Bio


Colin Ophus is an Associate Professor in the Department of Materials Science and Engineering and a Center Fellow at the Precourt Institute for Energy, Stanford University. He previously worked as a Staff Scientist at the National Center for Electron Microscopy (NCEM), part of the Molecular Foundry, at Lawrence Berkeley Lab. He was awarded a US Department of Energy (DOE) Early Career award in 2018, and the Burton medal from the Microscopy Society of America (MSA) in 2018. His research focuses on experimental methods, reconstruction algorithms, and software codes for simulation, analysis, and instrument design of transmission electron microscopy (TEM) and scanning TEM (STEM).

Colin advocates for open science and his group has developed open-source scientific software including as the Prismatic STEM simulation code and py4DSTEM analysis toolkit. He has taught many workshops around the world on topics ranging from scientific visualization to large scale data analysis. He also is the founder and editor-in-chief for a new journal based on interactive science communication named Elemental Microscopy.

Academic Appointments


Honors & Awards


  • Burton Medal in Physical Sciences, Microscopy Society of America (2022)
  • Early Career Research Award, US Department of Energy (2018)

Stanford Advisees


All Publications


  • Tailored topotactic chemistry unlocks heterostructures of magnetic intercalation compounds. Nature communications Husremović, S., Gonzalez, O., Goodge, B. H., Xie, L. S., Kong, Z., Zhang, W., Ryu, S. H., Ribet, S. M., Fender, S. S., Bustillo, K. C., Song, C., Ciston, J., Taniguchi, T., Watanabe, K., Ophus, C., Jozwiak, C., Bostwick, A., Rotenberg, E., Bediako, D. K. 2025; 16 (1): 1208

    Abstract

    The construction of thin film heterostructures has been a widely successful archetype for fabricating materials with emergent physical properties. This strategy is of particular importance for the design of multilayer magnetic architectures in which direct interfacial spin-spin interactions between magnetic phases in dissimilar layers lead to emergent and controllable magnetic behavior. However, crystallographic incommensurability and atomic-scale interfacial disorder can severely limit the types of materials amenable to this strategy, as well as the performance of these systems. Here, we demonstrate a method for synthesizing heterostructures comprising magnetic intercalation compounds of transition metal dichalcogenides (TMDs), through directed topotactic reaction of the TMD with a metal oxide. The mechanism of the intercalation reaction enables thermally initiated intercalation of the TMD from lithographically patterned oxide films, giving access to a family of multi-component magnetic architectures through the combination of deterministic van der Waals assembly and directed intercalation chemistry.

    View details for DOI 10.1038/s41467-025-56467-9

    View details for PubMedID 39885123

    View details for PubMedCentralID PMC11782516

  • Accelerating the Electrochemical Formation of the δ Phase in Manganese-Rich Rocksalt Cathodes ADVANCED MATERIALS Holstun, T., Mishra, T. P., Huang, L., Hau, H., Anand, S., Yang, X., Ophus, C., Bustillo, K., Ma, L., Ehrlich, S., Ceder, G. 2024: e2412871

    Abstract

    Mn-rich disordered rocksalt materials with Li-excess (DRX) materials have emerged as a promising class of earth-abundant and energy-dense next-generation cathode materials for lithium-ion batteries. Recently, an electrochemical transformation to a spinel-like "δ" phase has been reported in Mn-rich DRX materials, with improved capacity, rate capability, and cycling stability compared with previous DRX compositions. However, this transformation unfolds slowly over the course of cycling, complicating the development and understanding of these materials. In this work, it is reported that the transformation of Mn-rich DRX materials to the promising δ phase can be promoted to occur much more rapidly by electrochemical pulsing at elevated temperature, rate, and voltage. To extend this concept, micron-sized single-crystal DRX particles are also transformed to the δ phase by the same method, possessing greatly improved cycling stability in the first demonstration of cycling for large, single-crystal DRX particles. To shed light on the formation and specific structure of the δ phase, X-ray diffraction, scanning electron nanodiffraction (SEND) and atomic resolution STEM-HAADF are used to reveal a nanodomain spinel structure with minimal remnant disorder.

