March 20, 2023
Away Team Tech: 3D Flora And Fauna At Your Fingertips

Away Team Tech: 3D flora and fauna at your fingertips – Astrobiology

A simplified diagram of the photogrammetry method. The slowly spinning object (Carassius auratus langsdorfii), suspended by a nylon fishing line, is photographed from several angles. The resulting 3D model is shown at or — Kyushu University

Citing research ideas and results, a Kyushu University researcher has developed a new technique for scanning various plants and animals and reconstructing them into highly detailed 3D models. To date, more than 1,400 models have been made available online for public use.

Open any nature textbook or magazine and you’ll find stunning high-resolution images of the diverse flora and fauna that encompass our world. From the botanical illustrations in Dioscorides’ De materia medica (AD 50-70) to Robert Hooke’s sketches of the microscopic world in Micrographia (1665), scientists and artists have worked meticulously to depict the true grandeur of nature.

The advent of photography has given us even more detailed images of animals and plants both large and small, in some cases providing new information about an organism’s morphology. As technology developed, digital libraries began to develop, giving us almost unlimited access to valuable data, with methods such as CT or CT and MRI becoming powerful tools for studying the internal structure of such creatures.

“Although powerful, MRI and CT methods are prohibitively expensive. You also cannot collect vital information such as organism color,” explains Yuichi Kano, associate professor of Kyushu University’s Graduate Education and Research Program in Decision Science for a Sustainable Society. “So we developed ‘bio-photogrammetry’ as a way to incorporate photogrammetry that could scan and render a high-quality 3D image of an organism.”

Photogrammetry is a method by which you can obtain information and measurements about objects by analyzing photographs or other images. Today it is commonly used to scan everything from landscapes to sculptures to build digital 3D models, similar to what you find in Google Earth.

Kano used the same methodology to make thousands of models of various organisms.

“We hung the specimen on a fishing line and took pictures from several angles. We would end up taking hundreds of photos of the sample and input up to 500 of the best ones into the photogrammetry program,” explains Kano. “It’s similar to how the bullet time sequences in the first Matrix movie were shot, except Keanu Reeves is on a line surrounded by cameras, we’re using an octopus.”

While Kano works on a variety of organisms, including insects, plants, and even fungi, he currently focuses on aquatic animals such as fish and amphibians. To date, there are over 1,400 samples available all free to use under the CC BY 4.0 license.

There are some limitations to the current methodology, such as the difficulty of capturing transparent creatures or making models very small (<5 mm) ή μεγάλων (>1 m) organizations, but some improvements in software and protocols could help solve such issues.

“I hope to see this work continue to be developed and used in various fields such as taxonomy, morphology and ecology. It’s free to the public so you can use it in training or even plug it into a VR machine and explore these organisms up close. I’d like to see what some people can come up with,” Kano concludes.

For more information on this research, see “Bio-photogrammetry: digital archiving of color 3D data of creature morphology and related challenges”, Yuichi Kano, Research Ideas and Outcomes (2022).

About Kyushu University

Kyushu University has been one of Japan’s leading higher education research institutes since its establishment in 1911. Home to approximately 19,000 students and 8,000 faculty and staff, Kyushu U’s world-class research centers cover a wide range of study areas and research fields, from the humanities and arts to engineering and medical sciences. Its multiple campuses—including the largest in Japan—are located around the city of Fukuoka, a coastal metropolis on the southwestern Japanese island of Kyushu often ranked among the world’s most livable cities and historically known as the gateway to Asia.


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