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In academic English the preferred plural of index is indices, for most scientific and mathematical if not all purposes. (See the article on -es in Latin.) You may sometimes see indexes; you may hear it more often. But I would advise you to use indices as your usual form. Index was originally a Latin word, and academics should stick to Latin forms wherever appropriate.

OED does say that indexes is the more usual plural form for the 'alphabetical list[s], placed (usually) at the end of a book, of the names, subjects, etc. occurring in it, with indication of the places in which they occur'; but this is not universal in academic circles.