    View details for DOI 10.1002/adma.202412871

    View details for Web of Science ID 001381572300001

    View details for PubMedID 39711222

  • Reducing crystal symmetry to generate out-of-plane Dzyaloshinskii-Moriya interaction NATURE COMMUNICATIONS Niu, H., Kwon, H., Ma, T., Cheng, Z., Ophus, C., Miao, B., Sun, L., Wu, Y., Liu, K., Parkin, S. P., Won, C., Schmid, A. K., Ding, H., Chen, G. 2024; 15 (1): 10199

    Abstract

    The Dzyaloshinskii-Moriya antisymmetric exchange interaction (DMI) stabilises topological spin textures with promising future spintronics applications. According to crystal symmetry, the DMI can be categorized as four different types that favour different chiral textures. Unlike the other three extensively-investigated types, out-of-plane DMI, as the last type that favours in-plane chirality, remained missing so far. Here we apply point-group-dependent DMI matrix analysis to show that out-of-plane DMI exists under reduced crystal symmetry. Through strain and structure engineering, we show how Cs symmetry is realized in ultrathin magnets and observe the out-of-plane DMI stabilised in-plane chirality using spin-polarized electron microscopy. Our results show that extremely low out-of-plane DMI strengths at µeV/atom are sufficient to stabilise topological spin textures, including merons and bimerons. We also demonstrate field-induced reversible control of the in-plane chirality and merons. Our findings open up untapped paths on topological magnetic textures and their potential applications.

    View details for DOI 10.1038/s41467-024-54521-6

    View details for Web of Science ID 001364059600020

    View details for PubMedID 39587066

    View details for PubMedCentralID PMC11589593

  • Streaming Large-Scale Microscopy Data to a Supercomputing Facility MICROSCOPY AND MICROANALYSIS Welborn, S. S., Harris, C., Ribet, S. M., Varnavides, G., Ophus, C., Enders, B., Ercius, P. 2024

    Abstract

    Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy generates data at a nominal rate of 480 Gbit s-1 (87,000 frames s-1), producing a 700 GB dataset in 15 s. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera's data acquisition system to supercomputing nodes at the National Energy Research Scientific Computing Center, bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a postmortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions.

    View details for DOI 10.1093/mam/ozae109

    View details for Web of Science ID 001354785800001

    View details for PubMedID 39541183

  • Grain boundary engineering for efficient and durable electrocatalysis. Nature communications Geng, X., Vega-Paredes, M., Wang, Z., Ophus, C., Lu, P., Ma, Y., Zhang, S., Scheu, C., Liebscher, C. H., Gault, B. 2024; 15 (1): 8534

    Abstract

    Grain boundaries in noble metal catalysts have been identified as critical sites for enhancing catalytic activity in electrochemical reactions such as the oxygen reduction reaction. However, conventional methods to modify grain boundary density often alter particle size, shape, and morphology, obscuring the specific role of grain boundaries in catalytic performance. This study addresses these challenges by employing gold nanoparticle assemblies to control grain boundary density through the manipulation of nanoparticle collision frequency during synthesis. We demonstrate a direct correlation between increased grain boundary density and enhanced two-electron oxygen reduction reaction activity, achieving a significant improvement in both specific and mass activity. Additionally, the gold nanoparticle assemblies with high grain boundary density exhibit remarkable electrochemical stability, attributed to boron segregation at the grain boundaries, which prevents structural degradation. This work provides a promising strategy for optimizing the activity, selectivity, and stability of noble metal catalysts through precise grain boundary engineering.

