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In academic English, the plural of helix should always be helices.

Helix is a word used in mathematical descriptions, or descriptions echoing mathematics. It means 'a coil, a spiral, [such] as an electromagnetic coil of wire, the thread of a screw, a tendril'¦ [more accurately] 'anything of a spiral or coiled form, whether in one plane (like a watch-spring), or advancing around an axis (like a corkscrew), but more usually applied to the latter' (http://www.oed.com/). Its most famous use in modern English is in the phrase 'the double helix' to describe the molecular structure of DNA.

Helix was originally a Greek word which was then taken into Latin. (See -es in Latin.) In academic English, use the Latin or Greek forms of words that still 'feel' as if they are Latin or Greek, as far as you can.