Friday, June 13, 2025

Bones to pick: New Australian animal 3D database comes to life

Flinders University

Morphosource — video:
Screen recording of the Ozboneviz collection on MorphoSource.org.

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Credit: Flinders University

For the first time, the remarkable features of Australia’s unique wildlife – from platypus, bilby, kangaroo, koala and emu to mammals gone extinct – are available for all to see, via their bones and skeletons in a new free online collection.

Using 3D imaging technology, Flinders University and partners have launched the ‘Ozboneviz’ virtual database, which goes ‘inside’ the anatomy of dozens of Australia’s most famous animals for the public, schools, researchers, artists, nature-lovers and others to access.

Described in a new article published in the journal BioScience, the new collection of more than 1600 specimens has been collated and uploaded on to the high-tech MorphoSource repository, by Flinders University Associate Professor Vera Weisbecker’s ‘Bones and Biodiversity Lab’ and colleagues around Australia.

“We are all fascinated by bones and this new database is a way to go behind the glass cases at the museum, see specimens up close and understand their special features,” says Associate Professor Weisbecker, who hopes

Ozboneviz will fuel better scientific and public appreciation of Australia’s amazing mammals around the world.

“Australia leads the world in mammal extinctions, but we are losing far more than a few fluffy rat-like critters. Our mammals have evolved in isolation for nearly 40 million years - there is simply nothing like them anywhere else.

“Victorian-era scientists deemed Australian wildlife ‘primitive’, but now we can marvel at the elongated leg bones that make the kangaroo the largest hopping animal ever, or the bizarre shovel-like arms of the marsupial mole, and chances are that you will change your mind!

“3D models of skeletons are a charismatic way to engage adults and children alike with Australia’s precious fauna, making it a key asset in science communication and school education.”

Now Australia’s largest open-access library of 3D biodiversity data, the project was funded by the Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), with support from the Australian Museum, SA and NT museums, the Australian National Wildlife Collection, and several universities.

“Our core team spent three years travelling to four Australian museums and three universities. We mostly used surface scanners to digitise ten key bones of 189 iconic Australasian species: the skull, shoulder blade, pelvis and limb bones,” explains CABAH and Flinders archaeologist Dr Erin Mein.

Jacob van Zoelen, PhD candidate at Flinders University and digitisation manager, says: “We used a structured light scanner to image the outside of most bones. But for particularly rare species, like the presumed-extinct ngudlukanta or desert rat-kangaroo, we opted for computed tomography, because it also images the internal structure of the bones at resolutions of 10-50 micrometers.”

The resulting 3D files are deposited on the MorphoSource platform, which is important for scientists because it has the same rigorous cataloguing as any physical museum. But the files are open access, with anyone able to download them for non-commercial use.

To facilitate public access, Dr Mein also built a Sketchfab site with more than 500 of the most precious and informative bones, with examples including the skull of an extinct marsupial tiger, or thylacine, the pig-footed bandicoot, desert-rat kangaroo and rare marsupial mole.

“This means the public can compare the cranium of a fox to a thylacine and dingo, for example, and compare the size and shape of limb bones of common marsupials,” adds Dr Mein. “There are also plenty of annotations to help non-specialist users learn about vertebrate anatomy and compare anatomical attributes between species.”

As well as the focus on large native mammals such as kangaroos, possums, and bandicoots, the database includes some non-native mammals that people tend to come across, like goats and sheep, as well as a selection of large birds, lizards and frogs.

The MorphoSource collection includes a number of specimens with interesting features or stories, including:

The skeleton of Billie, the Port River dolphin well known to Adelaide residents.
An Attenborough’s long-beaked Echidna (Zaglossus attenboroughi)- previously considered extinct but was reobserved in the wild around the time the specimen was scanned.
The extinct pig-footed bandicoot (Chaeropus ecaudatus), the only marsupial with something like hooves.
CT scan of two whole marsupial moles (genus Notoryctes), which is Australia’s “weirdest skeleton,” according to Associate Professor Weisbecker.

Associate Professor Weisbecker says there is no Australian precedent for open-access databases of this kind.

“Hopefully this will lead the way to an even wider use of digitisation to make Australia’s unique local biodiversity accessible to the global public.”

The article, ‘Ozboneviz: An Australian precedent in FAIR 3D imagery and extended biodiversity collections’ (2025) by Vera Weisbecker (Flinders University), Diana Fusco (Flinders), Sandy Ingleby (Australian Museum), Ariana BJ Lambrides (James Cook University), Tiina Manne (University of Queensland), Keith Maguire (South Australian Museum), Sue O’Connor (ANU), Thomas J Peachey (Australian Museum), Sofia C Samper Carro (ANU), David Stemmer (SA Museum), Jorgo Ristevski (Griffith University and Max Planck Institute of Geoanthropology), Jacob D van Zoelen (Flinders), Pietro Viacava (CSIRO), Adam M Yates (Museum and Art Gallery of the NT) and Erin Mein (Flinders) has been published in Bioscience (Oxford University Press). DOI: 10.1093/biosci/biaf064. https://doi.org/10.1093/biosci/biaf064

Photos / 3D images: Ozboneviz_media_release_assets - Google Drive
Vertebrate cranial anatomy animation (Sketchfab) https://skfb.ly/oWMF9

Journal

BioScience

DOI

10.1093/biosci/biaf064

Method of Research

Meta-analysis

Subject of Research

Animals

Article Title

Ozboneviz: An Australian precedent in FAIR 3D imagery and extended biodiversity collections

Article Publication Date

11-Jun-2025

Jacob van Zoelen [VIDEO]

Jacob van Zoelen, PhD candidate at Flinders University and digitisation manager, surface scans bones from a national collection.