    View details for DOI 10.1038/s41467-024-52919-w

    View details for PubMedID 39358376

  • The hierarchical structure of organic mixed ionic-electronic conductors and its evolution in water. Nature materials Tsarfati, Y., Bustillo, K. C., Savitzky, B. H., Balhorn, L., Quill, T. J., Marks, A., Donohue, J., Zeltmann, S. E., Takacs, C. J., Giovannitti, A., McCulloch, I., Ophus, C., Minor, A. M., Salleo, A. 2024

    Abstract

    Polymeric organic mixed ionic-electronic conductors underpin several technologies in which their electrochemical properties are desirable. These properties, however, depend on the microstructure that develops in their aqueous operational environment. We investigated the structure of a model organic mixed ionic-electronic conductor across multiple length scales using cryogenic four-dimensional scanning transmission electron microscopy in both its dry and hydrated states. Four-dimensional scanning transmission electron microscopy allows us to identify the prevalent defects in the polymer crystalline regions and to analyse the liquid crystalline nature of the polymer. The orientation maps of the dry and hydrated polymers show that swelling-induced disorder is mostly localized in discrete regions, thereby largely preserving the liquid crystalline order. Therefore, the liquid crystalline mesostructure makes electronic transport robust to electrolyte ingress. This study demonstrates that cryogenic four-dimensional scanning transmission electron microscopy provides multiscale structural insights into complex, hierarchical structures such as polymeric organic mixed ionic-electronic conductors, even in their hydrated operating state.

    View details for DOI 10.1038/s41563-024-02016-6

    View details for PubMedID 39333273

    View details for PubMedCentralID 4991841

  • Random forest prediction of crystal structure from electron diffraction patterns incorporating multiple scattering PHYSICAL REVIEW MATERIALS Gleason, S. P., Rakowski, A., Ribet, S. M., Zeltmann, S. E., Savitzky, B. H., Henderson, M., Ciston, J., Ophus, C. 2024; 8 (9)
  • Earth-abundant Li-ion cathode materials with nanoengineered microstructures. Nature nanotechnology Hau, H., Mishra, T., Ophus, C., Huang, T., Bustilo, K., Sun, Y., Yang, X., Holstun, T., Zhao, X., Wang, S., Ha, Y., Lee, G., Song, C., Turner, J., Bai, J., Ma, L., Chen, K., Wang, F., Yang, W., McCloskey, B. D., Cai, Z., Ceder, G. 2024

    Abstract

    Manganese-based materials have tremendous potential to become the next-generation lithium-ion cathode as they are Earth abundant, low cost and stable. Here we show how the mobility of manganese cations can be used to obtain a unique nanosized microstructure in large-particle-sized cathode materials with enhanced electrochemical properties. By combining atomic-resolution scanning transmission electron microscopy, four-dimensional scanning electron nanodiffraction and in situ X-ray diffraction, we show that when a partially delithiated, high-manganese-content, disordered rocksalt cathode is slightly heated, it forms a nanomosaic of partially ordered spinel domains of 3-7nm in size, which impinge on each other at antiphase boundaries. The short coherence length of these domains removes the detrimental two-phase lithiation reaction present near 3V in a regular spinel and turns it into a solid solution. This nanodomain structure enables good rate performance and delivers 200mAhg-1 discharge capacity in a (partially) disordered material with an average primary particle size of 5m. The work not only expands the synthesis strategies available for developing high-performance Earth-abundant manganese-based cathodes but also offers structural insights into the ability to nanoengineer spinel-like phases.

    View details for DOI 10.1038/s41565-024-01787-y

    View details for PubMedID 39300225

  • Integrated rocksalt-polyanion cathodes with excess lithium and stabilized cycling NATURE ENERGY Huang, Y., Dong, Y., Yang, Y., Liu, T., Yoon, M., Li, S., Wang, B., Zheng, E., Lee, J., Sun, Y., Han, Y., Ciston, J., Ophus, C., Song, C., Penn, A., Liao, Y., Ji, H., Shi, T., Liao, M., Cheng, Z., Xiang, J., Peng, Y., Ma, L., Xiao, X., Kan, W., Chen, H., Yin, W., Guo, L., Liu, W., Muruganantham, R., Yang, C., Zhu, Y., Li, Q., Li, J. 2024
  • Considerations for extracting moiré-level strain from dark field intensities in transmission electron microscopy JOURNAL OF APPLIED PHYSICS Craig, I. M., Van Winkle, M., Ophus, C., Bediako, D. 2024; 136 (7)

