Coral structures analyzed by computers

We all know that Earth's coral reefs are threatened by human activities, especially the global warming effect. And to study coral colonies, biologists either did manual measurements or used photographs. But now, Dutch researchers are using computers to measure coral structures and open source software to visualize them. Read more...

We all know that Earth's coral reefs are threatened by human activities, especially the global warming effect. And to study coral colonies, biologists either had to do manual measurements or look at photographs. But now, Dutch researchers are using computers to measure coral structures. Coral specimens are first scanned before being reduced to a skeleton analyzed by a computer to detect various branches. The open source software developed by the researchers provides 3-D interactive simulations of the corals. And they expect it will help to conserve the Earth's coral reefs. Read more...

Let's start with a short introduction about coral species.

Corals can, for instance, be ball-shaped or formed like a tree. The same species of coral can look completely different depending on environmental factors, which influence the growth pattern. To compare and classify specimens, it is important to make very precise measurements of coral thickness and branch distances. Biologists used to do this by hand, which takes a lot of time, and can cause unwanted errors.

Obviously, coral biologists need more modern methods. This is why Krzysztof Kruszynski (CWI) and Jaap Kaandorp (Universiteit van Amsterdam) developed a semi-automatic method for the quantification of branching coral shape.

Coral specimens are scanned in a CT scanner. The scan data are filtered, segmented and transformed to a centerline skeleton. This method simplifies detection of features like branches, branching locations, and endpoints. The skeleton is then measured by the computer, and the results are subjected to statistical analysis; the measurements include thickness, angles, lengths, and spacing of branches

As an example, below is a series of pictures of coral structures. From left to right, you can see the volume rendering of the CT scan, theiso-surface of the segmentation and the skeleton (Credit: CWI).

A series of coral structures

According to the researchers, their method is not perfect, even if it's much faster than current manual ones. Here are some the problems they faced.

Noise comes from CT scanner ray scattering, decayed parts of the coral and creatures growing on it. Branches broken during transport are reattached with glue, influencing the measurements. It is difficult to fill holes -- made by worms or human drilling -- making it hard to distinguish the inside of the coral from the background. 'Skeleton loops' -- due to low scanner resolution or branches growing back together -- make branch ordering, and thus measurement, impossible. Noise filtering might affect the shape, but the noise itself influences the measurements, and must thus be reduced.

OK, the method is not perfect. But it's still better than current ones. Personally, I think these researchers did a great job which will help us to better understand -- and conserve -- corals.

For more information, please read a technical paper called "An Interactive Visualization System for Quantifying Coral Structures (PDF format, 8 pages, 269 KB). The above illustration has been extracted from this paper.

Sources: Chris Kruszynski and Annette Kik, in ERCIM News, Issue 66, July, 2006; and various web sites

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