51
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High spatiotemporal resolution and low photo-toxicity fluorescence imaging in live cells and in vivo. Biochem Soc Trans 2020; 47:1635-1650. [PMID: 31829403 DOI: 10.1042/bst20190020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022]
Abstract
Taking advantage of high contrast and molecular specificity, fluorescence microscopy has played a critical role in the visualization of subcellular structures and function, enabling unprecedented exploration from cell biology to neuroscience in living animals. To record and quantitatively analyse complex and dynamic biological processes in real time, fluorescence microscopes must be capable of rapid, targeted access deep within samples at high spatial resolutions, using techniques including super-resolution fluorescence microscopy, light sheet fluorescence microscopy, and multiple photon microscopy. In recent years, tremendous breakthroughs have improved the performance of these fluorescence microscopies in spatial resolution, imaging speed, and penetration. Here, we will review recent advancements of these microscopies in terms of the trade-off among spatial resolution, sampling speed and penetration depth and provide a view of their possible applications.
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52
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Zdańkowski P, Trusiak M, McGloin D, Swedlow JR. Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging. ACS NANO 2020; 14:394-405. [PMID: 31841303 DOI: 10.1021/acsnano.9b05891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In stimulated emission depletion (STED) nanoscopy, the major origin of decreased signal-to-noise ratio within images can be attributed to sample photobleaching and strong optical aberrations. This is due to STED utilizing a high-power depletion laser (increasing the risk of photodamage), while the depletion beam is very sensitive to sample-induced aberrations. Here, we demonstrate a custom-built STED microscope with automated aberration correction that is capable of 3D super-resolution imaging through thick, highly aberrating tissue. We introduce and investigate a state of the art image denoising method by block-matching and collaborative 3D filtering (BM3D) to numerically enhance fine object details otherwise mixed with noise and further enhance the image quality. Numerical denoising provides an increase in the final effective resolution of the STED imaging of 31% using the well established Fourier ring correlation metric. Results achieved through the combination of aberration correction and tailored image processing are experimentally validated through super-resolved 3D imaging of axons in differentiated induced pluripotent stem cells growing under an 80 μm thick layer of tissue with lateral and axial resolution of 204 and 310 nm, respectively.
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Affiliation(s)
- Piotr Zdańkowski
- Centre for Gene Regulation and Expression, School of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
- SUPA, School of Science and Engineering , University of Dundee , Dundee DD1 4HN , United Kingdom
- Institute of Micromechanics and Photonics , Warsaw University of Technology , 8 A. Boboli Street , Warsaw 02-525 , Poland
| | - Maciej Trusiak
- Institute of Micromechanics and Photonics , Warsaw University of Technology , 8 A. Boboli Street , Warsaw 02-525 , Poland
| | - David McGloin
- SUPA, School of Science and Engineering , University of Dundee , Dundee DD1 4HN , United Kingdom
- School of Electrical and Data Engineering , University of Technology Sydney , Ultimo , New South Wales 2007 , Australia
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
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53
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Abstract
Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Jinhan Ren
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
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54
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Salter PS, Booth MJ. Adaptive optics in laser processing. LIGHT, SCIENCE & APPLICATIONS 2019; 8:110. [PMID: 31814967 PMCID: PMC6884496 DOI: 10.1038/s41377-019-0215-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/11/2019] [Accepted: 10/30/2019] [Indexed: 05/11/2023]
Abstract
Adaptive optics are becoming a valuable tool for laser processing, providing enhanced functionality and flexibility for a range of systems. Using a single adaptive element, it is possible to correct for aberrations introduced when focusing inside the workpiece, tailor the focal intensity distribution for the particular fabrication task and/or provide parallelisation to reduce processing times. This is particularly promising for applications using ultrafast lasers for three-dimensional fabrication. We review recent developments in adaptive laser processing, including methods and applications, before discussing prospects for the future.
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Affiliation(s)
- Patrick S. Salter
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ UK
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ UK
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55
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Advances in adaptive optics-based two-photon fluorescence microscopy for brain imaging. Lasers Med Sci 2019; 35:317-328. [PMID: 31729608 DOI: 10.1007/s10103-019-02908-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/18/2019] [Indexed: 12/20/2022]
Abstract
Deep tissue imaging using two-photon fluorescence (TPF) techniques have revolutionized the optical imaging community by providing in depth molecular information at the single-cell level. These techniques provide structural and functional aspects of mammalian brain at unprecedented depth and resolution. However, wavefront distortions introduced by the optical system as well as the biological sample (tissue) limit the achievable fluorescence signal-to-noise ratio and resolution with penetration depth. In this review, we discuss on the advances in TPF microscopy techniques for in vivo functional imaging and offer guidelines as to which technologies are best suited for different imaging applications with special reference to adaptive optics.
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56
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Polzer C, Ness S, Mohseni M, Kellerer T, Hilleringmann M, Rädler J, Hellerer T. Correlative two-color two-photon (2C2P) excitation STED microscopy. BIOMEDICAL OPTICS EXPRESS 2019; 10:4516-4530. [PMID: 31565507 PMCID: PMC6757464 DOI: 10.1364/boe.10.004516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
We present a two-color two-photon stimulated emission depletion microscopy technique (2C2P-STED) that correlates a confocal image with a super-resolved image employing the inherent self-referencing mechanism of nonlinear excitation. The novel approach overcomes the substantial challenge posed by two different imaging modalities in laser-scanning fluorescence microscopy for colocalization on the nanometer scale. Demonstrating the principle of 2C2P-STED, we show for the first time super-resolved images of the gram-positive bacteria Streptococcus pneumoniae TIGR4 pilus type-1. A signal-to-noise ratio (SNR) greater than 10 was achieved in 2C2P excitation mode and approximately 70 nm details were resolved in 2P-STED.
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Affiliation(s)
- Christoph Polzer
- Multiphoton Imaging Lab, Munich University of Applied Sciences, 80335 Munich, Germany
- Faculty of Physics, Soft Condensed Matter, Ludwig-Maximilians-University, 80539 Munich, Germany
| | - Stefan Ness
- FG Protein Biochemistry & Cellular Microbiology, University of Applied Sciences Munich, 80335 Munich, Germany
| | - Mojtaba Mohseni
- Multiphoton Imaging Lab, Munich University of Applied Sciences, 80335 Munich, Germany
| | - Thomas Kellerer
- Multiphoton Imaging Lab, Munich University of Applied Sciences, 80335 Munich, Germany
| | - Markus Hilleringmann
- FG Protein Biochemistry & Cellular Microbiology, University of Applied Sciences Munich, 80335 Munich, Germany
| | - Joachim Rädler
- Faculty of Physics, Soft Condensed Matter, Ludwig-Maximilians-University, 80539 Munich, Germany
| | - Thomas Hellerer
- Multiphoton Imaging Lab, Munich University of Applied Sciences, 80335 Munich, Germany
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57
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Trebbia JB, Baby R, Tamarat P, Lounis B. 3D optical nanoscopy with excited state saturation at liquid helium temperatures. OPTICS EXPRESS 2019; 27:23486-23496. [PMID: 31510625 DOI: 10.1364/oe.27.023486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/09/2019] [Indexed: 06/10/2023]
Abstract
We present a 3D fluorescence nanoscopy method operating at cryogenic temperatures, based on optical saturation of the excited state of individual molecules. Using a focused laser beam structured with a zero-intensity central region surrounded by intensity gradients in the three space directions, we achieve a sub-30 nm 3D optical resolution. Moreover, the analysis of the fluorescence scanning images of single molecules reveals the 3D orientation of their transition dipole with an accuracy of a few degrees. This method provides a valuable tool for locating neighboring molecules with overlapping optical transitions in order to study their interactions.
