Here is an interesting article on current development of creature pipeline at Weta Digital. They mention how new standalone custom software Tissue developped at Weta during production of Avatar is used for accurate deformation and simulation of character surfaces, consisting of realistic anatomical model of bones, muscles and fat. Also how in recent movies like Planet of Apes or Tin Tin dynamic simulation similar to cloth is used in facial animation post-process.
http://www.cgw.com/Publications/CGW/2011/Volume-34-Issue-9-Dec-Jan-2012-/Animation-Evolution.aspx
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