Solution is to add option=>'quantum:polarity=min-is-white' to the image object like this:
my $image = Image::Magick->new(magick=>'TIFF', option=>'quantum:polarity=min-is-white');
This is the perl equivalent (found after hours of searching the net :) of the convert.exe command line:
convert file.tif -define quantum:polarity=min-is-white -resample 200x200 [...]
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