objects anymore (if the background is transparent) and it doesn't extract them.
So I'm stuck at doing 3. after 2., which doesn't work anymore
(3. however works without removing the background, but this is not what I want)
How do I combine the removal of the black background and the "extract objects" of gmic so I can do both after each other? I don't want to use the "select by color" on all created layers by gmic one by one.