After talking to @nethahussain we decided I'll upload one category of files to one of the empty categories in https://commons.wikimedia.org/wiki/Category:SMART-Servier_Medical_Art, preferably Intracellural components as all the metadata for these images has been prepared. Then we'll evaluate it together to make sure we have a process that can be applied to the rest of the collection.
Category: https://commons.wikimedia.org/wiki/Category:SMART-Servier_Medical_Art_-_Intracellular_components