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58
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Barbotin A, Galiani S, Urbančič I, Eggeling C, Booth MJ. Adaptive optics allows STED-FCS measurements in the cytoplasm of living cells. OPTICS EXPRESS 2019; 27:23378-23395. [PMID: 31510616 PMCID: PMC6825603 DOI: 10.1364/oe.27.023378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 05/18/2023]
Abstract
Fluorescence correlation spectroscopy in combination with super-resolution stimulated emission depletion microscopy (STED-FCS) is a powerful tool to investigate molecular diffusion with sub-diffraction resolution. It has been of particular use for investigations of two dimensional systems like cell membranes, but has so far seen very limited applications to studies of three-dimensional diffusion. One reason for this is the extreme sensitivity of the axial (z) STED depletion pattern to optical aberrations. We present here an adaptive optics-based correction method that compensates for these aberrations and allows STED-FCS measurements in the cytoplasm of living cells.
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Affiliation(s)
- Aurélien Barbotin
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
| | - Silvia Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
| | - Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- “Jožef Stefan” Institute, Jamova cesta 39, SI-1000 Ljubljana,
Slovenia
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena,
Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745 Jena,
Germany
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
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59
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Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods 2019; 174:27-41. [PMID: 31344404 DOI: 10.1016/j.ymeth.2019.07.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/28/2019] [Accepted: 07/17/2019] [Indexed: 12/17/2022] Open
Abstract
Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.
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60
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Abstract
STimulated emission depletion (STED) nanoscopy has been proposed to extend greatly our capability of using light to study a variety of biological problems with nanometer-scale resolution. However, in practice the unwanted background noise degrades the STED image quality and precludes quantitative analysis. Here, we discuss the underlying sources of the background noise in STED images, and review current approaches to alleviate this problem, such as time-gating, anti-Stokes excitation removal, and off-focus incomplete depletion suppression. Progress in correcting uncorrelated background photons in fluorescence correlation spectroscopy combined with STED (STED-FCS) will also be discussed.
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Affiliation(s)
- Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America.,Departments of Biophysics and Biophysical Chemistry, Biophysics, Johns Hopkins University, Baltimore, MD, United States of America.,Howard Hughes Medical Institute, Baltimore, MD, United States of America.,Author to whom any correspondence should be addressed
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61
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Dai Y, Antonello J, Booth MJ. Calibration of a phase-only spatial light modulator for both phase and retardance modulation. OPTICS EXPRESS 2019; 27:17912-17926. [PMID: 31252743 DOI: 10.1364/oe.27.017912] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Liquid crystal spatial light modulators (SLMs) are usually configured and calibrated for phase modulation. However, as they are variable retarders, they also have application as polarization modulators. We show that conventional phase-only calibrations are insufficient for this purpose, and a separate retardance calibration is needed. To overcome this shortcoming we report a simple Twyman-Green interferometer-based setup to realize SLM phase and retardance calibration. For phase calibration, we identify the non-linear, spatially variant response to the drive voltage of the SLM using fringe analysis and both horizontally and vertically polarized incident light. For retardance calibration, we use incident light polarized at 45° and assess the intensity variation. The methods presented are compatible with in situ calibration of SLMs.
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62
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Zhang Y, Wu C, Song Y, Si K, Zheng Y, Hu L, Chen J, Tang L, Gong W. Machine learning based adaptive optics for doughnut-shaped beam. OPTICS EXPRESS 2019; 27:16871-16881. [PMID: 31252906 DOI: 10.1364/oe.27.016871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
The doughnut-shaped beam has been widely applied in the field of super-resolution microscopic imaging, micro-nanostructure lithography, ultra-high-density storage, and laser trapping. However, how to maintain the doughnut-shaped focus inside the scattering medium becomes a challenge, due to the wavefront aberrations. Here we demonstrate a machine learning based adaptive optics method to recover the doughnut-shaped focus with high speed. In our method, the relationship between the distorted doughnut-shaped intensity point spread function and the coefficients of the first 15 Zernike modes for phase correction is established. Experimental results show that the wavefront aberration with 101,784 optical control elements can be predicted within ~17 ms even using a personal computer, and 97.5% correction accuracy can be achieved in 200 repeated tests. Besides, we successfully apply this method in the scanning microscopy theoretically. With a large number of optical control elements and fast operation speed, our method may pave the way for many important applications in bioimaging, such as deep tissue stimulated emission depletion (STED) microscopy.
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63
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Turcotte R, Liang Y, Tanimoto M, Zhang Q, Li Z, Koyama M, Betzig E, Ji N. Dynamic super-resolution structured illumination imaging in the living brain. Proc Natl Acad Sci U S A 2019; 116:9586-9591. [PMID: 31028150 PMCID: PMC6511017 DOI: 10.1073/pnas.1819965116] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells in the brain act as components of extended networks. Therefore, to understand neurobiological processes in a physiological context, it is essential to study them in vivo. Super-resolution microscopy has spatial resolution beyond the diffraction limit, thus promising to provide structural and functional insights that are not accessible with conventional microscopy. However, to apply it to in vivo brain imaging, we must address the challenges of 3D imaging in an optically heterogeneous tissue that is constantly in motion. We optimized image acquisition and reconstruction to combat sample motion and applied adaptive optics to correcting sample-induced optical aberrations in super-resolution structured illumination microscopy (SIM) in vivo. We imaged the brains of live zebrafish larvae and mice and observed the dynamics of dendrites and dendritic spines at nanoscale resolution.
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Affiliation(s)
- Raphaël Turcotte
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
- Department of Physics, University of California, Berkeley, CA 94720
| | - Yajie Liang
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Masashi Tanimoto
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Qinrong Zhang
- Department of Physics, University of California, Berkeley, CA 94720
| | - Ziwei Li
- Department of Physics, University of California, Berkeley, CA 94720
| | - Minoru Koyama
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147
| | - Eric Betzig
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147;
- Department of Physics, University of California, Berkeley, CA 94720
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Na Ji
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147;
- Department of Physics, University of California, Berkeley, CA 94720
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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64
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Wang X, Fells JAJ, Yip WC, Ali T, Lin JD, Welch C, Mehl GH, Booth MJ, Wilkinson TD, Morris SM, Elston SJ. Fast and low loss flexoelectro-optic liquid crystal phase modulator with a chiral nematic reflector. Sci Rep 2019; 9:7016. [PMID: 31064999 PMCID: PMC6504954 DOI: 10.1038/s41598-019-42831-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/05/2019] [Indexed: 11/09/2022] Open
Abstract
In this paper, we demonstrate a flexoelectro-optic liquid crystal phase-only device that uses a chiral nematic reflector to achieve full 2π phase modulation. This configuration is found to be very tolerant to imperfections in the chiral nematic reflector provided that the flexoelectro-optic LC layer fulfils the half-wave condition. Encouragingly, the modulation in the phase, which operates at kHz frame rates, is also accompanied by low amplitude modulation. The configuration demonstrated herein is particularly promising for the development of next-generation liquid crystal on silicon spatial light modulators.
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Affiliation(s)
- Xiuze Wang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Julian A J Fells
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Wing C Yip
- Department of Engineering, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Taimoor Ali
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jia-de Lin
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Chris Welch
- Department of Chemistry, University of Hull, Hull, HU6 7RX, UK
| | - Georg H Mehl
- Department of Chemistry, University of Hull, Hull, HU6 7RX, UK
| | - Martin J Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | | | - Stephen M Morris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
| | - Steve J Elston
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
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65
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Combs CA, Sackett DL, Knutson JR. A simple empirical algorithm for optimising depletion power and resolution for dye and system specific STED imaging. J Microsc 2019; 274:168-176. [PMID: 31012103 DOI: 10.1111/jmi.12795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/28/2022]
Abstract
Here we show an easy method for determining an effective dye saturation factor ('PSTED ') for STED (Stimulated Emission Depletion) microscopy. We define PSTED to be a combined microscope system plus dye factor (analogous to the traditional ground truth Is measurement, which is microscope independent) that is functionally defined as the power in the depletion beam that provides a resolution enhancement of 41% compared to confocal, according to the modified Abbe's formula for STED resolution enhancement. We show that the determination of PSTED provides insight not only into the suitability of a particular dye and the best imaging parameters to be used for an experiment, but also sets the critical value for correctly determining the point spread function (PSF) used in deconvolution of STED images. PSTED can be a function of many experimental variables, both microscope and sample related. Here we show the utility of doing PSTED determinations by (1) exploiting the simple relationship between width and a threshold-defined area provided by a Gaussian PSF, for either linear or spherical objects and (2) linearising the normally inverse hyperbolic function of resolution versus power that can determine PSTED . We show that this rearrangement allows us to determine PSTED using only a few measurements: either at a few relatively low depletion powers, on traditional bead size measurements or by finding the total area of a naturally occurring sub-limit sized biological feature (in this case, microtubules). We show the derivation of these equations and methods and the utility of its use by characterising several dyes and a local imaging parameter relevant to STED microscopy. This information is used to predict the enhancement of resolution of the point spread function necessary for post-processing deconvolution. LAY DESCRIPTION: Stimulated Emission Depletion (STED) microscopy is a fluorescence imaging superresolution technique that achieves tens of nanometres resolution. This is done by utilising a depletion laser to effectively quench (deplete) fluorescence in a donut shape overlapping the normally excited fluorescence spot. The size of the remaining (undepleted) central fluorescence spot is power dependent allowing 'tunable' resolution with the power of the STED depletion laser. This depletion power versus resolution relationship is dye and instrument dependent. We have developed a method for quickly measuring this relationship to optimise experiments based on individual dyes and microscope specific parameters. This allows for quickly optimising microscope settings and for correctly postprocessing images.
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Affiliation(s)
- Christian A Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Dan L Sackett
- NICHD Division of Basic and Translational Biophysics, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jay R Knutson
- NHLBI Laboratory for Advanced Microscopy and Biophotonics, National Institutes of Health, Bethesda, Maryland, U.S.A
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66
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Zdankowski P, McGloin D, Swedlow JR. Full volume super-resolution imaging of thick mitotic spindle using 3D AO STED microscope. BIOMEDICAL OPTICS EXPRESS 2019; 10:1999-2009. [PMID: 31086714 PMCID: PMC6484978 DOI: 10.1364/boe.10.001999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 05/08/2023]
Abstract
Stimulated emission depletion (STED) nanoscopy is one of a suite of modern optical microscopy techniques capable of bypassing the conventional diffraction limit in fluorescent imaging. STED makes use of a spiral phase mask to enable 2D super-resolution imaging whereas to achieve full volumetric 3D super-resolution an additional bottle-beam phase mask must be applied. The resolution achieved in biological samples 10 µm or thicker is limited by aberrations induced mainly by scattering due to refractive index heterogeneity in the sample. These aberrations impact the fidelity of both types of phase mask, and have limited the application of STED to thicker biological systems. Here we apply an automated adaptive optics solution to correct the performance of both STED masks, enhancing robustness and expanding the capabilities of this nanoscopic technique. Corroboration in terms of successful high-quality imaging of the full volume of a 15µm mitotic spindle with resolution of 50nm x 50nm x 150nm achieved in all three dimensions is presented.
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Affiliation(s)
- Piotr Zdankowski
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
- SUPA, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN UK
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 A. Boboli St., 02-525 Warsaw, Poland
| | - David McGloin
- SUPA, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN UK
- School of Electrical and Data Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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67
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Wang Y, Wang F, Liu R, Zhang P, Gao H, Li F. Sub-Rayleigh resolution single-pixel imaging using Gaussian- and doughnut-spot illumination. OPTICS EXPRESS 2019; 27:5973-5981. [PMID: 30876191 DOI: 10.1364/oe.27.005973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
In this paper, we propose an approach to achieve a sub-Rayleigh resolution image in a single-pixel imaging system. In our scheme, Gaussian- and doughnut-shaped spots are used to alternatively illuminate an object and a single-pixel detector located after the object is employed to collect the transmitted light as two bucket signals, respectively. The image is reconstructed by assigning the difference of the bucket signals to the central position of the illumination spot. In this way, the spatial resolution of the resulting image is determined by the width of subtraction of the two spots. Combined with the deconvolution algorithm, we achieve a spatial resolution beyond the Rayleigh limit of single-pixel imaging by a factor of 22. We also propose a differential algorithm to keep the visibility of single-pixel imaging at a high level, which will be more suitable for applications.
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68
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Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 540] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
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Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
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69
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Wang L, Yan W, Li R, Weng X, Zhang J, Yang Z, Liu L, Ye T, Qu J. Aberration correction for improving the image quality in STED microscopy using the genetic algorithm. NANOPHOTONICS 2018; 7:1971-1980. [PMID: 32123648 PMCID: PMC7051000 DOI: 10.1515/nanoph-2018-0133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
With a purely optical modulation of fluorescent behaviors, stimulated emission depletion (STED) microscopy allows for far-field imaging with a diffraction-unlimited resolution in theory. The performance of STED microscopy is affected by many factors, of which aberrations induced by the optical system and biological samples can distort the wave front of the depletion beam at the focal plane to greatly deteriorate the spatial resolution and the image contrast. Therefore, aberration correction is imperative for STED imaging, especially for imaging thick specimens. Here, we present a wave front compensation approach based on the genetic algorithm (GA) to restore the distorted laser wave front for improving the quality of STED images. After performing aberration correction on two types of zebrafish samples, the signal intensity and the imaging resolution of STED images were both improved, where the thicknesses were 24 μm and 100 μm in the zebrafish retina sample and the zebrafish embryo sample, respectively. The results showed that the GA-based wave front compensation approach has the capability of correction for both system-induced and sample-induced aberrations. The elimination of aberrations can prompt STED imaging in deep tissues; therefore, STED microscopy can be expected to play an increasingly important role in super-resolution imaging related to the scientific research in biological fields.
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Affiliation(s)
| | | | - Runze Li
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, P.R. China
| | - Xiaoyu Weng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P.R. China
| | - Jia Zhang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P.R. China
| | - Zhigang Yang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P.R. China
| | - Liwei Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P.R. China
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70
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Szydlowski NA, Go JS, Hu YS. Chromatin imaging and new technologies for imaging the nucleome. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1442. [PMID: 30456928 DOI: 10.1002/wsbm.1442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulated emission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global and sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Nicole A Szydlowski
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Jane S Go
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
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71
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Görlitz F, Guldbrand S, Runcorn TH, Murray RT, Jaso-Tamame AL, Sinclair HG, Martinez-Perez E, Taylor JR, Neil MAA, Dunsby C, French PMW. easySLM-STED: Stimulated emission depletion microscopy with aberration correction, extended field of view and multiple beam scanning. JOURNAL OF BIOPHOTONICS 2018; 11:e201800087. [PMID: 29978591 DOI: 10.1002/jbio.201800087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/01/2018] [Accepted: 07/05/2018] [Indexed: 05/06/2023]
Abstract
We demonstrate a simplified set-up for STED microscopy with a straightforward alignment procedure that uses a single spatial light modulator (SLM) with collinear incident excitation and depletion beams to provide phase modulation of the beam profiles and correction of optical aberrations. We show that this approach can be used to extend the field of view for STED microscopy by correcting chromatic aberration that otherwise leads to walk-off between the focused excitation and depletion beams. We further show how this arrangement can be adapted to increase the imaging speed through multibeam excitation and depletion. Fine adjustments to the alignment can be accomplished using the SLM only, conferring the potential for automation.
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Affiliation(s)
- Frederik Görlitz
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Stina Guldbrand
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Timothy H Runcorn
- Femtosecond Optics Group, Department of Physics, Imperial College London, London, UK
| | - Robert T Murray
- Femtosecond Optics Group, Department of Physics, Imperial College London, London, UK
| | | | - Hugo G Sinclair
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | | | - James R Taylor
- Femtosecond Optics Group, Department of Physics, Imperial College London, London, UK
| | - Mark A A Neil
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Centre for Pathology, Imperial College London, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
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72
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Hrabetova S, Cognet L, Rusakov DA, Nägerl UV. Unveiling the Extracellular Space of the Brain: From Super-resolved Microstructure to In Vivo Function. J Neurosci 2018; 38:9355-9363. [PMID: 30381427 PMCID: PMC6706003 DOI: 10.1523/jneurosci.1664-18.2018] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 11/21/2022] Open
Abstract
The extracellular space occupies approximately one-fifth of brain volume, molding a spider web of gaps filled with interstitial fluid and extracellular matrix where neurons and glial cells perform in concert. Yet, very little is known about the spatial organization and dynamics of the extracellular space, let alone its influence on brain function, owing to a lack of appropriate techniques (and a traditional bias toward the inside of cells, not the spaces in between). At the same time, it is clear that understanding fundamental brain functions, such as synaptic transmission, memory, sleep, and recovery from disease, calls for more focused research on the extracellular space of the brain. This review article highlights several key research areas, covering recent methodological and conceptual progress that illuminates this understudied, yet critically important, brain compartment, providing insights into the opportunities and challenges of this nascent field.
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Affiliation(s)
- Sabina Hrabetova
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203
| | - Laurent Cognet
- Université de Bordeaux, Laboratoire Photonique Numérique et Nanosciences, F-33400 Talence, France
- Institut d'Optique and Centre National de la Recherche Scientifique, F-33400 Talence, France
| | - Dmitri A Rusakov
- Institute of Neurology, University College London, London WC1N 3BG, United Kingdom
| | - U Valentin Nägerl
- Institut Interdisciplinaire des Neurosciences, Université de Bordeaux, 33077 Bordeaux, France, and
- Institut Interdisciplinaire des Neurosciences, Centre National de la Recherche, 33077 Bordeaux, France
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73
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Fells JAJ, Wang X, Elston SJ, Welch C, Mehl GH, Booth MJ, Morris SM. Flexoelectro-optic liquid crystal analog phase-only modulator with a 2π range and 1 kHz switching. OPTICS LETTERS 2018; 43:4362-4365. [PMID: 30211871 DOI: 10.1364/ol.43.004362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
We present a flexoelectro-optic liquid crystal (LC) analog phase modulator with >2π phase range at a 1 kHz switching frequency. The chiral nematic LC mixture consists of the bimesogen CBC7CB with chiral dopant R5011, aligned in the uniform lying helix mode. The mixture exhibits >±π/4 rotation of the optic axis for a drive voltage of ±21.5 V (E=±4.5 V μm-1). The rotation of the optic axis is converted into a phase modulation with the aid of a reflective device configuration incorporating a ∼5 μm LC cell, a polarizer, two quarter-wave plates, and a mirror. The residual amplitude modulation is found to be <23%. This flexoelectro-optic phase modulator combination has the potential to enable analog spatial light modulators with very fast frame rates suitable for a range of applications.
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74
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Zhu D, Liu W, Zhang Z, Zheng C, Chen Y, Li C, Kuang C, Fan J, Xu Y, Liu X, Hussain A. Enhancement of fluorescence emission difference microscopy using conjugated vortex phase modulation. J Microsc 2018; 272:151-159. [PMID: 30338534 DOI: 10.1111/jmi.12756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/09/2018] [Accepted: 08/18/2018] [Indexed: 11/25/2022]
Abstract
In this paper, we propose and demonstrate an improved fluorescence emission difference microscopy (FED) method, exploiting programmable phase modulation for image enhancement. The main novelty of the proposed approach lies in the matched size and intensity of two excitation spots. The proposed method improves the FED performance on image quality via artefact elimination. We demonstrate the feasibility of this method through theoretical studies and experimental tests. The experimental results of nanobeads and cells validate the practical performance of this method, which can enable reliable observations at superresolution in biomedical studies. LAY DESCRIPTION: In this paper, we propose a method to improve the imaging quality of regular fluorescence emission difference (FED) microscopy. In regular FED imaging, a solid and a doughnut excitation beam are successively used to acquire two images which are then subtracted with each other to improve the resolution of confocal microscopy. The doughnut beam can be generated by modulating the excitation beam with a vortex phase mask. Note that both of the excitation beam and the vortex phase mask must have the same handed direction in regular FED microscopy. However, some negative values may be produced and some information may be lost due to the subtraction process in regular FED imaging, which is mainly caused by the mismatched size and intensity of these two excitation spots. To address this issue, we propose conjugated FED (cFED) microscopy which additionally uses a conjugated vortex phase mask to modulate the solid beam to extend its focal spot size to be matched with the doughnut spot, which means the handed direction of the solid beam and the vortex phase mask is different. Besides, in order not to damage the resolution, the doughnut beam needs to be saturated to some degree. The experiment results show that, at the same resolution level, the negative values and the information loss in cFED image are all less than that of regular FED image.
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Affiliation(s)
- D Zhu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - W Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Z Zhang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - C Zheng
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Y Chen
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Instrumentation Science & Dynamic Measurement of Ministry of Education, North University of China, Taiyuan, China
| | - C Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - C Kuang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - J Fan
- Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Hangzhou, China
| | - Y Xu
- Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Hangzhou, China
| | - X Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - A Hussain
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Quantum Optics Lab, Department of Physics, COMSATS University, Islamabad, Pakistan
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75
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Mlodzianoski MJ, Cheng-Hathaway PJ, Bemiller SM, McCray TJ, Liu S, Miller DA, Lamb BT, Landreth GE, Huang F. Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections. Nat Methods 2018; 15:583-586. [PMID: 30013047 PMCID: PMC6071422 DOI: 10.1038/s41592-018-0053-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
Single Molecule Switching Nanoscopy (SMSN) beyond the coverslip surface poses significant challenges. The sample-induced aberrations distort and blur single-molecule emission patterns. Combining active point-spread function shaping and efficient adaptive optics enables robust 3D-SMSN imaging at large depths. This development allowed us to image through 30-μm thick brain sections, visualize the morphology and the nanoscale details of amyloid-β filaments in a mouse model of Alzheimer’s disease and reconstruct their volumetric arrangements.
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Affiliation(s)
- Michael J Mlodzianoski
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.,Centre for Dynamic Imaging, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Paul J Cheng-Hathaway
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Shane M Bemiller
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tyler J McCray
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - David A Miller
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Bruce T Lamb
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Gary E Landreth
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA. .,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
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76
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Pfeiffer T, Poll S, Bancelin S, Angibaud J, Inavalli VK, Keppler K, Mittag M, Fuhrmann M, Nägerl UV. Chronic 2P-STED imaging reveals high turnover of dendritic spines in the hippocampus in vivo. eLife 2018; 7:34700. [PMID: 29932052 PMCID: PMC6014725 DOI: 10.7554/elife.34700] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/05/2018] [Indexed: 11/13/2022] Open
Abstract
Rewiring neural circuits by the formation and elimination of synapses is thought to be a key cellular mechanism of learning and memory in the mammalian brain. Dendritic spines are the postsynaptic structural component of excitatory synapses, and their experience-dependent plasticity has been extensively studied in mouse superficial cortex using two-photon microscopy in vivo. By contrast, very little is known about spine plasticity in the hippocampus, which is the archetypical memory center of the brain, mostly because it is difficult to visualize dendritic spines in this deeply embedded structure with sufficient spatial resolution. We developed chronic 2P-STED microscopy in mouse hippocampus, using a ‘hippocampal window’ based on resection of cortical tissue and a long working distance objective for optical access. We observed a two-fold higher spine density than previous studies and measured a spine turnover of ~40% within 4 days, which depended on spine size. We thus provide direct evidence for a high level of structural rewiring of synaptic circuits and new insights into the structure-dynamics relationship of hippocampal spines. Having established chronic super-resolution microscopy in the hippocampus in vivo, our study enables longitudinal and correlative analyses of nanoscale neuroanatomical structures with genetic, molecular and behavioral experiments.
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Affiliation(s)
- Thomas Pfeiffer
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Stefanie Poll
- Neuroimmunology and Imaging Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Stephane Bancelin
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Julie Angibaud
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Vvg Krishna Inavalli
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Kevin Keppler
- Light Microscope Facility, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Manuel Mittag
- Neuroimmunology and Imaging Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Martin Fuhrmann
- Neuroimmunology and Imaging Group, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - U Valentin Nägerl
- Interdisciplinary Institute for Neuroscience, CNRS UMR 5297, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
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77
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Optical imaging featuring both long working distance and high spatial resolution by correcting the aberration of a large aperture lens. Sci Rep 2018; 8:9165. [PMID: 29907794 PMCID: PMC6003919 DOI: 10.1038/s41598-018-27289-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/31/2018] [Indexed: 11/22/2022] Open
Abstract
High-resolution optical imaging within thick objects has been a challenging task due to the short working distance of conventional high numerical aperture (NA) objective lenses. Lenses with a large physical diameter and thus a large aperture, such as microscope condenser lenses, can feature both a large NA and a long working distance. However, such lenses suffer from strong aberrations. To overcome this problem, we present a method to correct the aberrations of a transmission-mode imaging system that is composed of two condensers. The proposed method separately identifies and corrects aberrations of illumination and collection lenses of up to 1.2 NA by iteratively optimizing the total intensity of the synthetic aperture images in the forward and phase-conjugation processes. At a source wavelength of 785 nm, we demonstrated a spatial resolution of 372 nm at extremely long working distances of up to 1.6 mm, an order of magnitude improvement in comparison to conventional objective lenses. Our method of converting microscope condensers to high-quality objectives may facilitate increases in the imaging depths of super-resolution and expansion microscopes.
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78
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Chojnacki J, Eggeling C. Super-resolution fluorescence microscopy studies of human immunodeficiency virus. Retrovirology 2018; 15:41. [PMID: 29884197 PMCID: PMC5994058 DOI: 10.1186/s12977-018-0424-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
Super-resolution fluorescence microscopy combines the ability to observe biological processes beyond the diffraction limit of conventional light microscopy with all advantages of the fluorescence readout such as labelling specificity and non-invasive live-cell imaging. Due to their subdiffraction size (< 200 nm) viruses are ideal candidates for super-resolution microscopy studies, and Human Immunodeficiency Virus type 1 (HIV-1) is to date the most studied virus by this technique. This review outlines principles of different super-resolution techniques as well as their advantages and disadvantages for virological studies, especially in the context of live-cell imaging applications. We highlight the findings of super-resolution based HIV-1 studies performed so far, their contributions to the understanding of HIV-1 replication cycle and how the current advances in super-resolution microscopy may open new avenues for future virology research.
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Affiliation(s)
- Jakub Chojnacki
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Institute of Applied Optics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745, Jena, Germany
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79
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Otomo K, Hibi T, Fang YC, Hung JH, Tsutsumi M, Kawakami R, Yokoyama H, Nemoto T. Advanced easySTED microscopy based on two-photon excitation by electrical modulations of light pulse wavefronts. BIOMEDICAL OPTICS EXPRESS 2018; 9:2671-2680. [PMID: 30258682 PMCID: PMC6154199 DOI: 10.1364/boe.9.002671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 05/28/2023]
Abstract
We developed a compact stimulated emission depletion (STED) two-photon excitation microscopy that utilized electrically controllable components. Transmissive liquid crystal devices inserted directly in front of the objective lens converted the STED light into an optical vortex while leaving the excitation light unaffected. Light pulses of two different colors, 1.06 and 0.64 μm, were generated by laser diode-based light sources, and the delay between the two pulses was flexibly controlled so as to maximize the fluorescence suppression ratio. In our experiments, the spatial resolution of this system was up to three times higher than that obtained without STED light irradiation, and we successfully visualize the fine microtubule network structures in fixed mammalian cells without causing significant photo-damage.
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Affiliation(s)
- Kohei Otomo
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14 Nishi 9, Kita-ku, Sapporo 060-0814, Japan
| | - Terumasa Hibi
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
| | - Yi-Cheng Fang
- New Industry Creation Hatchery Center (NICHe), Tohoku University, Aramaki-Aoba 6-6-10, Aoba-ku, Sendai 980-8579, Japan
| | - Jui-Hung Hung
- New Industry Creation Hatchery Center (NICHe), Tohoku University, Aramaki-Aoba 6-6-10, Aoba-ku, Sendai 980-8579, Japan
| | - Motosuke Tsutsumi
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
| | - Ryosuke Kawakami
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14 Nishi 9, Kita-ku, Sapporo 060-0814, Japan
| | - Hiroyuki Yokoyama
- New Industry Creation Hatchery Center (NICHe), Tohoku University, Aramaki-Aoba 6-6-10, Aoba-ku, Sendai 980-8579, Japan
| | - Tomomi Nemoto
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14 Nishi 9, Kita-ku, Sapporo 060-0814, Japan
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80
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Man T, Wan Y, Yan W, Wang XH, Peterman EJG, Wang D. Adaptive optics via self-interference digital holography for non-scanning three-dimensional imaging in biological samples. BIOMEDICAL OPTICS EXPRESS 2018; 9:2614-2626. [PMID: 30258677 PMCID: PMC6154187 DOI: 10.1364/boe.9.002614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 05/18/2023]
Abstract
Three-dimensional imaging in biological samples usually suffers from performance degradation caused by optical inhomogeneities. Here we proposed an approach to adaptive optics in fluorescence microscopy where the aberrations are measured by self-interference holographic recording and then corrected by a post-processing optimization procedure. In our approach, only one complex-value hologram is sufficient to measure and then correct the aberrations, which results in fast acquisition speed, lower exposure time, and the ability to image in three-dimensions without the need to scan the sample or any other element in the system. We show proof-of-principle experiments on a tissue phantom containing fluorescence particles. Furthermore, we present three-dimensional reconstructions of actin-labeled MCF7 breast cancer cells, showing improved resolution after the correction of aberrations. Both experiments demonstrate the validity of our method and show the great potential of non-scanning adaptive three-dimensional microscopy in imaging biological samples with improved resolution and signal-to-noise ratio.
