Thumbnail descriptions that do not match either of the patterns listed above are presumed to be manually uploaded thumbnails. These thumbnails will not be replaced even if the -f option is passed to the filter media process.
DSpaces uses JPEG as format for thumbnails. While JPEG doesn't support transparency, PDF, PNG and other formats does. As those formats are used as outgoing material in DSpace, DSpace has to care about transparency during the generation of the thumbnails. In combination of special versions of ImageMagick and Ghostscript it may occur, that completely transparent areas will become black. As solution ImageMagick recommends to flatten images extracted from PDFs before they are stored as JPEG. Since DSpace 5.2 the ImageMagick media filter flatten thumbnails extracted from PDFs. If you run in to problems you lead back to flattening of the extracted images, you can switch the flattening off by setting the following property in dspace.cfg to false:
org.dspace.app.mediafilter.ImageMagickThumbnailFilter.flatten = false
The ImageMagick conversion software provides a large number of conversion options. Subclasses of these media filters could be written to take advantage of the additional conversion properties available in the software.