    View details for DOI 10.1063/5.0222102

    View details for Web of Science ID 001293864000008

  • Electronic structure along Sm2Co3Ge5 twin boundaries ACTA MATERIALIA Kennedy, E., Kyrk, T. M., Ophus, C., McCandless, G. T., Chan, J. Y., Scott, M. C. 2024; 270
  • Structural Study of Hydrated Organic Mixed Ionic Electronic Conductors Using Cryogenic 4D-STEM. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada Tsarfati, Y., Bustillo, K. C., Savitzky, B. H., Ophus, C., McCulloch, I., Salleo, A., Minor, A. M. 2023; 29 (Supplement_1): 264-265

    View details for DOI 10.1093/micmic/ozad067.119

    View details for PubMedID 37613608

  • Multimodal Characterization of Crystal Structure and Formation in Rubrene Thin Films Reveals Erasure of Orientational Discontinuities ADVANCED FUNCTIONAL MATERIALS Tan, J. A., Dull, J. T., Zeltmann, S. E., Tulyagankhodjaev, J. A., Johnson, H. M., Liebman-Pelaez, A., Folie, B. D., Donges, S. A., Khatib, O., Raybin, J. G., Roberts, T. D., Hamerlynck, L. M., Tanner, C. N., Lee, J., Ophus, C., Bustillo, K. C., Raschke, M. B., Ohldag, H., Minor, A. M., Rand, B. P., Ginsberg, N. S. 2023
  • Spatially resolved structural order in low-temperature liquid electrolyte. Science advances Xie, Y., Wang, J., Savitzky, B. H., Chen, Z., Wang, Y., Betzler, S., Bustillo, K., Persson, K., Cui, Y., Wang, L. W., Ophus, C., Ercius, P., Zheng, H. 2023; 9 (2): eadc9721

    Abstract

    Determining the degree and the spatial extent of structural order in liquids is a grand challenge. Here, we are able to resolve the structural order in a model organic electrolyte of 1 M lithium hexafluorophosphate (LiPF6) dissolved in 1:1 (v/v) ethylene carbonate:diethylcarbonate by developing an integrated method of liquid-phase transmission electron microscopy (TEM), cryo-TEM operated at -30°C, four-dimensional scanning TEM, and data analysis based on deep learning. This study reveals the presence of short-range order (SRO) in the high-salt concentration domains of the liquid electrolyte from liquid phase separation at the low temperature. Molecular dynamics simulations suggest the SRO originates from the Li+-(PF6-)n (n > 2) local structural order induced by high LiPF6 salt concentration.

    View details for DOI 10.1126/sciadv.adc9721

    View details for PubMedID 36638171

  • Correlative image learning of chemo-mechanics in phase-transforming solids. Nature materials Deng, H. D., Zhao, H., Jin, N., Hughes, L., Savitzky, B. H., Ophus, C., Fraggedakis, D., Borbely, A., Yu, Y., Lomeli, E. G., Yan, R., Liu, J., Shapiro, D. A., Cai, W., Bazant, M. Z., Minor, A. M., Chueh, W. C. 2022