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Affiliation(s)
- Tianlong Man
- Institute of Information Photonics Technology, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
- College of Applied Sciences, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
| | - Yuhong Wan
- Institute of Information Photonics Technology, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
- College of Applied Sciences, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
| | - Wujuan Yan
- Laboratory for Biomedical Photonics, Institute of Laser Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiu-Hong Wang
- Laboratory for Biomedical Photonics, Institute of Laser Engineering, Beijing University of Technology, Beijing 100124, China
| | - Erwin J. G. Peterman
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
- LaserLaB Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands
| | - Dayong Wang
- Institute of Information Photonics Technology, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
- College of Applied Sciences, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124, China
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81
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Heine J, Wurm CA, Keller-Findeisen J, Schönle A, Harke B, Reuss M, Winter FR, Donnert G. Three dimensional live-cell STED microscopy at increased depth using a water immersion objective. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:053701. [PMID: 29864829 DOI: 10.1063/1.5020249] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Modern fluorescence superresolution microscopes are capable of imaging living cells on the nanometer scale. One of those techniques is stimulated emission depletion (STED) which increases the microscope's resolution many times in the lateral and the axial directions. To achieve these high resolutions not only close to the coverslip but also at greater depths, the choice of objective becomes crucial. Oil immersion objectives have frequently been used for STED imaging since their high numerical aperture (NA) leads to high spatial resolutions. But during live-cell imaging, especially at great penetration depths, these objectives have a distinct disadvantage. The refractive index mismatch between the immersion oil and the usually aqueous embedding media of living specimens results in unwanted spherical aberrations. These aberrations distort the point spread functions (PSFs). Notably, during z- and 3D-STED imaging, the resolution increase along the optical axis is majorly hampered if at all possible. To overcome this limitation, we here use a water immersion objective in combination with a spatial light modulator for z-STED measurements of living samples at great depths. This compact design allows for switching between objectives without having to adapt the STED beam path and enables on the fly alterations of the STED PSF to correct for aberrations. Furthermore, we derive the influence of the NA on the axial STED resolution theoretically and experimentally. We show under live-cell imaging conditions that a water immersion objective leads to far superior results than an oil immersion objective at penetration depths of 5-180 μm.
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Affiliation(s)
- Jörn Heine
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Christian A Wurm
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Andreas Schönle
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Benjamin Harke
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Matthias Reuss
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Franziska R Winter
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Gerald Donnert
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
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82
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Wang R, Brustlein S, Mailfert S, Fabre R, Fallet M, Sivankutty S, Rigneault H, Marguet D. A straightforward STED-background corrected fitting model for unbiased STED-FCS analyses. Methods 2018; 140-141:212-222. [DOI: 10.1016/j.ymeth.2018.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/22/2017] [Accepted: 02/09/2018] [Indexed: 11/16/2022] Open
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83
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Dlasková A, Engstová H, Špaček T, Kahancová A, Pavluch V, Smolková K, Špačková J, Bartoš M, Hlavatá LP, Ježek P. 3D super-resolution microscopy reflects mitochondrial cristae alternations and mtDNA nucleoid size and distribution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:829-844. [PMID: 29727614 DOI: 10.1016/j.bbabio.2018.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
3D super-resolution microscopy based on the direct stochastic optical reconstruction microscopy (dSTORM) with primary Alexa-Fluor-647-conjugated antibodies is a powerful method for accessing changes of objects that could be normally resolved only by electron microscopy. Despite the fact that mitochondrial cristae yet to become resolved, we have indicated changes in cristae width and/or morphology by dSTORM of ATP-synthase F1 subunit α (F1α). Obtained 3D images were analyzed with the help of Ripley's K-function modeling spatial patterns or transferring them into distance distribution function. Resulting histograms of distances frequency distribution provide most frequent distances (MFD) between the localized single antibody molecules. In fasting state of model pancreatic β-cells, INS-1E, MFD between F1α were ~80 nm at 0 and 3 mM glucose, whereas decreased to 61 nm and 57 nm upon glucose-stimulated insulin secretion (GSIS) at 11 mM and 20 mM glucose, respectively. Shorter F1α interdistances reflected cristae width decrease upon GSIS, since such repositioning of F1α correlated to average 20 nm and 15 nm cristae width at 0 and 3 mM glucose, and 9 nm or 8 nm after higher glucose simulating GSIS (11, 20 mM glucose, respectively). Also, submitochondrial entities such as nucleoids of mtDNA were resolved e.g. after bromo-deoxyuridine (BrDU) pretreatment using anti-BrDU dSTORM. MFD in distances distribution histograms reflected an average nucleoid diameter (<100 nm) and average distances between nucleoids (~1000 nm). Double channel PALM/dSTORM with Eos-lactamase-β plus anti-TFAM dSTORM confirmed the latter average inter-nucleoid distance. In conclusion, 3D single molecule (dSTORM) microscopy is a reasonable tool for studying mitochondrion.
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Affiliation(s)
- Andrea Dlasková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Engstová
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Špaček
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anežka Kahancová
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vojtěch Pavluch
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarína Smolková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jitka Špačková
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Bartoš
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic; Alef Ltd, Prague, Czech Republic
| | - Lydie Plecitá Hlavatá
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Ježek
- Department of Mitochondrial Physiology, No. 75, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic.
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84
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Le Marois A, Suhling K. Quantitative Live Cell FLIM Imaging in Three Dimensions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1035:31-48. [PMID: 29080129 DOI: 10.1007/978-3-319-67358-5_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this chapter, the concept of fluorescence lifetime and its utility in quantitative live cell imaging will be introduced, along with methods to record and analyze FLIM data. Relevant applications in 3D tissue and live cell imaging, including multiplexed FLIM detection, will also be detailed.
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Affiliation(s)
- Alix Le Marois
- Department of Physics, King's College London, Strand, London, WC2R 2LS, UK
| | - Klaus Suhling
- Department of Physics, King's College London, Strand, London, WC2R 2LS, UK.
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85
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Optimal model-based sensorless adaptive optics for epifluorescence microscopy. PLoS One 2018; 13:e0194523. [PMID: 29558510 PMCID: PMC5860766 DOI: 10.1371/journal.pone.0194523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 03/05/2018] [Indexed: 11/19/2022] Open
Abstract
We report on a universal sample-independent sensorless adaptive optics method, based on modal optimization of the second moment of the fluorescence emission from a point-like excitation. Our method employs a sample-independent precalibration, performed only once for the particular system, to establish the direct relation between the image quality and the aberration. The method is potentially applicable to any form of microscopy with epifluorescence detection, including the practically important case of incoherent fluorescence emission from a three dimensional object, through minor hardware modifications. We have applied the technique successfully to a widefield epifluorescence microscope and to a multiaperture confocal microscope.
