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AFORO adds 3D otoliths to identify fish species

AFORO is a well known online catalogue of otoliths (internal structures of the fish ear). Now it has started a new stage, AFORO 3D, in which three-dimensional models of otoliths are added to the catalogue. This opens the door to new possibilities that were unimaginable until now.

Fish and otoliths. Above,  Zeus Faber or John dory. Below, Paracanthurus hepatus or surgeonfishSince  2002, scientists at the Institut de Cièncias del Mar of the CSIC and at the Universitat Politècnica de Catalunya have developed a system of image analysis and a database to automatically identify fish species through the otoliths’ shapes. Its website, AFORO is open to specialists to search and identify directly using images of otholits.

AFORO is the acronym of Shape Analysis of Fish Otoliths in Spanish (Análisis de FORmas de Otolitos). Its image classification system offers a good rate for identification: 70 % at species level and 90% at genus and family level.

The scientists have recently started to add three dimensional pictures, which will offer more reliability for the identification of otoliths. Also, and most importantly, it will make it possible to have virtual 3D models of the otoliths, making it therefore possible to study them without having them physically. Also, these 3D models can be applied to biomechanical studies of the fish ear.

Like the identity card of the fish

Otoliths, the internal structures of the fish ear, are formed of calcium carbonate crystals basically made up of aragonite crystals. They don’t easily degrade. “Otoliths are like the identity card of fish”, explains Antoni Lombarte, CSIC scientist at the Institut de Ciències del Mar and leader of the AFORO project. “Otholits allow us to identify not only the species of fish but other things, such as the age or their movements”.

On one hand, explains the expert, otoliths register how the fish grow every year, similarly to the rings within a tree's trunk, and the daily growth. Therefore, they make it possible to know the age of the fish with great accuracy. On the other hand, the chemical composition of otolith depends on the water characteristics, which reveals in what kind of water the fish has been. This is useful also for environmental studies, to detect alterations in water through otoliths. 

Also, otoliths are useful  in archaeological excavations, where food remains have been found, to identify which fish species our antecessors used to eat; or in paleontological excavations, to identify species from the past. Or for trophic structure studies, to analise the diet of animals that hunt fish and the only sample available is the stomach content.
Another interesting area, points out Antoni Lombarte, is fisheries management, when there are species externally so similar that a morphological tool is necessary to reliably differentiate them.

From 2D to 3D

First descriptions of otoliths were based on anatomical characteristics and represented by drawings. “With the arrival of image analysis systems, the concept of form analysis started to be introduced in the descriptive studies of otoliths”, says Lombarte.

The website AFORO, created in 2002, has a database of 4.100 images of otoliths, which correspond to 1.250 species. Most of them come from the biological collection of the Institut de Ciències del Mar, which compiles 5.000 samples. Others come from autors that have offered their images.

But comparing bi-dimensional images has limitations. That’s why scientists started to add 3D images. The project counts on the collaboration of the Universitat Politècnica de Catalunya, and the Universitat de Vic. The issue is to create three-dimensional morphological descriptors and to develop 3D analysis tools.

A special 3D scanner has been created, able to scan the small otoliths, whose sizes go from one millimetre to a few centimetres

A very special scanner

A special scanner has been created, able to scan the small otoliths, whose sizes go from one millimetre to a few centimetres. The prototype works with a single camera and a beam of LED light. It has been developed by the group of Computer and Robotics Vision at the Universitat de Girona and the company AQSENSE.

Using this device, scientists at the Institut de Ciències del Mar have started to obtain virtual 3D models of otoliths, 30 until now, with a high resolution. “They have been digitalized with a precision of 40 micrometres”, says Lombarte, “So they can be used  as a models in computer simulation, in biomechanical studies of the ear”.

“The same could be done with teeth or bones, and therefore to have the possibility of working with virtual models without using the samples”, points out the expert. This opens great possibilities for studies in the fields of paleontology, archaeology, biomechanics, and to create reference  collections of virtual models

3D videos and pictures of otoliths at: