W. E. Moerner
· ProfessorVerifiedStanford University · Applied Physics
Active 1973–2026
About
Professor W. E. Moerner is the Principal Investigator of the Moerner Lab at Stanford University, where his research focuses on physical chemistry and chemical physics. His work centers on the study of individual molecules in condensed phases and single biomolecules in cells, utilizing far-field and near-field optical imaging and spectroscopy techniques. Professor Moerner's research includes the development and application of controllable fluorophores and three-dimensional methods for superresolution imaging within cells. Additionally, his lab investigates the trapping and study of single antenna proteins and enzymes in solution, as well as the use of nanoantennas to enhance interactions between light and matter. The Moerner Lab emphasizes excellence in research within an open, collaborative, and respectful environment that values the ideas and contributions of all members.
Research topics
- Chemistry
- Biology
- Cell biology
- Computer Science
- Biochemistry
- Artificial Intelligence
- Materials science
- Biophysics
- Optics
- Data science
- Computational biology
- Physics
- Nanotechnology
- Pathology
- Immunology
Selected publications
bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-27
articleOpen accessSenior authorCorrespondingis a single-celled eukaryotic parasite with prolific invasion capability. The parasite uses an apical complex comprised of proteinaceous structures and secretory organelles to efficiently enter host cells. As a result, the apical complex remains a vital structure of interest, with many studies dedicated to understanding its protein organization. One such protein is the motor Myosin H (MyoH), which is indispensable for parasite motility and host cell invasion. Given the small size of the complex, roughly a diffraction-limited volume in the visible, high-resolution techniques are required to make precise determinations of protein organization. In this work, we use 3D single-molecule localization microscopy in both traditionally fixed and gel-expanded parasites to localize the indispensable motor Myosin H within the apical complex. Labeling of the N- and C-terminus of MyoH in fixed parasites resolved the orientation of the motor protein in the apical complex, showing the motor head radially exterior to the tail. Two-color imaging of MyoH with tubulin in fixed parasites allowed for localization of the MyoH termini relative to the conoid, a barrel of tubulin-based fibers in the apical complex and showed the MyoH tail toward the interior face of the conoid and the head at the conoid exterior. Gel expansion showed improved labeling density for both tubulin and MyoH but altered MyoH localization, highlighting the nuanced effects of gel expansion on protein organization. Statement of Significance: . While previous studies have provided high-resolution views of the parasite's invasion machinery, MyoH has remained elusive at the nanoscale. We resolved differences in radial organization between the N- and C-termini of the motor, thus determining the orientation of the protein in the apical space. Two-color imaging revealed the organization of the motor in the greater context of the parasite's invasion complex. 3D single-molecule imaging in gel-expanded samples revealed an increase in labeling efficiency but perturbed localization of only the MyoH C-terminus, highlighting the nuanced effects of gel expansion on protein organization.
Zenodo (CERN European Organization for Nuclear Research) · 2026-04-21 · 1 citations
datasetOpen accessSenior authorExample raw data, 3D single-molecule localizations, and data processing scripts supporting Organization of Myosin H in the Apical Complex of Toxoplasma Gondii Revealed by 3D Single-Molecule Super-Resolution Microscopy. See read_me.txt for full descriptions.
Zenodo (CERN European Organization for Nuclear Research) · 2026-04-21
datasetOpen accessSenior authorExample raw data, 3D single-molecule localizations, and data processing scripts supporting Organization of Myosin H in the Apical Complex of Toxoplasma Gondii Revealed by 3D Single-Molecule Super-Resolution Microscopy. See read_me.txt for full descriptions.
CRISPR–Cas-based live cell imaging of genome dynamics
Nature Reviews Genetics · 2026-04-08
article2025-03-19
articleSenior authorWe present an enhanced confocal interferometric scattering microscopy (iSCAT) technique for label-free imaging of live cells. By integrating confocal illumination and detection, iSCAT overcomes challenges related to speckle from complex scattering media, achieving high-quality nanoscale imaging. A unique scanning mirror system further improves field homogeneity and allows for higher acquisition rates. This method provides shot-noise limited detection and visualization of intracellular organelles without the need of a label. Our results demonstrate the potential of confocal iSCAT for long-term live cell studies, with the ability to combine with fluorescence microscopy when additional specificity is required.
A Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells
bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-18 · 1 citations
preprintOpen accessSenior authorCorrespondingThe spatial organization of viral and host components dictates the course of infection, yet the nanoscale architecture of the SARS-CoV-2 life cycle remains largely uncharted. Here, we present a comprehensive super-resolution Atlas of SARS-CoV-2 infection, systematically mapping the localization of nearly all viral proteins and RNAs in human cells. This resource reveals that the viral main protease, nsp5, localizes to the interior of double-membrane vesicles (DMVs), challenging existing models and suggesting that polyprotein processing is a terminal step in replication organelle maturation. We identify previously undescribed features of the infection landscape, including thin dsRNA "connectors" that physically link DMVs, and large, membrane-less dsRNA granules decorated with replicase components, reminiscent of viroplasms. Finally, we show that the antiviral drug nirmatrelvir induces the formation of persistent, multi-layered bodies of uncleaved polyproteins. This spatial Atlas provides a foundational resource for understanding coronavirus biology and offers crucial insights into viral replication, assembly, and antiviral mechanisms.
2025-08-01
articleSenior authorWe present an enhanced confocal interferometric scattering microscopy (C-iSCAT) technique for label-free imaging of live cells. By integrating confocal illumination and detection, C-iSCAT overcomes challenges related to speckle from complex scattering media, achieving high-quality nanoscale imaging in cells. A unique scanning mirror system further improves field homogeneity and allows for higher acquisition rates. This method provides shot-noise limited detection and visualization of intracellular organelles without the need of a label. Our approach is ideal for long-term live-cell studies and can be integrated with fluorescence microscopy for additional molecular specificity.
Biophysical Journal · 2025-02-01
articleSenior authorEfficient Double Helix Detection with Steerable Filters
bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-20 · 2 citations
preprintOpen accessSenior authorAbstract We present an efficient detection scheme for localization of Double Helix point-spread functions for 3D single-molecule localization microscopy or tracking. Using steerable filters, we extract both 2D position and lobe orientation (axial position) estimates using just 7 convolutions, orders of magnitude less than used in deep-learning-based approaches. We pair this detection with a fitter and implement both as a plug-in for the open source PYthon Microscopy Environment (PYME), which features percentile-based background subtraction, signal-to-noise-based detection thresholding, and performant parallel analysis. Our complete localization analysis pipeline achieves state-of-the-art performance with minimal user input.
bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-21 · 1 citations
preprintOpen accessSenior authorCorrespondingAbstract Light microscopy remains indispensable in life sciences for visualizing cellular structures and dynamics in live specimens. Yet, conventional fluorescence imaging can suffer from phototoxicity, limited labeling efficiency, or perturbation of biological function. Label-free techniques such as interferometric scattering microscopy (iSCAT) offer a powerful alternative by detecting nanoscale structures based on their light scattering, without the need for dyes or genetic tags. iSCAT has enabled high-sensitivity detection of single proteins and viruses on clean surfaces. More recently, its application to live cells has been extended by using confocal illumination and detection, allowing suppression of out-of-focus light, yielding subcellular structures with high contrast. This development laid the foundation for biologically relevant label-free imaging. Here, we introduce interferometric image scanning microscopy (iISM). This next-generation technique combines interferometric detection with image scanning microscopy to achieve about 120 nm lateral resolution while operating at tenfold lower incident illumination power per diffraction limited spot, significantly reducing photodamage while enhancing signal-to-noise and contrast. Using iISM, we are able to visualize intracellular organelles such as the endoplasmic reticulum, actin cytoskeleton, mitochondria, and vesicles in live cells at essentially unlimited observation times. Importantly, iISM can be readily combined with confocal fluorescence microscopy, enabling correlation of label-free dynamics and structural information with molecular specificity. Our approach opens new avenues for studying dynamic biological processes, such as host-pathogen interactions, intracellular trafficking, or cytoskeletal rearrangements, under label-free, near-native conditions. iISM thus offers a powerful new tool for high-resolution, low-impact imaging of live cells, paving the way for new biological insights.
Recent grants
NIH · $414k · 2005
NIH · $366k · 2007
NIH · $538k · 2010
SGER: Trapping and Controlling Single Nanoscale Objects
NSF · $158k · 2006–2007
Subcellular architecture of regulatory protein complexes at the bacterial pole
NIH · $4.7M · 2008–2016
Frequent coauthors
- 150 shared
Robert J. Twieg
Kent State University
- 58 shared
Lucy Shapiro
- 54 shared
Peter D. Dahlberg
Stanford Synchrotron Radiation Lightsource
- 50 shared
Samuel J. Lord
University of California, San Francisco
- 47 shared
G. C. Bjorklund
- 36 shared
Matthew D. Lew
Washington University in St. Louis
- 33 shared
D. Wright
- 30 shared
Katherine A. Willets
Temple University
Labs
Physical chemistry/chemical physics: individual molecules in condensed phases, single biomolecules in cells probed by far-field and near-field optical imaging and spectroscopy; controllable fluorophores and 3D methods for superresolution imaging in cells; trapping and studying single antenna proteins and enzymes in solution; nanoantennas to produce enhanced interactions between light and matter.
Education
- 1984
Ph.D., Physics
Stanford University
- 1979
B.S., Physics
University of California, Berkeley
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