Upgrade scikit-image, numexpr, numpy

[derdualist]

At the moment we do not use the latest versions of scikit-image and numexpr, because the padding logic does not work with the numpy dependency version of scikit-image.

We need to upgrade scikit-image and refactor the padding logic. np.pad can probably not be used anymore for that.
Idea for the new logic: create a red frame of type numpy.ndarray and insert the actual image into that frame as a new image.

https://stackoverflow.com/questions/53931455/how-to-merge-a-transparent-png-image-with-another-image-using-scikit-image