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Pyroteuthis margaritifera has morphologically distinctive photophores on the tentacles, eyeball and in the mantle cavity. The photogenic tissue in each photophore is identical, has a blue-green fluorescence and luminesces on treatment with dilute hydrogen peroxide. The photocytes frequently contain organized fibrillar material akin to that in the photocytes of certain other cephalopods. Several different types of blood vessel are present among the photocytes, including some, apparently restricted to the photophores, with a microvillous endothelium. Haemocyanin is present not only within identifiable blood vessels but also in some intercellular spaces.

On the basis of their characteristic optical systems the photophores can be separated into three types: (1) tentacular; (2) ocular and anal; (3) branchial and median abdominal. The tentacular photophores have collagenous reflector and light guide systems and the median ones are double organs. The ocular and anal organs do not have collagenous optical structures but an elaborate variety of reflective iridosomes. Those in the aperture of the photophores appear to act as interference filters. The branchial and abdominal organs have iridosomes as the major reflective tissue but collagenous fibrils function as light guides in the aperture of these organs and their emission is diffuse rather than collimated.