Lauren Mason – STROBE

X-Ray and Electron Tomography: From Images to Volumes to Knowledge

Abstract: One of the ultimate goals of microscopy is to understand the structure of materials from the images we obtain. Recent advances in X-ray and electron microscopy—including smaller probes, efficient detectors, and advanced computational imaging tools—are bringing us closer to this goal. However, most imaging workflows remain two-dimensional (2D), providing only projected information from inherently three-dimensional (3D) objects. By acquiring full 3D data sets and applying tomographic reconstruction, one can recover the true structure of a sample. In this talk, I will present the workflow and limitations of nanoscale tomography using X-ray and electron microscopy—from optimizing 2D image contrast, to acquiring tomographic data, to reconstructing 3D volumes. Drawing on examples from STROBE projects, I will show how structural knowledge gained from these volumes—such as atomic models, nanoporosity, and magnetic fields—provides critical insights across a wide range of scientific disciplines.

Speaker Bio: Colum earned his bachelor’s degree in physics from Trinity College Dublin and completed a PhD in Materials Science at the University of Oxford. In 2020, he joined UCLA as a STROBE Postdoctoral Fellow in the Miao Group, where he advanced ptychography and tomography techniques for 3D imaging of individual light atoms. Colum recently joined SLAC National Accelerator Laboratory as a Research Associate, where he focuses on multiscale, multimodal imaging approaches for microelectronics.

Building Materials from the Nanocrystal Up

Using the Advanced Light Source (ALS), researchers clarified the mechanism—an unusual intermediate state—that accelerates the transformation of nanocrystals into a superlattice with fewer defects using a two-step, instead of a one-step, process.

“Nanoscale Imaging: Soft X-ray STXM and Ptychography at the ALS”

Abstract: Advancements in materials research increasingly require visualization of structure, composition, and functionality at the nanometer scale. Soft X-ray Ptychography and Scanning Transmission X-ray Microscopy (STXM) are two complementary techniques that leverage the brightness and coherence of synchrotron radiation at the Advanced Light Source (ALS) to probe materials with high spatial resolution and enhanced chemical sensitivity. This seminar offers conceptual insights and practical guidance for designing and executing STXM and ptychography experiments, illustrated with examples such as precipitate formation in catalytic particles, chemical dynamics in battery materials, and labyrinth domain formation in magnetic thin films. The experimental workflow is outlined, from sample preparation and data acquisition to common challenges and management of beam time. Finally, the seminar covers data processing and interpretation, including ptychographic reconstructions, X-ray absorption spectroscopy (XAS) analysis, and tomographic reconstructions.

Speaker Bio: Jayden Plumb completed his undergraduate studies at the University of Utah and earned his graduate degree from the University of California, Santa Barbara. Currently a postdoctoral researcher at the Advanced Light Source at LBNL, he specializes in 3D imaging techniques using soft X-rays. He is currently interested in imaging novel nanoscale magnetic structures and nanoscale devices.

Congratulations to Jose Rodriguez for Receiving the Inaugural UCLA Academic Senate Service Rising Star Award

The UCLA Academic Senate selected Prof. Jose Rodriguez to receive the inaugural Academic Senate Service Rising Star Award. This award celebrates and recognizes UCLA Senate faculty who are in an early stage of their Senate service and have demonstrated a noteworthy contribution to the Academic Senate. A noteworthy contribution may include activities such as consistent and meaningful participation in committee or council meetings or projects; effective chairship of a subcommittee, special committee or task force; championing shared governance; or demonstrating Senate leadership potential. Preference is given to Senate members who have not yet chaired a standing committee or council. Current committee and council chairs, Senate Leadership and Senate staff are eligible to nominate candidates. Congratulations, Jose!