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86
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Vangindertael J, Camacho R, Sempels W, Mizuno H, Dedecker P, Janssen KPF. An introduction to optical super-resolution microscopy for the adventurous biologist. Methods Appl Fluoresc 2018; 6:022003. [DOI: 10.1088/2050-6120/aaae0c] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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87
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Combs CA, Shroff H. Fluorescence Microscopy: A Concise Guide to Current Imaging Methods. ACTA ACUST UNITED AC 2018; 79:2.1.1-2.1.25. [DOI: 10.1002/cpns.29] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Christian A. Combs
- NHLBI Light Microscopy Facility, National Institutes of Health Bethesda Maryland
| | - Hari Shroff
- NIBIB Section on High Resolution Optical Imaging, National Institutes of Health Bethesda Maryland
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88
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Miller H, Zhou Z, Shepherd J, Wollman AJM, Leake MC. Single-molecule techniques in biophysics: a review of the progress in methods and applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:024601. [PMID: 28869217 DOI: 10.1088/1361-6633/aa8a02] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
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Affiliation(s)
- Helen Miller
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
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89
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Tønnesen J, Inavalli VK, Nägerl UV. Super-Resolution Imaging of the Extracellular Space in Living Brain Tissue. Cell 2018; 172:1108-1121.e15. [DOI: 10.1016/j.cell.2018.02.007] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 11/08/2017] [Accepted: 02/01/2018] [Indexed: 01/07/2023]
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90
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Antonello J, Burke D, Booth MJ. Aberrations in stimulated emission depletion (STED) microscopy. OPTICS COMMUNICATIONS 2017; 404:203-209. [PMID: 29861506 PMCID: PMC5962904 DOI: 10.1016/j.optcom.2017.06.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Like all methods of super-resolution microscopy, stimulated emission depletion (STED) microscopy can suffer from the effects of aberrations. The most important aspect of a STED microscope is that the depletion focus maintains a minimum, ideally zero, intensity point that is surrounded by a region of higher intensity. It follows that aberrations that cause a non-zero value of this minimum intensity are the most detrimental, as they inhibit fluorescence emission even at the centre of the depletion focus. We present analysis that elucidates the nature of these effects in terms of the different polarisation components at the focus for two-dimensional and three-dimensional STED resolution enhancement. It is found that only certain low-order aberration modes can affect the minimum intensity at the Gaussian focus. This has important consequences for the design of adaptive optics aberration correction systems.
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Affiliation(s)
- Jacopo Antonello
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford, OX1 3SR, UK
| | - Daniel Burke
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford, OX1 3SR, UK
| | - Martin J. Booth
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford, OX1 3SR, UK
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Corresponding author.
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91
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Heller JP, Rusakov DA. The Nanoworld of the Tripartite Synapse: Insights from Super-Resolution Microscopy. Front Cell Neurosci 2017; 11:374. [PMID: 29225567 PMCID: PMC5705901 DOI: 10.3389/fncel.2017.00374] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022] Open
Abstract
Synaptic connections between individual nerve cells are fundamental to the process of information transfer and storage in the brain. Over the past decades a third key partner of the synaptic machinery has been unveiled: ultrathin processes of electrically passive astroglia which often surround pre- and postsynaptic structures. The recent advent of super-resolution (SR) microscopy has begun to uncover the dynamic nanoworld of synapses and their astroglial environment. Here we overview and discuss the current progress in our understanding of the synaptic nanoenvironment, as gleaned from the imaging methods that go beyond the diffraction limit of conventional light microscopy. We argue that such methods are essential to achieve a new level of comprehension pertinent to the principles of signal integration in the brain.
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Affiliation(s)
- Janosch P Heller
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Dmitri A Rusakov
- UCL Institute of Neurology, University College London, London, United Kingdom.,Institute of Neuroscience, University of Nizhny Novgorod, Nizhny Novgorod, Russia
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92
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Klauss A, Conrad F, Hille C. Binary phase masks for easy system alignment and basic aberration sensing with spatial light modulators in STED microscopy. Sci Rep 2017; 7:15699. [PMID: 29147005 PMCID: PMC5691043 DOI: 10.1038/s41598-017-15967-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/03/2017] [Indexed: 12/22/2022] Open
Abstract
The use of binary phase patterns to improve the integration and optimization of spatial light modulators (SLM) in an imaging system, especially a confocal microscope, is proposed and demonstrated. The phase masks were designed to create point spread functions (PSF), which exhibit specific sensitivity to major disturbances in the optical system. This allows direct evaluation of misalignment and fundamental aberration modes by simple visual inspection of the focal intensity distribution or by monitoring the central intensity of the PSF. The use of proposed phase masks is investigated in mathematical modelling and experiment for the use in a stimulated emission depletion (STED) microscope applying wavefront shaping by a SLM. We demonstrate the applicability of these phase masks for modal wavefront sensing of low order aberration modes up to the third order of Zernike polynomials, utilizing the point detector of a confocal microscope in a 'guide star' approach. A lateral resolution of ~25 nm is shown in STED imaging of the confocal microscope retrofitted with a SLM and a STED laser and binary phase mask based system optimization.
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Affiliation(s)
- André Klauss
- University of Potsdam, Institute of Chemistry, Potsdam, D-14476, Germany.
| | - Florian Conrad
- University of Potsdam, Institute of Chemistry, Potsdam, D-14476, Germany
| | - Carsten Hille
- University of Potsdam, Institute of Chemistry, Potsdam, D-14476, Germany.
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93
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Gould TJ, Tóth K, Mücke N, Langowski J, Hakusui AS, Olins AL, Olins DE. Defining the epichromatin epitope. Nucleus 2017; 8:625-640. [PMID: 28960120 DOI: 10.1080/19491034.2017.1380141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Epichromatin is identified by immunostaining fixed and permeabilized cells with particular bivalent anti-nucleosome antibodies (mAbs PL2-6 and 1H6). During interphase, epichromatin resides adjacent to the inner nuclear membrane; during mitosis, at the outer surface of mitotic chromosomes. By STED (stimulated emission depletion) microscopy, PL2-6 stained interphase epichromatin is ∼76 nm thick and quite uniform; mitotic epichromatin is more variable in thickness, exhibiting a "wrinkled" surface with an average thickness of ∼78 nm. Co-immunostaining with anti-Ki-67 demonstrates Ki-67 deposition between the PL2-6 "ridges" of mitotic epichromatin. Monovalent papain-derived Fab fragments of PL2-6 yield a strikingly different punctate "chromomeric" immunostaining pattern throughout interphase nuclei and along mitotic chromosome arms. Evidence from electrophoretic mobility shift assay (EMSA) and from analytical ultracentrifugation characterize the Fab/mononucleosome complex, supporting the concept that there are two binding sites per nucleosome. The peptide sequence of the Hv3 region (heavy chain variable region 3) of the PL2-6 antibody binding site strongly resembles other nucleosome acidic patch binding proteins (especially, LANA and CENPC), supporting that the nucleosome acidic patch is included within the epichromatin epitope. It is speculated that the interphase epichromatin epitope is "exposed" with favorable geometric arrangements for binding bivalent PL2-6 at the surface chromatin; whereas, the epitope is "hidden" within internal chromatin. Furthermore, it is suggested that the "exposed" nucleosome surface of mitotic epichromatin may play a role in post-mitotic nuclear envelope reformation.
