1
|
Temma K, Oketani R, Kubo T, Bando K, Maeda S, Sugiura K, Matsuda T, Heintzmann R, Kaminishi T, Fukuda K, Hamasaki M, Nagai T, Fujita K. Selective-plane-activation structured illumination microscopy. Nat Methods 2024; 21:889-896. [PMID: 38580844 DOI: 10.1038/s41592-024-02236-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
The background light from out-of-focus planes hinders resolution enhancement in structured illumination microscopy when observing volumetric samples. Here we used selective plane illumination and reversibly photoswitchable fluorescent proteins to realize structured illumination within the focal plane and eliminate the out-of-focus background. Theoretical investigation of the imaging properties and experimental demonstrations show that selective plane activation is beneficial for imaging dense microstructures in cells and cell spheroids.
Collapse
Affiliation(s)
- Kenta Temma
- Department of Applied Physics, Osaka University, Osaka, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Ryosuke Oketani
- Department of Applied Physics, Osaka University, Osaka, Japan
- Department of Chemistry, Kyushu University, Fukuoka, Japan
| | - Toshiki Kubo
- Department of Applied Physics, Osaka University, Osaka, Japan
| | - Kazuki Bando
- Department of Applied Physics, Osaka University, Osaka, Japan
| | - Shunsuke Maeda
- Department of Applied Physics, Osaka University, Osaka, Japan
| | - Kazunori Sugiura
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Tomoki Matsuda
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller University Jena, Jena, Germany
| | - Tatsuya Kaminishi
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koki Fukuda
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Takeharu Nagai
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
- Research Institute for Electronic Science, Hokkaido University, Hokkaido, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, Osaka, Japan.
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Osaka, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.
| |
Collapse
|
2
|
Gardini L, Vignolini T, Curcio V, Pavone FS, Capitanio M. Optimization of highly inclined illumination for diffraction-limited and super-resolution microscopy. OPTICS EXPRESS 2023; 31:26208-26225. [PMID: 37710487 DOI: 10.1364/oe.492152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 09/16/2023]
Abstract
In HILO microscopy, a highly inclined and laminated light sheet is used to illuminate the sample, thus drastically reducing background fluorescence in wide-field microscopy, but maintaining the simplicity of the use of a single objective for both illumination and detection. Although the technique has become widely popular, particularly in single molecule and super-resolution microscopy, a limited understanding of how to finely shape the illumination beam and of how this impacts on the image quality complicates the setting of HILO to fit the experimental needs. In this work, we build up a simple and comprehensive guide to optimize the beam shape and alignment in HILO and to predict its performance in conventional fluorescence and super-resolution microscopy. We model the beam propagation through Gaussian optics and validate the model through far- and near-field experiments, thus characterizing the main geometrical features of the beam. Further, we fully quantify the effects of a progressive reduction of the inclined beam thickness on the image quality of both diffraction-limited and super-resolution images and we show that the most relevant impact is obtained by reducing the beam thickness to sub-cellular dimensions (< 3 µm). Based on this, we present a simple optical solution that exploits a rectangular slit to reduce the inclined beam thickness down to 2.6 µm while keeping a field-of-view dimension suited for cell imaging and allowing an increase in the number of localizations in super-resolution imaging of up to 2.6 folds.
Collapse
|
3
|
Dhakal A, Gyawali R, Wang L, Cheng J. CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529443. [PMID: 36865277 PMCID: PMC9980126 DOI: 10.1101/2023.02.21.529443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is currently the most powerful technique for determining the structures of large protein complexes and assemblies. Picking single-protein particles from cryo-EM micrographs (images) is a key step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though the emerging machine learning-based particle picking can potentially automate the process, its development is severely hindered by lack of large, high-quality, manually labelled training data. Here, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for single protein particle picking and analysis to address this bottleneck. It consists of manually labelled cryo-EM micrographs of 32 non-redundant, representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). It includes 9,089 diverse, high-resolution micrographs (∼300 cryo-EM images per EMPIAR dataset) in which the coordinates of protein particles were labelled by human experts. The protein particle labelling process was rigorously validated by both 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of machine learning and artificial intelligence methods for automated cryo-EM protein particle picking. The dataset and data processing scripts are available at https://github.com/BioinfoMachineLearning/cryoppp.
