X-RAY MICRO COMPUTED TOMOGRAPHY SEMINAR & WORKSHOP
Wednesday, September 27, 2023 Hosted by the Department of Earth Sciences at the University of Southern California
Registration | Program | Presenters | Location | Recording
In this seminar, you will learn about various applications of X-ray micro computed tomography (CT) in geology and archeology from the top researchers making the most of X-ray CT in their fields. You can also participate in the workshop to see a demonstration of CT data collection and data analysis, followed by a tour of the Natural History Museum of Los Angeles County.
Program
8:30 AM - 9:00 AM
Registration - Room ZHS 265
9:00 AM - 9:15 AM
Opening Remarks - Room ZHS 265
9:15 AM - 10:00 AM
Integrating microCT to improve research and pedagogy in Earth Sciences - Room ZHS 265
10:00 AM - 10:45 AM
Assessing trabecular bone architecture at the divergence of bird-line (Avemetatarsalia) and croc-line (Pseudosuchia) archosaurs to reveal cardiopulmonary evolution and soft tissue relationships. - Room ZHS 265
10:45 AM - 11:00 AM
Coffee Break - Room ZHS 265
11:00 AM - 11:45 AM
Deep Learning Automated Image Segmentation - No expertise required - Room ZHS 265
11:45 Am - 12:30 PM
Ion exchange processes and crystal imaging of Pb sequestration in clinoptilolite - Room ZHS 265
12:30 PM - 1:30 PM
Lunch Break - Room ZHS 265
1:30 PM - 3:30 PM
Workshop - Room ZHS 319
Seminar Program
Integrating microCT to improve research and pedagogy in Earth Sciences
Emily Cooperdock (Invited speaker)
Assistant Professor, Department of Earth, Environmental & Planetary Sciences
Brown University
Research in Earth sciences strives to understand the processes that shape the Earth in 3D; however, we are often limited to making observations in 2D. As educators in academia, one of our goals is to teach students to think of 3D processes that occur over deep time and expose them to cutting edge research techniques. In this talk, I will describe how we use the Rigaku CT Lab HX benchtop instrument to enhance research in the fields of geochronology, petrology, and structural geology by being able to make direct 3D observations of the materials we work with. I will also show how we developed a new curriculum for a required undergraduate course in mineralogy at USC that exposed students to hands-on research with microCT data.
Assessing trabecular bone architecture at the divergence of bird-line (Avemetatarsalia) and croc-line (Pseudosuchia) archosaurs to reveal cardiopulmonary evolution and soft tissue relationships.
Paul Byrne (Invited speaker)
Ph.D. Student, Dinosaur Institute
University of Southern California
Birds and crocodilians today have highly specialized cardiopulmonary systems that are fine-tuned for energetically costly flight and underwater sit-and-wait ambush hunting (respectively). However, similarities in embryonic development suggest a shared common origin for this paired system. Reconstructing cardiopulmonary anatomy in the last common ancestor of bird-line (Avemetatarsalia) and croc-line (Pseudosuchia) archosaurs to pinpoint when cardiopulmonary anatomy diverged has been challenging due to a lack of preserved soft tissue in the fossil record + insufficient computational techniques needed to visualize the bone/soft tissue interface. Postcranial skeletal pneumaticity (external foramina leading to hollow concavities within intertrabecular space) is hypothesized to have allowed for the lightning and strengthening of bone to aid in energetics and has been stated to be a reliable osteological correlate for pulmonary diverticula in avian and nonavian dinosaurs. However, this has led to a fallacious link assuming all pneumatic instances equate to the presence of the avian air sac system in the fossil record. Thus, it is unclear if variation within the trabecular architecture itself can reveal interaction with diverticula, or if this variation exists solely due to locomotor or behavioral modifications influencing bone structure. I hypothesize that, if specific trabecular architectural morphologies can be identified based on pulmonary diverticula interacting with bone, then trabecular morphology can be sorted into the following categories: a. interaction with diverticula, or b. locomotory style. When incorporating fossil taxa before and after the divergence point between Avemetatarsalia and Pseudosuchia, the cause of variation within trabecular bone architecture can be better resolved. These preliminary results suggest that fine-tuned microCT visualization methods can allow a better understanding of cardiopulmonary evolution in extinct organisms and can allow for a better understanding of the acquisition of the unique cardiopulmonary systems present today in birds and crocodilians.
Deep Learning Automated Image Segmentation - No expertise required
Dr. Mike Marsh (Invited speaker)
Director of Product Management, Dragonfly
Object Research Systems, Inc.
We will look at examples of how a user-friendly Deep Learning platform can fully automate image segmentation on images that would otherwise take countless hours of effort to fully label. We’ll see how a variety of biological and materials science samples are easily managed by Deep Learning, even by users who have no expertise or background in machine learning/deep learning. Finally, we’ll explore some questions and best practices in how to optimize performance so users can get highly robust models with minimal effort spent preparing ground truth.
Ion exchange processes and crystal imaging of Pb sequestration in clinoptilolite
Dr. Aaron Celestian (Invited speaker)
Curator, Natural History Museum & Adjunct Professor
University of Southern California
The goal of the proposed study is to visualize Pb incorporation into clinoptilolite (a common microporous mineral) using data collected from in situ tomography, spectroscopy, and crystallography to better understand Pb entombment. We used a mutli-modal approach with micro computed tomography (microCT), Raman spectroscopy, and X-ray diffraction to investigate Pb absorption in individual clinoptilolite crystals. microCT produced a series of grayscale images that relate to density and atomic number of a material. The image stacks can be reconstructed for 3D visualization of the internal composition and structure of a specimen. We found that increasing Pb-contamination in crystals will correlate with brighter X-ray grayscale values in microCT. Time-resolved Raman spectroscopy measured real-time structural changes in clinoptilolite during Pb ion exchange, and the back-exchange response when treated with stimulated stomach acid (buffer pH=1.5, to mimic accidental ingestion). Once preliminary structural changes were mapped, single crystal X-ray diffraction was used to determine the crystal structure of clinoptilolite and the crystallographic locations of Pb.