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Micro-CT Workshop Venue: Fritz-‐Loewe Theatre, School of Earth Sciences The University of Melbourne
Date, Time: 7th November 2018, 9:00-‐13:00.
Full Program 9:00 Introductory Remarks Welcome from the TrACEES platform manager and members of the steering committee. 9:15 Introduction to Micro-‐CT / Highlights from 2018 X-‐Ray Computed Tomography (XCT) is a technique for the non-‐destructive 3D visualization of the internal structure of objects using 2D X-‐ray snapshots from different angles of an object to reconstruct a 3D volume of the objects internal features. Contrast between the different features within an object is achieved due to a difference in the X-‐ray absorption by these features, which is impacted by a features density and composition. Instruments utilizing this method range from medical CAT scan instruments with a coarse resolution (>100 micrometer per voxel, a 3D pixel) to instruments classified as nano-‐ or micro-‐CT scanners that can achieve resolutions in the sub-‐micrometer to micrometer range. The TrACEES platform at the University of Melbourne currently operates a GE Phoenix Nanotom M micro-‐CT scanner with a resolution ranging from 1 micrometer to 70 micrometer on an object 1 mm3 to ~3000 cm3 in size. This workshop will highlight research from 2018 using micro-‐CT data collected through the TrACEES platform and will host a forum for discussion of micro-‐CT applications, data management and analysis.
Dr. Jay Black Jay is an experimental geochemist with a PhD in Inorganic Chemistry from Monash University (2005) and joined the School of Earth Sciences at the University of Melbourne in 2013 to pursue his research into carbon storage in deep saline aquifers. From 2016 Jay has worked for the TrACEES platform as operator of the micro-‐CT instrument specializing in the analysis of micro-‐CT data. TrACEES Platform, School of Earth Sciences, The University of Melbourne [email protected]
9:30 Old Material, New Technologies: X-‐ray CT scanning at Museums Victoria The last two decades have seen a revolution in digital imaging techniques for non-‐destructive sampling of museum collections. These approaches offer an unprecedented view of external and internal features of whole objects in three dimensions – objects that we would otherwise not handle for fear of damaging them (E.g. Seastar in figure to right). X-‐ray computed tomography, or CT (similar to CAT scanning), has become a primary tool for interacting with these unique materials, be it ethanol-‐preserved organisms or ancient mineralised fossils. In this talk I describe the discovery and applications of X-‐ray radiation in scientific research, and how we are using it at Museums Victoria to unlock hidden aspects of our vast natural history collections.
Dr. Christy Hipsley Christy is an ARC DECRA Fellow and Research Associate at Museums Victoria, where she uses their extensive collections to reconstruct Australia’s evolutionary past. Her current research focuses on the long-‐term impacts of climate change on Australia’s fossil record, by measuring variation in lizard and frog communities over geological time. School of BioSciences, The University of Melbourne; Museums Victoria [email protected]
Seastar from Museums Victoria collection. False coloured 3D renderings of micro-‐CT data from top-‐down (A) and bottom-‐up (B); Cross sections through specimen (C-‐E) with red line indicating location. (scalebar = 5 mm) O’Hara et al. (2018) Zoo. J. Linn. Soc.
9:45 Development of the Extinct Tasmanian Tiger Pouch Young Revealed by X-‐ray Computed Tomography The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was an iconic Australian marsupial predator that looked like a large dog or wolf but raised its young in a pouch. Falsely labelled as a ‘sheep killer', the thylacine was hunted to extinction through a government bounty scheme in the early 20th century, with the last known individual tragically dying in captivity in 1936. The eradication of the thylacine also promoted trading of whole animals, bones and pelts, and now over 800 specimens exist in institutions worldwide. To learn more about the biology and development of the thylacine we sourced all known thylacine pouch young joeys and applied non-‐invasive digital x-‐ray computed tomography. For the very first time, we have digitally reconstructed the complete developmental trajectory of this extinct marsupial, and using this series shed light on its unique development strategies to develop into a large predator.
Dr. Axel Newton Axel recently completed his PhD in the School of BioSciences, University of Melbourne, and at Museums Victoria under the supervision of A/Prof Andrew Pask and Dr. Christy Hipsley. His thesis utilized a combination of genetics, molecular biology and morphometrics to examine the basis of convergent skull evolution between the thylacine and canids (dogs and wolves). School of BioSciences, The University of Melbourne [email protected]
10:00 Millions of Years, Dozens of Samples, One Single Scan How on Earth did we end up with over 800 species of lizards and almost 250 species of amphibians only here in Australia? Well, the answer might not be “on” but “buried underneath” in the fossil records across the country. Millions of years ago, many species left their footprint on this vast land and became preserved as fossils. The State of Queensland is a gem that can provide us with millions of micro-‐fossils to study changes in morphology, ecology and distribution of lizards and frogs. These studies may shed light on past and future extinctions, and help to identify the drivers of diversification. But how can we visualize and compare so many small specimens within a project budget? Here I present several techniques I have developed over time to maximise the quantity of samples per scan in order to obtain high quality 3D models of these miniscule pieces of bones, to be compared to their modern counterparts and analysed using geometric morphometric methods.
Rocio Aguilar Rocio did her BSc/MSc at the National University of Comahue on habitat use and thermal biology of geckos, and her PhD at the National University of Cuyo (Argentina) on the thermal ecophysiology of iguanids. She worked for 6 years as a RA with Dr. Mike Kearney (University of Melbourne) and Dr. Christy Hipsley (University of Melbourne/Museum Victoria) studying the eco-‐physiology, eco-‐morphology and conservation of Australian lizards. She currently is part of an ARC Linkage Project CT scanning Australian lizard species to find out about their morphology, ecology and diversification working with Dr. David Chapple and Dr. Alistair Evans from Monash University; and Dr. Jane Melville, Dr. Joanna Sumner, Dr. Katie Date and Dr. Christy Hipsley from Museums Victoria.
School of Biological Sciences, Monash University; Museums Victoria [email protected] 10:15 Morning Tea
Renderings of Tasmanian tiger pouch young CT data showing false coloured organs (top) and white skeleton (bottom). (scalebar = 20 mm.) Newton et al. (2018) R. Soc. open sci. 5: 171914
“Fossil Whirlpool”: Australian skink dentaries and maxillae.
(scalebar = 5 mm)
10:40 Investigating Bioturbator Galleries and their Effects on Sub-‐surface Sediment Structure Bioturbation activity by macroinvertebrates in freshwaters may influence the hyporheic exchange processes in river systems. In this study we focused on understanding how the upward conveyor macroinvertebrate Lumbriculus Variegatus (a freshwater worm) may impact the hyporheic processes through physical alterations of the sediment structure. We aim at investigating spatial distribution of the bioturbators in sandy bedforms by using Micro-‐CT scans of sediment cores. Experiments were conducted in a recirculating perspex flume 2.5m (L) x 0.2m (W) x 0.3m (H) in dimension filled with triple washed sand of 0.2mm average grain size and clogged with clay particles with an average grain size of 0.002mm. The population density of worms in the flume are expected to concentrate mostly in the downwelling zones/troughs of bedforms. Galleries were imaged using the micro-‐CT by taking core samples along the flume and scanning the top 5 cm of the core. This study can help us understand the need and importance to protect the bioturbator communities for river restoration and healthy functioning of the ecosystem.