Collapse
Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
| | - Rajan Gyawali
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO 65211, USA. Fax: 573-882-8318
| |
Collapse
|
4
|
splitSMLM, a spectral demixing method for high-precision multi-color localization microscopy applied to nuclear pore complexes. Commun Biol 2022; 5:1100. [PMID: 36253454 PMCID: PMC9576791 DOI: 10.1038/s42003-022-04040-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022] Open
Abstract
Single molecule localization microscopy (SMLM) with a dichroic image splitter can provide invaluable multi-color information regarding colocalization of individual molecules, but it often suffers from technical limitations. Classical demixing algorithms tend to give suboptimal results in terms of localization precision and correction of chromatic errors. Here we present an image splitter based multi-color SMLM method (splitSMLM) that offers much improved localization precision and drift correction, compensation of chromatic distortions, and optimized performance of fluorophores in a specific buffer to equalize their reactivation rates for simultaneous imaging. A novel spectral demixing algorithm, SplitViSu, fully preserves localization precision with essentially no data loss and corrects chromatic errors at the nanometer scale. Multi-color performance is further improved by using optimized fluorophore and filter combinations. Applied to three-color imaging of the nuclear pore complex (NPC), this method provides a refined positioning of the individual NPC proteins and reveals that Pom121 clusters act as NPC deposition loci, hence illustrating strength and general applicability of the method. The development of an image splitter based multi-colour single-molecule localization microscopy method (splitSMLM) in combination with a spectral demixing algorithm improves localization accuracy as exemplified by three-colour imaging of nuclear pore complex proteins.
Collapse
|
5
|
Hung ST, Llobet Rosell A, Jurriens D, Siemons M, Soloviev O, Kapitein LC, Grußmayer K, Neukomm LJ, Verhaegen M, Smith C. Adaptive optics in single objective inclined light sheet microscopy enables three-dimensional localization microscopy in adult Drosophila brains. Front Neurosci 2022; 16:954949. [PMID: 36278016 PMCID: PMC9583434 DOI: 10.3389/fnins.2022.954949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) enables the high-resolution visualization of organelle structures and the precise localization of individual proteins. However, the expected resolution is not achieved in tissue as the imaging conditions deteriorate. Sample-induced aberrations distort the point spread function (PSF), and high background fluorescence decreases the localization precision. Here, we synergistically combine sensorless adaptive optics (AO), in-situ 3D-PSF calibration, and a single-objective lens inclined light sheet microscope (SOLEIL), termed (AO-SOLEIL), to mitigate deep tissue-induced deteriorations. We apply AO-SOLEIL on several dSTORM samples including brains of adult Drosophila. We observed a 2x improvement in the estimated axial localization precision with respect to widefield without aberration correction while we used synergistic solution. AO-SOLEIL enhances the overall imaging resolution and further facilitates the visualization of sub-cellular structures in tissue.
Collapse
Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Arnau Llobet Rosell
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Lukas J. Neukomm
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Michel Verhaegen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Carlas Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
- *Correspondence: Carlas Smith
| |
Collapse
|
6
|
Tang WC, Liu YT, Yeh CH, Lu CH, Tu CH, Lin YL, Lin YC, Hsu TL, Gao L, Chang SW, Chen P, Chen BC. Optogenetic manipulation of cell migration with high spatiotemporal resolution using lattice lightsheet microscopy. Commun Biol 2022; 5:879. [PMID: 36028551 PMCID: PMC9418249 DOI: 10.1038/s42003-022-03835-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/09/2022] [Indexed: 12/02/2022] Open
Abstract
Lattice lightsheet microscopy (LLSM) featuring three-dimensional recording is improved to manipulate cellular behavior with subcellular resolution through optogenetic activation (optoLLSM). A position-controllable Bessel beam as a stimulation source is integrated into the LLSM to achieve spatiotemporal photoactivation by changing the spatial light modulator (SLM) patterns. Unlike the point-scanning in a confocal microscope, the lattice beams are capable of wide-field optical sectioning for optogenetic activation along the Bessel beam path.We show that the energy power required for optogenetic activations is lower than 1 nW (or 24 mWcm-2) for time-lapses of CRY2olig clustering proteins, and membrane ruffling can be induced at different locations within a cell with subcellular resolution through light-triggered recruitment of phosphoinositide 3-kinase. Moreover, with the epidermal growth factor receptor (EGFR) fused with CRY2olig, we are able to demonstrate guided cell migration using optogenetic stimulation for up to 6 h, where 463 imaging volumes are collected, without noticeable cellular damages. Using a Bessel beam as a simulation source allows the use of lattice lightsheet microscopy for spatiotemporal control of photoactivation, illustrated by the control of cellular migration behavior.
Collapse
Affiliation(s)
- Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Han Yeh
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiao-Hui Tu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Tsui-Ling Hsu
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Liang Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Physics, Academia Sinica, Taipei, 11529, Taiwan.
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
7
|
Gan Y, Ma Y, Gong W, Liu W, Wang Z, Hao X, Han Y, Kuang C, Liu X. Enhanced axial resolution of lattice light sheet microscopy by fluorescence differential detection. OPTICS EXPRESS 2022; 30:27381-27394. [PMID: 36236910 DOI: 10.1364/oe.462516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/01/2022] [Indexed: 06/16/2023]
Abstract
Lattice light-sheet microscopy (LLSM) is promising in long-term biological volumetric imaging due to its high spatiotemporal resolution and low phototoxicity. However, three-dimensional (3D) isotropic spatial resolution remains an unmet goal in LLSM because of its poorer axial resolution. Combing LLSM with fluorescence differential detection, namely LLSDM, has been proposed to improve the axial resolution of LLSM in simulation. It demonstrates the possibility of further enhancing the axial resolution in 3D volumetric imaging with LLSM by specifically discarding the off-focus photons captured using a complementary optical lattice (OL) profile generated with additional 0-π phase modulation at the objective pupil plane. The direct generation of the complementary lattice profile using the binary phase modulator conjugated to the sample plane for amplitude modulation, as used in LLSM, is also permittable. Nevertheless, the previously proposed configuration fails to provide a symmetric complementary lattice pattern along the axial axis, thus leading to the imbalanced off-focus photon suppression in the reconstructed images after subtraction [Opt. Lett.45, 2854 (2020)10.1364/OL.393378]. Here, we modified the LLSDM theory which can produce an ideal complementary lattice pattern with central zero intensity and symmetrically distributed sidelobes. We also analyzed the impact of numerical aperture matching between the original and complementary lattice patterns and presented the consistency between the simulated and experimental results. As demonstrated by imaging the distribution of fluorescent beads and microtubules in fixed U2OS cells, as well as the dynamics of filopodia in live U2OS cells, LLSDM provides about 1.5 times improvement in axial resolution, and higher imaging contrast compared with traditional LLSM.
Collapse
|
8
|
Live microscopy: cracking the challenge to image biology unfolding in cells, tissues, and organs. Commun Biol 2022; 5:665. [PMID: 35799060 PMCID: PMC9262930 DOI: 10.1038/s42003-022-03601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
9
|
Kohmura Y, Yang SM, Chen HH, Takano H, Chang CJ, Wang YS, Lee TT, Chiu CY, Yang KE, Chien YT, Hu HM, Su TL, Petibois C, Chen YY, Hsu CH, Chen P, Hueng DY, Chen SJ, Yang CL, Chin AL, Low CM, Tan FCK, Teo A, Tok ES, Cai XX, Lin HM, Boeckl J, Stampfl AP, Yamada J, Matsuyama S, Ishikawa T, Margaritondo G, Chiang AS, Hwu Y. The new X-ray/visible microscopy MAXWELL technique for fast three-dimensional nanoimaging with isotropic resolution. Sci Rep 2022; 12:9668. [PMID: 35690597 PMCID: PMC9188605 DOI: 10.1038/s41598-022-13377-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Microscopy by Achromatic X-rays With Emission of Laminar Light (MAXWELL) is a new X-ray/visible technique with attractive characteristics including isotropic resolution in all directions, large-volume imaging and high throughput. An ultrathin, laminar X-ray beam produced by a Wolter type I mirror irradiates the sample stimulating the emission of visible light by scintillating nanoparticles, captured by an optical system. Three-dimensional (3D) images are obtained by scanning the specimen with respect to the laminar beam. We implemented and tested the technique with a high-brightness undulator at SPring-8, demonstrating its validity for a variety of specimens. This work was performed under the Synchrotrons for Neuroscience-an Asia-Pacific Strategic Enterprise (SYNAPSE) collaboration.