Deep Learning to Overcome Physical Limits in CryoEM and CryoET

Abstract: CryoEM and cryoET enable imaging of biological specimens frozen in vitreous ice, revealing 3D molecular or cellular structures at high resolution and in their native state. However, cryoET is limited by the “missing-wedge” problem due to restricted tilt angles, and cryoEM often suffers from preferred orientation, resulting in uneven sampling of angular views and leaving parts of Fourier space poorly covered. We developed IsoNet and spIsoNet to address these inverse problems through data-driven, self-supervised deep learning: both methods learn from collected data alone, using well-sampled orientations to infer under-represented ones. IsoNet restores isotropy in tomograms by reconstructing missing information; spIsoNet adapts these principles to single-particle and subtomogram averaging workflows, improving angular coverage and alignment. Together, our deep learning methods reliably mitigate previously challenging physical constraints in cryoEM/cryoET.

Speaker Bio: Yun-Tao Liu completed his undergraduate and graduate studies at the University of Science and Technology of China. He then pursued postdoctoral research in Professor Hong Zhou’s lab at UCLA. His work focuses on developing deep learning tools to tackle fundamental problems in structural biology, as well as investigating the mechanisms of nucleic acid processing and cellular processes in nervous systems.

How low can dose go? Applications in ultra low dose electron diffraction of molecular crystals.

Abstract: Electron diffraction enables atomic structure determination from nano- or microcrystals, allowing for rapid structural analysis of crystalline powders or mixtures. However, electron dose is fundamentally limiting, especially for the determination of solvated molecular structures. Crystals of hydrated molecules often require lengthy optimization of vitrification conditions, an approach challenged by non-aqueous solvents. I will discuss my group’s efforts to enable room-temperature electron diffraction of microcrystals suspended in solvent, using simple liquid cells composed of two TEM grids “sandwiched” together with a liquid layer in between. As room-temperature, hydrated microcrystals are particularly prone to electron beam radiation damage, we have also implemented new hardware and software measures to minimize the beam fluence delivered to each crystal. Those tactics enable study of molecular conformations only accessible in a room-temperature solvated state, which are otherwise inaccessible by MicroED, but can be of particular relevance for research and pharmaceuticals.

Speaker Bio: Jose Rodriguez is a true bruin, having completed his undergraduate, graduate and postdoctoral training at UCLA. He is now a professor of Chemistry & Biochemistry at UCLA, where his group develops new structural biology and structural chemistry approaches, and applies them to pressing problems in biochemistry & adjacent fields.

UCLA Scientists Break Imaging Barrier to Unlock Secrets of Deadly “Chaotic” Viruses

The findings could pave the way to new treatments for some of our most lethal diseases. For years, graduate student Lily Taylor and her advisor, Professor Jose Rodriguez, have been working on something big: a novel technique that would finally allow scientists to look closely at some of the most “chaotic” viruses in the world. Now, in Taylor’s first published paper as first author, they have done it…

Congratulations to Gabriella (Gabi) Seifert for Receiving an NSF Graduate Research Fellowship

The NSF GRFP recognizes and supports outstanding graduate students in NSF-supported STEM disciplines who are pursuing research-based master’s and doctoral degrees at accredited US institutions. The purpose of the NSF Graduate Research Fellowship Program (GRFP) is to ensure the quality, vitality, and diversity of the scientific and engineering workforce of the United States. The five-year fellowship provides three years of financial support including an annual stipend of $37,000.

Congratulations to Benjamin Hammel for receiving Best Poster Award at the Mountain States Society of Electron Microscopists (MSSEM) Fall 2024 Conference.

Benjamin Hammel, a graduate student in Gordana Dukovic’s group at CU Boulder, received the Best Poster Award at the Mountain States Society of Electron Microscopists (MSSEM) Fall 2024 Conference. Congratulations, Ben!

Congratulations to Jianwei (John) Miao for Being Elected as a 2025 Fellow of the Materials Research Society (MRS)

Professor John (Jianwei) Miao at UCLA has been elected as a 2025 Fellow of the Materials Research Society (MRS) for his research in pioneering coherent diffractive imaging for a wide range of material systems and atomic electron tomography for determining the three-dimensional atomic structure of crystal defects and amorphous materials. Congratulations, John!

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About Lauren Mason