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SkyScan 1173 from Micro Photonics being used to digitize all species of fish

With more than 25,000 species identified worldwide, fish demonstrate more species diversity than all other kinds of vertebrates. A unique project using a SkyScan 1173 Micro-CT Scanner from Micro Photonics is changing the way scientists, teachers, students, and amateur ichthyologists will be able to study any fish from around the globe. This innovative use of micro-CT technology and scientific collaboration will enable anyone to look at the fine details of any fish online or produce an exact replica using 3D printing.

Fish

A scan of the spotfin hatchetfish (Thoracocorax stellatus). Credit: University of Washington, Adam P. Summers

 

University of Washington professor of biology and aquatic and fishery sciences, Adam Summers has undertaken the daunting task of scanning and digitizing each species of fish through collaboration with other scientists, creating high-resolution, 3-D images that will be available for free online. “These scans are transforming the way we think about 3-D data and accessibility,” said Summers. “It’s been so fun to throw this data up on the web and have people actually use it.”

Summers, based at the UW’s Friday Harbor Laboratories, uses a SkyScan 1173 Micro-CT Scanner from Micro Photonics to generate scans from fish specimens gathered around the world. The SkyScan 1173 is a flexible microtomography (micro-CT) scanner which offers a large field of view for big  and dense objects and also has the flexibility to image low-density materials.

Although smaller than a standard CT scanner used in hospitals, the SkyScan 1173 works similarly. First, a series of X-ray images is taken from different angles, converted to 2D slices and the images are then combined to create three-dimensional images. Prior to this there wasn’t an affordable way for scientists to get detailed, three-dimensional scans of fish or other creatures nondistructively.

Since acquiring the SkyScan 1173 for his lab, Summers has established a policy that scanning on the machine is free and open to other scientists as long as the fish come from museum-accessioned collections. The online database now comprises scans of fish from the UW’s Burke Museum of Natural History and Culture, the National Academy of Sciences in Philadelphia, Ohio State University, Western Australian Museum, and many more.

Summers has developed a great deal of expertise in the processes involved in the project and in the sharing of the finished scans. He begins by scanning multiple fish at once, rolling the specimens together in a cylinder that is placed in the scanner. After running a single scan, Summers digitally separates the 3-D images into individual files. Since most scientists don’t need the maximum of detailed data that could be scanned, Summers saves time and digital space by scanning at a somewhat lower resolution. This makes online access easier as well. “The way transformative ideas do, these just instantly changed the way we think about scanning specimens. We went from, ‘Is this possible?’ to scanning whole series of fishes quickly,” said Summers.

As of this writing, more than 500 fish species have been scanned, with many posted online to Open Science Framework (https://osf.io/), an open-source sharing website for scientists. Summers anticipates that all of the fish species in the world will be scanned in about three years.

As with all our SkyScan users, Micro Photonics technical staff is pleased to collaborate on projects such as this with technical support and resources as needed.

For more information, see “Professor digitizing every fish species in the world,” by Michelle Ma:   http://phys.org/news/2016-07-professor-digitizing-fish-species-world.html .

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