Collapse
Affiliation(s)
| | - Shun-Min Yang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Hsiang-Hsin Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | | | - Chia-Ju Chang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Ya-Sian Wang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Tsung-Tse Lee
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Ching-Yu Chiu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Kai-En Yang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yu-Ting Chien
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Huan-Ming Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Tzu-Ling Su
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Cyril Petibois
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yi-Yun Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Cheng-Huan Hsu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Peilin Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Dueng-Yuan Hueng
- Department of Surgery, School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, Tainan, Taiwan
| | - Chi Lin Yang
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - An-Lun Chin
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Chian-Ming Low
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Francis Chee Kuan Tan
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alvin Teo
- School of Chemical and Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Eng Soon Tok
- ƐMaGIC-Lab, Department of Physics, National University of Singapore, Singapore, Singapore
| | - Xu Xiang Cai
- Mechanical and Materials Department, Tatung University, Taipei, Taiwan
| | - Hong-Ming Lin
- Mechanical and Materials Department, Tatung University, Taipei, Taiwan
| | - John Boeckl
- US Air Force Research Laboratory, Materials and Manufacturing Directorate, WPAFB, Fairborn, OH, 43455, USA
| | - Anton P Stampfl
- Australian Nuclear Science and Technology Organisation, Sydney, NSW, 2234, Australia
| | | | - Satoshi Matsuyama
- Department of Materials Physics, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603, Japan
| | | | | | - Ann-Shyn Chiang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Yeukuang Hwu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan. .,Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan.
| |
Collapse
|
10
|
Hung ST, Cnossen J, Fan D, Siemons M, Jurriens D, Grußmayer K, Soloviev O, Kapitein LC, Smith CS. SOLEIL: single-objective lens inclined light sheet localization microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:3275-3294. [PMID: 35781973 PMCID: PMC9208595 DOI: 10.1364/boe.451634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
High-NA light sheet illumination can improve the resolution of single-molecule localization microscopy (SMLM) by reducing the background fluorescence. These approaches currently require custom-made sample holders or additional specialized objectives, which makes the sample mounting or the optical system complex and therefore reduces the usability of these approaches. Here, we developed a single-objective lens-inclined light sheet microscope (SOLEIL) that is capable of 2D and 3D SMLM in thick samples. SOLEIL combines oblique illumination with point spread function PSF engineering to enable dSTORM imaging in a wide variety of samples. SOLEIL is compatible with standard sample holders and off-the-shelve optics and standard high NA objectives. To accomplish optimal optical sectioning we show that there is an ideal oblique angle and sheet thickness. Furthermore, to show what optical sectioning delivers for SMLM we benchmark SOLEIL against widefield and HILO microscopy with several biological samples. SOLEIL delivers in 15 μm thick Caco2-BBE cells a 374% higher intensity to background ratio and a 54% improvement in the estimated CRLB compared to widefield illumination, and a 184% higher intensity to background ratio and a 20% improvement in the estimated CRLB compared to HILO illumination.
Collapse
Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Jelmer Cnossen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Daniel Fan
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience and Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Flexible Optical B.V., Polakweg 10-11, 2288 GG Rijswijk, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Carlas S. Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
| |
Collapse
|
11
|
Engelbrecht L, Ollewagen T, de Swardt D. Advances in fluorescence microscopy can reveal important new aspects of tissue regeneration. Biochimie 2022; 196:194-202. [DOI: 10.1016/j.biochi.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/19/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
|
12
|
Teranikar T, Lim J, Ijaseun T, Lee J. Development of Planar Illumination Strategies for Solving Mysteries in the Sub-Cellular Realm. Int J Mol Sci 2022; 23:ijms23031643. [PMID: 35163562 PMCID: PMC8835835 DOI: 10.3390/ijms23031643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has vastly expanded the frontiers of structural and functional biology, due to the non-invasive probing of dynamic volumes in vivo. However, traditional widefield microscopy illuminating the entire field of view (FOV) is adversely affected by out-of-focus light scatter. Consequently, standard upright or inverted microscopes are inept in sampling diffraction-limited volumes smaller than the optical system's point spread function (PSF). Over the last few decades, several planar and structured (sinusoidal) illumination modalities have offered unprecedented access to sub-cellular organelles and 4D (3D + time) image acquisition. Furthermore, these optical sectioning systems remain unaffected by the size of biological samples, providing high signal-to-noise (SNR) ratios for objective lenses (OLs) with long working distances (WDs). This review aims to guide biologists regarding planar illumination strategies, capable of harnessing sub-micron spatial resolution with a millimeter depth of penetration.
Collapse
Affiliation(s)
| | | | | | - Juhyun Lee
- Correspondence: ; Tel.: +1-817-272-6534; Fax: +1-817-272-2251
| |
Collapse
|
13
|
Sanchez-Arias JC, Carrier M, Frederiksen SD, Shevtsova O, McKee C, van der Slagt E, Gonçalves de Andrade E, Nguyen HL, Young PA, Tremblay MÈ, Swayne LA. A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. Front Neuroanat 2021; 15:722443. [PMID: 34949993 PMCID: PMC8691181 DOI: 10.3389/fnana.2021.722443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023] Open
Abstract
The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research.
Collapse
Affiliation(s)
| | - Micaël Carrier
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada
| | | | - Olga Shevtsova
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Emma van der Slagt
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Hai Lam Nguyen
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Penelope A Young
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.,Department of Molecular Medicine, Université de Laval, Québec City, QC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.,Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada
| |
Collapse
|
14
|
Lee CM, Tian X, Tsao C, Chen P, Huang TN, Hsueh YP, Chen BC. Macro Photography with Lightsheet Illumination Enables Whole Expanded Brain Imaging with Single-cell Resolution. Discoveries (Craiova) 2021; 9:e133. [PMID: 34849398 PMCID: PMC8626140 DOI: 10.15190/d.2021.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/26/2021] [Accepted: 07/13/2021] [Indexed: 01/19/2023] Open
Abstract
Macro photography allows direct visualization of the enlarged whole mouse brain by a combination of lightsheet illumination and expansion microscopy with single-cell resolution. Taking advantage of the long working distance of a camera lens, we imaged a 3.7 cm thick, transparent, fluorescently-labeled expanded brain. In order to improve 3D sectioning capability, we used lightsheet excitation confined as the depth of field of the camera lens. Using 4x sample expansion and 5x optical magnification, macro photography enables imaging of expanded whole mouse brain with an effective resolution of 300 nm, which provides the subcellular structural information at the organ level.
Collapse
Affiliation(s)
- Chia-Ming Lee
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan.,Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chieh Tsao
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Tzyy-Nan Huang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan.,Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
15
|
Liu Y, Patko D, Engelhardt I, George TS, Stanley-Wall NR, Ladmiral V, Ameduri B, Daniell TJ, Holden N, MacDonald MP, Dupuy LX. Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere. Proc Natl Acad Sci U S A 2021; 118:e2109176118. [PMID: 34819371 PMCID: PMC8640753 DOI: 10.1073/pnas.2109176118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants' large volume of influence. Here, we present the development of three-dimensional live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor-made, dual-illumination light sheet system acquired photons scattered from the plant while fluorescence emissions were simultaneously captured from transparent soil particles and labeled microorganisms, allowing the generation of quantitative data on samples ∼3,600 mm3 in size, with as good as 5 µm resolution at a rate of up to one scan every 30 min. The system tracked the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favored small pore spaces over the surface of soil particles, colonizing the root in a pulsatile manner. Migrations appeared to be directed toward the root cap, the point of "first contact," before the subsequent colonization of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.
Collapse
Affiliation(s)
- Yangminghao Liu
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Daniel Patko
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Ilonka Engelhardt
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
| | - Timothy S George
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | | | - Vincent Ladmiral
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Bruno Ameduri
- Institut Charles Gerhardt de Montpellier, Université de Montpellier, CNRS, ENSCM, Montpellier 34090, France
| | - Tim J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola Holden
- Northern Faculty, Scotland's Rural College, Aberdeen AB21 9YA, United Kingdom
| | - Michael P MacDonald
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom;
| | - Lionel X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom;
- Department of Conservation of Natural Resources, Neiker, Derio 48160, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain
| |
Collapse
|
16
|
Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
Collapse
Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
| |
Collapse
|
17
|
Lin PY, Hwang SPL, Lee CH, Chen BC. Two-photon scanned light sheet fluorescence microscopy with axicon imaging for fast volumetric imaging. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210219RR. [PMID: 34796706 PMCID: PMC8601431 DOI: 10.1117/1.jbo.26.11.116503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/01/2021] [Indexed: 05/31/2023]
Abstract
SIGNIFICANCE Two-photon microscopy has become the standard platform for deep-tissue fluorescence imaging. However, the use of point scanning in conventional two-photon microscopy limits the speed of volumetric image acquisition. AIM To obtain fast and deep volumetric images, we combine two-photon light sheet fluorescence microscopy (2p-LSFM) and axicon imaging that yields an extended depth of field (DOF) in 2p-LSFM. APPROACH Axicon imaging is achieved by imposing an axicon lens in the detection part of LSFM. RESULTS The DOF with axicon imaging is extended more than 20-fold over that of a conventional imaging lens, liberating the synchronized scanning in LSFM. We captured images of dynamic beating hearts and red blood cells in zebrafish larvae at volume acquisition rates up to 30 Hz. CONCLUSIONS We demonstrate the fast three-dimensional imaging capability of 2p-LSFM with axicon imaging by recording the rapid dynamics of physiological processes.
