Research Areas - (10) 3D Single-Molecule Localization Microscopy

Full path: Biology > Biophysics > Quantum Biology / Biosensing > Super-resolution Microscopy > 3D Single-Molecule Localization Microscopy

Department(s)/lab(s): Physics and Molecular & Cell Biology | Betzig Lab @ UCB
Summary:

Betzig shared the 2014 Nobel Prize in Chemistry for developing PALM, a single-molecule localization method that broke the optical diffraction limit, and subsequently invented lattice light-sheet and adaptive-optics microscopy to image subcellular dynamics in living organisms with minimal phototoxicity. His current work, split between Berkeley and Janelia, continues to push the spatial and temporal resolution of live-cell and developmental imaging beyond conventional limits.

Department(s)/lab(s): Chemistry | Cui Lab @ Stanford
Summary:

Cui develops vertical nanopillar electrode and optical sensor arrays that interface with the cell membrane to probe curvature-sensitive signaling, and pairs them with 3D super-resolution (single-molecule localization) microscopy to resolve nanoscale protein organization at the nano-bio interface with 10-20 nm precision, well past the optical diffraction limit.

Department(s)/lab(s): Physics & Astronomy – Photon Science Institute | Bioimaging and Microscopy Group (Dickinson Group) @ Manchester
Summary:

Dickinson's group develops advanced optical microscopy methods for biological and biomedical imaging. Research directions: (1) STORM super-resolution microscopy — stochastic optical reconstruction for nanoscale imaging of biological structures at ~20 nm lateral resolution; imaging cytoskeletal dynamics, cellular organelles, and pathological structures; (2) Optical coherence tomography (OCT) — depth-resolved, label-free imaging for biomedical diagnostics (retinal, cardiovascular tissues); (3) Laser speckle imaging — blood flow and perfusion measurements in tissues; (4) Multiphoton microscopy — second harmonic generation (SHG) and two-photon for collagen structure imaging in connective tissues and cancer. Part of the Manchester Photon Science Institute biophotonics theme.

Department(s)/lab(s): Molecular and Cellular Biology | Garner Lab @ Harvard
Summary:

Garner uses high-resolution, single-molecule tracking and localization microscopy (PALM-based) to study the dynamic spatial organization of the bacterial cytoskeleton and cell-wall synthesis machinery in live prokaryotic cells at nanometer precision.

Department(s)/lab(s): Imaging Physics (ImPhys) | Hoogenboom Lab (Integrated Microscopy) @ TU Delft
Summary:

Jacob Hoogenboom develops integrated correlative light and electron microscopy (CLEM) and molecular nanophotonic imaging. Research: (1) 3-in-1 microscopy combining light, electron beam, and ion beam for precise biological sample sectioning and protein localisation; (2) integrated CLEM for mapping proteins in cellular context; (3) single-molecule nanophotonic sensing using fluorescence. Relevant to advanced single-molecule biosensing approaches.

Department(s)/lab(s): Yusuf Hamied Department of Chemistry | The Lee Lab – Biophysical Chemistry @ Cambridge
Summary:

Lee leads TheLeeLab at Cambridge Chemistry, focused on developing cutting-edge biophysical single-molecule fluorescence methods to answer fundamental biological questions. Two major thrusts: (1) 3D super-resolution microscopy instrument development — the lab pioneered single-molecule light field microscopy (SMLFM) using a microlens array in the back focal plane, achieving ~10× speed improvement over double-helix PSF for volumetric imaging; also develops vortex light field microscopy (VLFM) for simultaneous 25 nm spatial / 3 nm spectral precision; (2) Biological applications — studying T-cell receptor signalling at the nanoscale (distribution of TCRs, microvilli-mediated close contacts), histone assembly during DNA replication and repair in fission yeast, and PSD-95 nanoclusters in mouse brain using 3D SMLM. A job posting (PDRA) was active in 2025 for T-cell imaging work with super-resolution and Fourier light-field microscopy.

Department(s)/lab(s): Imaging Physics (ImPhys) | Rieger Lab @ TU Delft
Summary:

Bernd Rieger works on computational super-resolution microscopy and live tissue imaging at the nanoscale. Research directions: (1) single-molecule localization microscopy (SMLM) algorithms and particle fusion; (2) 3D multi-label super-resolution imaging in tissue; (3) deep learning for biological image analysis. ERC grants; NL-BI Dutch Bioimaging consortium.

Department(s)/lab(s): School of Life Sciences (SV) | Schueder Lab (High-Resolution Microscopy) @ EPFL
Summary:

Schueder is a newly appointed (2025) EPFL Assistant Professor specializing in high-resolution microscopy and its biological applications. He played a key role in the development of DNA-PAINT, a super-resolution microscopy technique enabling nanometer-scale (~5 nm) visualization of cellular structures via transient programmable DNA hybridization. Research directions: (1) DNA-PAINT super-resolution — multiplexed, quantitative imaging of protein complexes in fixed and living cells with Exchange-PAINT; (2) Single-molecule localization below 5 nm resolution — resolving individual proteins within complexes; (3) Biological applications — imaging cytoskeletal networks, receptor clustering, chromatin organization; (4) Expanding to in situ structural biology — correlating super-resolution images with cryo-EM data. Transferred from ETH Zurich. Strong fit with EPFL imaging and structural biology ecosystem.

Department(s)/lab(s): Physics | Shaevitz Lab @ Princeton
Summary:

Shaevitz combines custom super-resolution and multifocal/3D imaging instrumentation with single-molecule tracking to make precision measurements of bacterial cell-shape mechanics, cytoskeletal dynamics (e.g. MreB), collective motility and pattern formation, and animal behavior quantification. His lab pioneered 3D live-cell imaging of bacterial shape during growth and continues to develop chromatic multifocal and localization-microscopy instrumentation in collaboration with the Yang and Gregor labs.

Department(s)/lab(s): Imaging Physics (ImPhys) | Stallinga Lab @ TU Delft
Summary:

Sjoerd Stallinga develops computational methods and hardware for super-resolution fluorescence microscopy. Research: (1) 3D single-molecule localization microscopy (3D SMLM) in living cells and tissue; (2) structured illumination microscopy (SIM) with noise-controlled reconstruction; (3) Fisher information framework for SMLM localization precision; (4) optical metrology for nanoscale structure characterization. ERC Advanced Grant for 3D super-resolution in living tissue.