    Abstract

    Constitutive laws underlie most physical processes in nature. However, learning such equations in heterogeneous solids (for example, due to phase separation) is challenging. One such relationship is between composition and eigenstrain, which governs the chemo-mechanical expansion in solids. Here we developed a generalizable, physically constrained image-learning framework to algorithmically learn the chemo-mechanical constitutive law at the nanoscale from correlative four-dimensional scanning transmission electron microscopy and X-ray spectro-ptychography images. We demonstrated this approach on LiXFePO4, a technologically relevant battery positive electrode material. We uncovered the functional form of the composition-eigenstrain relation in this two-phase binary solid across the entire composition range (0≤X≤1), including inside the thermodynamically unstable miscibility gap. The learned relation directly validates Vegard's law of linear response at the nanoscale. Our physics-constrained data-driven approach directly visualizes the residual strain field (by removing the compositional and coherency strain), which is otherwise impossible to quantify. Heterogeneities in the residual strain arise from misfit dislocations and were independently verified by X-ray diffraction line profile analysis. Our work provides the means to simultaneously quantify chemical expansion, coherency strain and dislocations in battery electrodes, which has implications on rate capabilities and lifetime. Broadly, this work also highlights the potential of integrating correlative microscopy and image learning for extracting material properties and physics.

    View details for DOI 10.1038/s41563-021-01191-0

    View details for PubMedID 35177785

  • Correlative analysis of structure and chemistry of LixFePO(4) platelets using 4D-STEM and X-ray ptychography MATERIALS TODAY Hughes, L. A., Savitzky, B. H., Deng, H. D., Jin, N. L., Lomeli, E. G., Yu, Y., Shapiro, D. A., Herring, P., Anapolsky, A., Chueh, W. C., Ophus, C., Minor, A. M. 2022; 52: 102-111
  • Design and synthesis of multigrain nanocrystals via geometric misfit strain. Nature Oh, M. H., Cho, M. G., Chung, D. Y., Park, I. n., Kwon, Y. P., Ophus, C. n., Kim, D. n., Kim, M. G., Jeong, B. n., Gu, X. W., Jo, J. n., Yoo, J. M., Hong, J. n., McMains, S. n., Kang, K. n., Sung, Y. E., Alivisatos, A. P., Hyeon, T. n. 2020; 577 (7790): 359–63

    Abstract

    The impact of topological defects associated with grain boundaries (GB defects) on the electrical, optical, magnetic, mechanical and chemical properties of nanocrystalline materials1,2 is well known. However, elucidating this influence experimentally is difficult because grains typically exhibit a large range of sizes, shapes and random relative orientations3-5. Here we demonstrate that precise control of the heteroepitaxy of colloidal polyhedral nanocrystals enables ordered grain growth and can thereby produce material samples with uniform GB defects. We illustrate our approach with a multigrain nanocrystal comprising a Co3O4 nanocube core that carries a Mn3O4 shell on each facet. The individual shells are symmetry-related interconnected grains6, and the large geometric misfit between adjacent tetragonal Mn3O4 grains results in tilt boundaries at the sharp edges of the Co3O4 nanocube core that join via disclinations. We identify four design principles that govern the production of these highly ordered multigrain nanostructures. First, the shape of the substrate nanocrystal must guide the crystallographic orientation of the overgrowth phase7. Second, the size of the substrate must be smaller than the characteristic distance between the dislocations. Third, the incompatible symmetry between the overgrowth phase and the substrate increases the geometric misfit strain between the grains. Fourth, for GB formation under near-equilibrium conditions, the surface energy of the shell needs to be balanced by the increasing elastic energy through ligand passivation8-10. With these principles, we can produce a range of multigrain nanocrystals containing distinct GB defects.

    View details for DOI 10.1038/s41586-019-1899-3

    View details for PubMedID 31942056

  • Short-range order and its impact on the CrCoNi medium-entropy alloy. Nature Zhang, R. n., Zhao, S. n., Ding, J. n., Chong, Y. n., Jia, T. n., Ophus, C. n., Asta, M. n., Ritchie, R. O., Minor, A. M. 2020; 581 (7808): 283–87

