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Ever wanted to compare a man with a mouse?

20 December 2010

Software developed by BBSRC-funded scientists to analyse bone structures is now being used by researchers in other disciplines to help tackle a range of challenges – including designing nuclear reactors.

Researchers at Imperial College London have developed a software plugin for the image analysis program ImageJ that measures bone geometry in animals of varying sizes.

Michael Doube and his team study bones from an evolutionary, comparative anatomy perspective and for biomedical purposes. The team was interested in how bones cope with the loads applied by animals of very different sizes. "Bone material and the basic skeletal layout is similar between quadrupeds, but an elephant is a million times more massive than a shrew," says Doube.

Doube's team wanted to know what modifications to bone shape could allow this range of body sizes to exist, but he found that existing bone analysis programs were expensive, inflexible and often unable to process the large image files produced by micro-CT scanners.

Trabecular thickness (Tb.Th) of a cube of trabecular bone from a horse.  Bright colours (yellow, orange) represent thick regions and dark colours (blue, purple) represent thinner regions. Image: Michael Doube

Trabecular thickness of a cube of trabecular bone from a horse. Bright colours (yellow, orange) represent thick regions and dark colours (blue, purple) represent thinner regions.
Image: Michael Doube

In order to overcome the issue, Doube and his team started work on developing a plugin for the image analysis program ImageJ. Doube says ImageJ is popular in scientific imaging because it is easily customised and is able to handle image formats that other programs struggle with. He was able to develop with ImageJ and its existing plugins because they are open source – anyone can look at the code and modify and improve it for wider use.

Many existing image analysis programs are only available in binary format and Doube explains that this does not allow the user to look at the code and see how their image data turns into their results. Doube describes the use of open source programs as "lifting the lid off the black box of scientific data analysis."

Thus, the team developed a bone analysis plugin for ImageJ and BoneJ (see external links) was born. The program was initially used to analyse trabecular bone, whole bones and osteocyte lacunae.

BoneJ is already being used for bone analysis by anthropologists and palaeontologists who are using the program to find out what bones and fossils have to tell us. The program's parameters are not limited to bone and it is able to provide analysis of food and soil samples due to their foamy structures that share characteristics of trabecular bone. "My favourite so far is the researcher who used BoneJ to develop the lining for nuclear fusion reactors," says Doube.

Doube hopes that BoneJ will become a reference for other scientists who write their own software for analysing bone structure but the program is, by its very nature, constantly in development. "There is a feature request list available on the BoneJ development website that anyone is welcome to come and work on," he says.


Natalie Waters

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fax: 01793 413382