Garima Lakhanpal Garima has recently submitted her Master’s thesis on “How bioturbation activity by macroinvertebrates affects the physical structure of sub-‐surface sediments in river systems” under the supervision of Prof. Michael Stewardson, Dr. Meenakshi Arora and Dr. Roser Casas-‐Mulet in the department of Infrastructure Engineering at the University of Melbourne. Infrastructure Engineering, The University of Melbourne [email protected]
10:55 Preferential Fluid Flow Pathways During Limestone Dissolution: Simulating fluid flow through segmented micro-‐CT data When a fluid flows through a porous media it takes the path of least resistance, forming preferential flow pathways. When this fluid is corrosive, it leads to mineral dissolution along these preferential pathways when in contact with the mineral surfaces. This heterogeneous process leads to changes in the structure of the pore domain, and depends highly on the tortuosity of the pore structure. There would be more dissolution along these preferential pathways as compared to the rest of the domain. As mineral dissolution continues it also leads to formation of new pathways in the pore structure. To study this dynamic process, a combination of laboratory experiments, digital imaging and numerical modelling is presented using a bioclastic limestone sample. Simulations based on the micro-‐CT imaging data are used to quantify the changes to fluid flow pathways developing due to the injection of acidic fluid through the sample.
Apoorv Jyoti Apoorv is pursuing his PhD through the Peter Cook Centre for CCS Research in the School of Earth Sciences at the University of Melbourne under the supervision of Prof. Ralf Haese and Prof. Stephan Matthai. He is a hydrogeologist by training and currently works on numerical modelling of fluid flow coupled with geochemistry at the pore scale. Peter Cook Centre for CCS Research, School of Earth Sciences, The University of Melbourne [email protected]
Perspective view of a core sample (transparent gray) containing worm galleries (orange burrows). (scalebar = 30 mm)
3D rendering of connected pore space through a section of carbonate rock (left) and preferential flow paths based on simulated fluid velocities through the pore space (right). (scalebar = 3 mm)
11:10 Data Munching on a Budget: Demonstrating a free workflow for processing micro-‐CT data While commercial data visualization and processing software offer attractive solutions for working with micro-‐CT datasets, the cost of these options can be prohibitive for most individual research users. In this talk, we present an alternative, demonstrating a complete workflow for processing micro-‐CT data using only free software.
Samuel Pinches Sam is pursuing his PhD through the department of Chemical Engineering at the University of Melbourne under the supervision of Prof. George Franks. He is currently investigating the internal cracking of complex shaped ceramic observed in components formed by freeze-‐casting. Access to micro-‐CT imaging has turned out to have been essential for this project in enabling breakthroughs in understanding.
Chemical Engineering, The University of Melbourne [email protected] 11:25 Forum: Micro-‐CT data processing, management and analysis tools; ethics of data sharing This open forum is a chance to discuss issues related to micro-‐CT data processing and managing the large datasets that are generated. The speakers from the workshop will be available to answer questions in regards to their experience working with micro-‐CT data and the various analysis tools they use. Despite the increasing application of digital imaging techniques to biological research and other fields, less than 10% of publications incorporating CT data make their digital images openly available. However, many journals now require all data, including CT images, to be open access and provided as part of the submission process. Dr. Christy HipsIey conducted a survey of over 100 researchers in the systematics community to identify the challenges to open access digital morphology data, and found that psychology, and not technology, remains our biggest obstacle. Here we hope to have an engaging discussion on the ethics and obstacles presented to open access data sharing. 12:00 Lab Tour Tour of the lab space and micro-‐CT instrument in the School of Earth Sciences including a show-‐and-‐tell of micro-‐CT datasets. Registration for this tour is required through the Eventbrite page: https://www.eventbrite.com/e/tracees-micro-ct-workshop-2018-tickets-50384817345 Tours will be conducted in small groups in 10-‐15 minute time blocks so some waiting may be required depending upon attendance.
Composite image of Alumina Ceramic Sample. Left: Raw single slice data from post-‐scan reconstruction; Right: Internal pore space segmented and exported to 3D volume file. The sample has a cylindrical diameter of ~22.5 mm.
Wordcloud of survey responses to the question:
“What do you see as the biggest obstacles to obtaining digital morphology data?”