    Abstract

    Traditional metallic alloys are mixtures of elements in which the atoms of minority species tend to be distributed randomly if they are below their solubility limit, or to form secondary phases if they are above it. The concept of multiple-principal-element alloys has recently expanded this view, as these materials are single-phase solid solutions of generally equiatomic mixtures of metallic elements. This group of materials has received much interest owing to their enhanced mechanical properties1-5. They are usually called medium-entropy alloys in ternary systems and high-entropy alloys in quaternary or quinary systems, alluding to their high degree of configurational entropy. However, the question has remained as to how random these solid solutions actually are, with the influence of short-range order being suggested in computational simulations but not seen experimentally6,7. Here we report the observation, using energy-filtered transmission electron microscopy, of structural features attributable to short-range order in the CrCoNi medium-entropy alloy. Increasing amounts of such order give rise to both higher stacking-fault energy and hardness. These findings suggest that the degree of local ordering at the nanometre scale can be tailored through thermomechanical processing, providing a new avenue for tuning the mechanical properties of medium- and high-entropy alloys.

    View details for DOI 10.1038/s41586-020-2275-z

    View details for PubMedID 32433617

  • The Materials Research Platform: Defining the Requirements from User Stories MATTER Aykol, M., Hummelshoj, J. S., Anapolsky, A., Aoyagi, K., Bazant, M. Z., Bligaard, T., Braatz, R. D., Broderick, S., Cogswell, D., Dagdelen, J., Drisdell, W., Garcia, E., Garikipati, K., Gavini, V., Gent, W. E., Giordano, L., Gomes, C. P., Gomez-Bombarelli, R., Gopal, C., Gregoire, J. M., Grossman, J. C., Herring, P., Hung, L., Jaramillo, T. F., King, L., Kwon, H., Maekawa, R., Minor, A. M., Montoya, J. H., Mueller, T., Ophus, C., Rajan, K., Ramprasad, R., Rohr, B., Schweigert, D., Shao-Horn, Y., Suga, Y., Suram, S. K., Viswanathan, V., Whitacre, J. F., Willard, A. P., Wodo, O., Wolverton, C., Storey, B. D. 2019; 1 (6): 1433–38
  • Diffraction imaging of nanocrystalline structures in organic semiconductor molecular thin films. Nature materials Panova, O. n., Ophus, C. n., Takacs, C. J., Bustillo, K. C., Balhorn, L. n., Salleo, A. n., Balsara, N. n., Minor, A. M. 2019

    Abstract

    The properties of organic solids depend on their structure and morphology, yet direct imaging using conventional electron microscopy methods is hampered by the complex internal structure of these materials and their sensitivity to electron beams. Here, we manage to observe the nanocrystalline structure of two organic molecular thin-film systems using transmission electron microscopy by employing a scanning nanodiffraction method that allows for full access to reciprocal space over the size of a spatially localized probe (~2 nm). The morphologies revealed by this technique vary from grains with pronounced segmentation of the structure-characterized by sharp grain boundaries and overlapping domains-to liquid-crystal structures with crystalline orientations varying smoothly over all possible rotations that contain disclinations representing singularities in the director field. The results show how structure-property relationships can be visualized in organic systems using techniques previously only available for hard materials such as metals and ceramics.

    View details for DOI 10.1038/s41563-019-0387-3

    View details for PubMedID 31160799

  • Multi-pass transmission electron microscopy SCIENTIFIC REPORTS Juffmann, T., Koppell, S. A., Klopfer, B. B., Ophus, C., Glaeser, R. M., Kasevich, M. A. 2017; 7

    Abstract

    Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulations to show that an electron microscope based on a multi-pass measurement protocol enables imaging of single proteins, without averaging structures over multiple images. While we demonstrate the method for particular imaging targets, the approach is broadly applicable and is expected to improve resolution and sensitivity for a range of electron microscopy imaging modalities, including, for example, scanning and spectroscopic techniques. The approach implements a quantum mechanically optimal strategy which under idealized conditions can be considered interaction-free.

    View details for DOI 10.1038/s41598-017-01841-x

    View details for Web of Science ID 000400886100039

    View details for PubMedID 28490730