1
|
COPELAND CRAIGR, PINTAR ADAML, DIXSON RONALDG, CHANANA ASHISH, SRINIVASAN KARTIK, WESTLY DARONA, ROBERT ILIC B, DAVANCO MARCELOI, STAVIS SAMUELM. Traceable localization enables accurate integration of quantum emitters and photonic structures with high yield. OPTICA QUANTUM 2024; 2:72-84. [PMID: 38741706 PMCID: PMC11089896 DOI: 10.1364/opticaq.502464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/02/2024] [Indexed: 05/16/2024]
Abstract
In a popular integration process for quantum information technologies, localization microscopy of quantum emitters guides lithographic placement of photonic structures. However, a complex coupling of microscopy and lithography errors degrades registration accuracy, severely limiting device performance and process yield. We introduce a methodology to solve this widespread but poorly understood problem. A new foundation of traceable localization enables rapid characterization of lithographic standards and comprehensive calibration of cryogenic microscopes, revealing and correcting latent systematic effects. Of particular concern, we discover that scale factor deviation and complex optical distortion couple to dominate registration errors. These novel results parameterize a process model for integrating quantum dots and bullseye resonators, predicting higher yield by orders of magnitude, depending on the Purcell factor threshold as a quantum performance metric. Our foundational methodology is a key enabler of the lab-to-fab transition of quantum information technologies and has broader implications to cryogenic and correlative microscopy.
Collapse
Affiliation(s)
- CRAIG R. COPELAND
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - ADAM L. PINTAR
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - RONALD G. DIXSON
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - ASHISH CHANANA
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - KARTIK SRINIVASAN
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Joint Quantum Institute, NIST/University of Maryland, College Park, Maryland 20742, USA
| | - DARON A. WESTLY
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - B. ROBERT ILIC
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- CNST NanoFab, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - MARCELO I. DAVANCO
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - SAMUEL M. STAVIS
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| |
Collapse
|
2
|
Mazal H, Wieser FF, Sandoghdar V. Insights into protein structure using cryogenic light microscopy. Biochem Soc Trans 2023; 51:2041-2059. [PMID: 38015555 PMCID: PMC10754291 DOI: 10.1042/bst20221246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.
Collapse
Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| |
Collapse
|
3
|
Barrantes FJ. Fluorescence microscopy imaging of a neurotransmitter receptor and its cell membrane lipid milieu. Front Mol Biosci 2022; 9:1014659. [PMID: 36518846 PMCID: PMC9743973 DOI: 10.3389/fmolb.2022.1014659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/01/2022] [Indexed: 05/02/2024] Open
Abstract
Hampered by the diffraction phenomenon, as expressed in 1873 by Abbe, applications of optical microscopy to image biological structures were for a long time limited to resolutions above the ∼200 nm barrier and restricted to the observation of stained specimens. The introduction of fluorescence was a game changer, and since its inception it became the gold standard technique in biological microscopy. The plasma membrane is a tenuous envelope of 4 nm-10 nm in thickness surrounding the cell. Because of its highly versatile spectroscopic properties and availability of suitable instrumentation, fluorescence techniques epitomize the current approach to study this delicate structure and its molecular constituents. The wide spectral range covered by fluorescence, intimately linked to the availability of appropriate intrinsic and extrinsic probes, provides the ability to dissect membrane constituents at the molecular scale in the spatial domain. In addition, the time resolution capabilities of fluorescence methods provide complementary high precision for studying the behavior of membrane molecules in the time domain. This review illustrates the value of various fluorescence techniques to extract information on the topography and motion of plasma membrane receptors. To this end I resort to a paradigmatic membrane-bound neurotransmitter receptor, the nicotinic acetylcholine receptor (nAChR). The structural and dynamic picture emerging from studies of this prototypic pentameric ligand-gated ion channel can be extrapolated not only to other members of this superfamily of ion channels but to other membrane-bound proteins. I also briefly discuss the various emerging techniques in the field of biomembrane labeling with new organic chemistry strategies oriented to applications in fluorescence nanoscopy, the form of fluorescence microscopy that is expanding the depth and scope of interrogation of membrane-associated phenomena.
Collapse
Affiliation(s)
- Francisco J. Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)–National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| |
Collapse
|
4
|
Kamiya N, Kuramoto K, Takishima K, Yumoto T, Oda H, Shimi T, Kimura H, Matsushita M, Fujiyoshi S. Superfluid helium nanoscope insert with millimeter working range. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:103703. [PMID: 36319353 DOI: 10.1063/5.0107395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
A superfluid helium insert was developed for cryogenic microscopy of millimeter-sized specimens. An optical-interferometric position sensor, cryogenic objective mirror, and piezo-driven cryogenic stage were fixed to an insert holder that was immersed in superfluid helium. The single-component design stabilized the three-dimensional position of the sample, with root-mean-square deviations of (x, lateral) 0.33 nm, (y, lateral) 0.29 nm, and (z, axial) 0.25 nm. Because of the millimeter working range of the optical sensor, the working range of the sample under the active stabilization was (x, y) 5 mm and (z) 3 mm in superfluid helium at 1.8 K. The insert was used to obtain the millimeter-sized fluorescence image of cell nuclei at 1.8 K without a sample exchange.
Collapse
Affiliation(s)
- Naoki Kamiya
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Kazuki Kuramoto
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Kento Takishima
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Tatsuya Yumoto
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Haruka Oda
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Takeshi Shimi
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Kimura
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Michio Matsushita
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Satoru Fujiyoshi
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| |
Collapse
|
5
|
Hartland GV. Virtual Issue on Super-Resolution Far-Field Optical Microscopy. J Phys Chem B 2021; 124:1581-1584. [PMID: 32131600 DOI: 10.1021/acs.jpcb.0c01501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
6
|
Ishida K, Naruse K, Mizouchi Y, Ogawa Y, Matsushita M, Shimi T, Kimura H, Fujiyoshi S. Variable immersion microscopy with a high numerical aperture. OPTICS LETTERS 2021; 46:856-859. [PMID: 33577531 DOI: 10.1364/ol.416006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
Three-dimensional (3D) optical microscopy with a high numerical aperture (NA) remains challenging for thick biological specimens owing to aberrations arising from interface refractions. We developed a variable immersion lens (VIL) to passively minimize these aberrations. A VIL is a high-NA concentric meniscus lens and was used in combination with an aberration-corrected high-NA reflecting objective (TORA-FUJI mirror). Wave-optics simulation at a wavelength of 488 nm showed that a VIL microscope enables diffraction-limited 1.2-NA imaging in water (refractive index of 1.34) at a depth of 0.3 mm by minimizing aberrations due to refraction of a sample interface. Another aberration due to the refractive index mismatching between a mounting medium, and an object can also be corrected by the VIL system, because various fluids with different refractive indices can be used as mounting media for the VIL. As a result of correcting the two aberrations at the same time, we experimentally demonstrated that a 6 µm diameter fluorescent bead can be imaged to the true dimensions in 3D.
Collapse
|
7
|
Furubayashi T, Ishida K, Nakata E, Morii T, Naruse K, Matsushita M, Fujiyoshi S. Cryogenic Far-Field Fluorescence Nanoscopy: Evaluation with DNA Origami. J Phys Chem B 2020; 124:7525-7536. [PMID: 32790384 DOI: 10.1021/acs.jpcb.0c04721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Far-field fluorescence localization nanoscopy of individual fluorophores at a temperature of 1.8 K was demonstrated using DNA origami as a one-nanometer-accurate scaffold. Red and near-infrared fluorophores were modified to the scaffold, and the fluorophores were 11 or 77 nm apart. We performed the localization nanoscopy of these two fluorophores at 1.8 K with a far-field fluorescence microscope. Under the cryogenic conditions, the fluorophores were perfectly immobilized and their photobleaching was drastically suppressed; consequently, the lateral spatial precision (a measure of reproducibility) was increased to 1 nm. However, the lateral spatial accuracy (a measure of trueness) remained tens of nanometers. We observed that the fluorophore centroids were laterally shifted as a function of the axial position. Because the orientation of the transition dipole of the fluorophores was fixed under cryogenic conditions, the anisotropic emission from the single fixed dipole had led to the lateral shift. This systematic error due to the dipole-orientation effect could be corrected by the three-dimensional localization of the individual fluorophores with spatial precisions of (lateral) 1 nm and (axial) 17 nm. In addition, the xy-error arising from the three-dimensional (3D) orientation of the scaffold with the two fluorophores 11 nm apart was estimated to be 0.3 nm. As a result, the individual fluorophores on the DNA origami were localized at the designed position, and the lateral spatial accuracy was quantified to be 4 nm in the standard error.
Collapse
Affiliation(s)
- Taku Furubayashi
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Keita Ishida
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kanta Naruse
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Michio Matsushita
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Satoru Fujiyoshi
- Department of Physics, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| |
Collapse
|
8
|
Hartland GV. Virtual Issue on Super-Resolution Far-Field Optical Microscopy. J Phys Chem A 2020; 124:1669-1672. [PMID: 32131601 DOI: 10.1021/acs.jpca.0c01500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|