Credit

Dr Erin Mein (Flinders University)

Photograph of postcranial skeletal elements of Thylacinus cynocephalus specimen MV-C5746 by Rodney Start for Museums Victoria. Copyright CC-BY 4.0 to Museums Victoria https://biocache.ala.org.au/occurrences/db4e9155-8742-4f3e-b3f5-1c88f6c52435

Credit

Rodney Start for Museums Victoria

Associate Professor Vera Weisbecker leads the ‘Bones and Biodiversity Lab’ at Flinders University and is part of the Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH).

Credit

Flinders University

An illustration of the extinct Tasmanian tiger (Thylacinus cynocephalus) by Nellie Pease for GoExtinct! Megafauna boardgame published by ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH). Copyright: CC-SA 4.0 https://commons.wikimedia.org/wiki/File:Tasmanian_Tiger_%28Thylacinus_cynocephalus%29.pn

Credit

Illustration by Nellie Pease for GoExtinct! Megafauna boardgame

Lawn story: Turfgrass data may improve urban greenhouse gas emission estimates

Penn State

UNIVERSITY PARK, Pa. — Data that has been lost in the weeds — or more accurately the turfgrass — could help improve estimates of carbon dioxide emissions from urban areas, according to a team led by scientists at Penn State.

As a part of a larger project to measure greenhouse gas emissions in Indianapolis, the researchers found that turfgrass lawns, like those surrounding our homes and in parks, golf courses and cemeteries, have impacts distinct from other urban vegetation, such as trees and wild grasslands. Adding turfgrass to simulations of urban ecosystems increases not only the understanding of vegetation’s role in carbon dioxide levels, but it could also improve estimates of human-caused emissions, the scientists reported in the Journal of Geophysical Research: Biogeosciences.

“This study has implications for guiding greenhouse gas policies and for reducing the amount of uncertainty when we’re trying to estimate anthropogenic emissions to guide those policy decisions,” said Jason Horne, a doctoral candidate in meteorology and atmospheric science at Penn State and lead author on the study. “There has been a push to better understand the processes that are going on in these areas, because it’s really complex.”

Urban greenhouse gas emissions result from humans burning fossil fuels while driving vehicles, powering factories and heating homes, but plants also play a role. Plants remove carbon dioxide from the atmosphere during photosynthesis, but they also produce carbon dioxide as they respire and decompose. Teasing out the impact of vegetation is important to produce accurate estimates of emissions from human activities, the scientists said.

“And for that, we need to have a good idea of what the biology is doing,” Horne said.

The work was part of the Indianapolis Flux Experiment (INFLUX), which has built emissions estimates for the city and its surroundings using an array of measurement techniques, including towers around the city that take continuous measurements of carbon dioxide.

“INFLUX is this long-running project that is one of three greenhouse gas testing sites in the United States,” Horne said. “It offers one of the best and most abundant and diverse records from urban areas compared to just about anywhere else in the world.”

In this study, Horne analyzed data collected from eddy covariance flux towers — instruments that can measure the exchange of gases between Earth’s surface and the atmosphere. One sensor was placed over a golf course and another over a cemetery lawn.

The researchers found that existing vegetation types that are already factored into their models could not capture seasonal patterns observed in the exchange of carbon dioxide from the ground to the atmosphere at these two turfgrass-covered locations.

For example, in winter months, when air temperatures dip below freezing, the models previously predicted no photosynthesis activity. But the team’s observations showed there is still photosynthesis in grass lawns removing some carbon dioxide from the atmosphere — even at subfreezing temperatures.

“Our models were not able to capture the carbon dioxide being removed from the atmosphere by photosynthesis in the middle of winter,” Horne said. “The model showed vegetation was a net source of carbon dioxide during the middle of the day.”

Using their observations, the researchers created a unique turfgrass vegetation type in the model. Including the new turfgrass representation allowed the model to capture the photosynthetic activity in the middle of winter as observed.

“Turfgrass photosynthesis is not highly active during the winter, but it’s active enough to make a difference in the models — and that could make a difference in how we understand every emission source,” Horne said.

He explained that if the models show that vegetation is putting more carbon dioxide into the atmosphere than it is removing — or acting as a source rather than a sink — then when scientists look at total emissions during that time frame, they may underestimate the impact of human-caused emissions, the scientists said.

And while the impact of photosynthesis from turfgrass in winter may be small, extrapolating that over the entire urban area means it can have a real impact, Horne said.

“Something like 20% to 30% of the surface area in Indianapolis is estimated to be turfgrass,” he said. “Even if we see a small drawdown of carbon dioxide in the middle of winter, it’s not insignificant. If you are not considering that, you may be underestimating anthropogenic emissions.”

The scientists noted differences between the two locations — the golf course’s grass is fertilized, mowed and irrigated, while the cemetery’s grass is less managed. Given the variability, they said additional studies are needed to further improve estimates of turfgrass impacts on carbon dioxide emissions.

“But it’s clear from our work that turfgrass lawns are worthy of dedicated study,” Horne said. "This could help reduce the amount of uncertainty when we're trying to estimate anthropogenic emissions to guide policy decisions.”

Also contributing from Penn State were Kenneth Davis, professor of atmospheric and climate science; Scott Richardson, research professor; Natasha Miles, research professor; and Samantha Murphy, doctoral candidate, all in the Department of Meteorology and Atmospheric Science.

Claire Jin, research assistant at Carnegie Mellon University, and Kai Wu, researcher at the Carbon Neutrality Research Center at the Chinese Academy of Sciences, also contributed.

The National Institute for Standards and Technology supported this work.