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Affiliation(s)
- Travis J Gould
- a Department of Physics & Astronomy , Bates College , Lewiston , ME , USA
| | - Katalin Tóth
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Norbert Mücke
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Langowski
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | | | - Ada L Olins
- c Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
| | - Donald E Olins
- c Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
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94
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Junker A, Brenner KH. Two-sided illumination in rigorous coupled-wave analysis applied to the 4π-microscope. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2017; 34:1769-1775. [PMID: 29036046 DOI: 10.1364/josaa.34.001769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
We apply the rigorous coupled-wave analysis (RCWA) to the simulation of 4π-microscopy. To achieve this, the concept of structured illumination [J. Opt. Soc. Am. A31, 2385 (2014)JOAOD60740-323210.1364/JOSAA.31.002385] is combined with the idea of coherent two-sided light incidence. We show how the latter can be integrated into the framework of the RCWA. Furthermore, we derive how light sources with different polarization types, such as linear, radial, or azimuthal polarization, can be realized in a general form. We combine these techniques to simulate two coherent counterpropagating converging beams incident upon a sample, as in 4π-microscopy.
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95
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Zheng W, Wu Y, Winter P, Fischer R, Nogare DD, Hong A, McCormick C, Christensen R, Dempsey WP, Arnold DB, Zimmerberg J, Chitnis A, Sellers J, Waterman C, Shroff H. Adaptive optics improves multiphoton super-resolution imaging. Nat Methods 2017. [PMID: 28628128 DOI: 10.1038/nmeth.4337] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We improve multiphoton structured illumination microscopy using a nonlinear guide star to determine optical aberrations and a deformable mirror to correct them. We demonstrate our method on bead phantoms, cells in collagen gels, nematode larvae and embryos, Drosophila brain, and zebrafish embryos. Peak intensity is increased (up to 40-fold) and resolution recovered (up to 176 ± 10 nm laterally, 729 ± 39 nm axially) at depths ∼250 μm from the coverslip surface.
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Affiliation(s)
- Wei Zheng
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA.,Research Laboratory for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yicong Wu
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter Winter
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert Fischer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Damian Dalle Nogare
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Amy Hong
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chad McCormick
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Ryan Christensen
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - William P Dempsey
- Department of Biology, Section of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Don B Arnold
- Department of Biology, Section of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Joshua Zimmerberg
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Ajay Chitnis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - James Sellers
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Clare Waterman
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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96
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Masuda S, Yanase Y, Usukura E, Ryuzaki S, Wang P, Okamoto K, Kuboki T, Kidoaki S, Tamada K. High-resolution imaging of a cell-attached nanointerface using a gold-nanoparticle two-dimensional sheet. Sci Rep 2017. [PMID: 28623338 PMCID: PMC5473937 DOI: 10.1038/s41598-017-04000-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This paper proposes a simple, effective, non-scanning method for the visualization of a cell-attached nanointerface. The method uses localized surface plasmon resonance (LSPR) excited homogeneously on a two-dimensional (2D) self-assembled gold-nanoparticle sheet. The LSPR of the gold-nanoparticle sheet provides high-contrast interfacial images due to the confined light within a region a few tens of nanometers from the particles and the enhancement of fluorescence. Test experiments on rat basophilic leukemia (RBL-2H3) cells with fluorescence-labeled actin filaments revealed high axial and lateral resolution even under a regular epifluorescence microscope, which produced higher quality images than those captured under a total internal reflection fluorescence (TIRF) microscope. This non-scanning-type, high-resolution imaging method will be an effective tool for monitoring interfacial phenomena that exhibit relatively rapid reaction kinetics in various cellular and molecular dynamics.
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Affiliation(s)
- Shihomi Masuda
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuhki Yanase
- Graduate School of Biomedical & Health Science, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima City Hiroshima, 734-8553, Japan
| | - Eiji Usukura
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Sou Ryuzaki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Pangpang Wang
- Education Center for Global Leaders in Molecular Systems for Devices, Kyushu University, Fukuoka, 819-0395, Japan
| | - Koichi Okamoto
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Thasaneeya Kuboki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Satoru Kidoaki
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kaoru Tamada
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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97
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Yan W, Yang Y, Tan Y, Chen X, Li Y, Qu J, Ye T. Coherent optical adaptive technique improves the spatial resolution of STED microscopy in thick samples. PHOTONICS RESEARCH 2017; 5:176-181. [PMID: 29400356 PMCID: PMC5791906 DOI: 10.1364/prj.5.000176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Stimulated emission depletion microscopy (STED) is one of far-field optical microscopy techniques that can provide sub-diffraction spatial resolution. The spatial resolution of the STED microscopy is determined by the specially engineered beam profile of the depletion beam and its power. However, the beam profile of the depletion beam may be distorted due to aberrations of optical systems and inhomogeneity of specimens' optical properties, resulting in a compromised spatial resolution. The situation gets deteriorated when thick samples are imaged. In the worst case, the sever distortion of the depletion beam profile may cause complete loss of the super resolution effect no matter how much depletion power is applied to specimens. Previously several adaptive optics approaches have been explored to compensate aberrations of systems and specimens. However, it is hard to correct the complicated high-order optical aberrations of specimens. In this report, we demonstrate that the complicated distorted wavefront from a thick phantom sample can be measured by using the coherent optical adaptive technique (COAT). The full correction can effectively maintain and improve the spatial resolution in imaging thick samples.
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Affiliation(s)
- Wei Yan
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Department of Bioengineering and the COMSET, Clemson University, Clemson, SC 29634, USA
| | - Yanlong Yang
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Science, Xi’an 710119, China
| | - Yu Tan
- Department of Bioengineering and the COMSET, Clemson University, Clemson, SC 29634, USA
| | - Xun Chen
- Department of Bioengineering and the COMSET, Clemson University, Clemson, SC 29634, USA
| | - Yang Li
- Department of Bioengineering and the COMSET, Clemson University, Clemson, SC 29634, USA
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Tong Ye
- Department of Bioengineering and the COMSET, Clemson University, Clemson, SC 29634, USA
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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98
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Adaptive optical fluorescence microscopy. Nat Methods 2017; 14:374-380. [DOI: 10.1038/nmeth.4218] [Citation(s) in RCA: 295] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/06/2017] [Indexed: 12/24/2022]
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99
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Affiliation(s)
- Hans Blom
- Royal Institute of Technology (KTH), Dept Applied Physics, SciLifeLab, 17165 Solna, Sweden
| | - Jerker Widengren
- Royal Institute of Technology (KTH), Dept Applied Physics, Albanova Univ Center, 10691 Stockholm, Sweden
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100
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Self-organizing actin patterns shape membrane architecture but not cell mechanics. Nat Commun 2017; 8:14347. [PMID: 28194011 PMCID: PMC5316839 DOI: 10.1038/ncomms14347] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/15/2016] [Indexed: 01/24/2023] Open
Abstract
Cell-free studies have demonstrated how collective action of actin-associated proteins can organize actin filaments into dynamic patterns, such as vortices, asters and stars. Using complementary microscopic techniques, we here show evidence of such self-organization of the actin cortex in living HeLa cells. During cell adhesion, an active multistage process naturally leads to pattern transitions from actin vortices over stars into asters. This process is primarily driven by Arp2/3 complex nucleation, but not by myosin motors, which is in contrast to what has been theoretically predicted and observed in vitro. Concomitant measurements of mechanics and plasma membrane fluidity demonstrate that changes in actin patterning alter membrane architecture but occur functionally independent of macroscopic cortex elasticity. Consequently, tuning the activity of the Arp2/3 complex to alter filament assembly may thus be a mechanism allowing cells to adjust their membrane architecture without affecting their macroscopic mechanical properties. In vitro models of actin organization show the formation of vortices, asters and stars. Here Fritzsche et al. show that such actin structures form in living cells in a manner dependent on the Arp2/3 complex but not myosin, and such structures influence membrane architecture but not cortex elasticity.
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