Collapse
Affiliation(s)
- Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping L. Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Hon Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
18
|
Haddad TS, Friedl P, Farahani N, Treanor D, Zlobec I, Nagtegaal I. Tutorial: methods for three-dimensional visualization of archival tissue material. Nat Protoc 2021; 16:4945-4962. [PMID: 34716449 DOI: 10.1038/s41596-021-00611-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
Analysis of three-dimensional patient specimens is gaining increasing relevance for understanding the principles of tissue structure as well as the biology and mechanisms underlying disease. New technologies are improving our ability to visualize large volume of tissues with subcellular resolution. One resource often overlooked is archival tissue maintained for decades in hospitals and research archives around the world. Accessing the wealth of information stored within these samples requires the use of appropriate methods. This tutorial introduces the range of sample preparation and microscopy approaches available for three-dimensional visualization of archival tissue. We summarize key aspects of the relevant techniques and common issues encountered when using archival tissue, including registration and antibody penetration. We also discuss analysis pipelines required to process, visualize and analyze the data and criteria to guide decision-making. The methods outlined in this tutorial provide an important and sustainable avenue for validating three-dimensional tissue organization and mechanisms of disease.
Collapse
Affiliation(s)
- Tariq Sami Haddad
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Peter Friedl
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Cancer GenomiCs.nl (CGC.nl), http://cancergenomics.nl, Utrecht, the Netherlands
| | | | - Darren Treanor
- Leeds Teaching Hospitals NHS Trust, Leeds, UK.,University of Leeds, Leeds, UK.,Department of Clinical Pathology, and Department of Clinical and Experimental Medicine, Linkoping University, Linköping, Sweden.,Center for Medical Imaging Science and Visualization (CMIV), Linköping, Sweden
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Iris Nagtegaal
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
19
|
Matryba P, Łukasiewicz K, Pawłowska M, Tomczuk J, Gołąb J. Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging? Int J Mol Sci 2021; 22:ijms22136730. [PMID: 34201632 PMCID: PMC8268743 DOI: 10.3390/ijms22136730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.
Collapse
Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Correspondence:
| | - Kacper Łukasiewicz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Tomczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| |
Collapse
|
20
|
Calovi S, Soria FN, Tønnesen J. Super-resolution STED microscopy in live brain tissue. Neurobiol Dis 2021; 156:105420. [PMID: 34102277 DOI: 10.1016/j.nbd.2021.105420] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
STED microscopy is one of several fluorescence microscopy techniques that permit imaging at higher spatial resolution than what the diffraction-limit of light dictates. STED imaging is unique among these super-resolution modalities in being a beam-scanning microscopy technique based on confocal or 2-photon imaging, which provides the advantage of superior optical sectioning in thick samples. Compared to the other super-resolution techniques that are based on widefield microscopy, this makes STED particularly suited for imaging inside live brain tissue, such as in slices or in vivo. Notably, the 50 nm resolution provided by STED microscopy enables analysis of neural morphologies that conventional confocal and 2-photon microscopy approaches cannot resolve, including all-important synaptic structures. Over the course of the last 20 years, STED microscopy has undergone extensive developments towards ever more versatile use, and has facilitated remarkable neurophysiological discoveries. The technique is still not widely adopted for live tissue imaging, even though one of its particular strengths is exactly in resolving the nanoscale dynamics of synaptic structures in brain tissue, as well as in addressing the complex morphologies of glial cells, and revealing the intricate structure of the brain extracellular space. Not least, live tissue STED microscopy has so far hardly been applied in settings of pathophysiology, though also here it shows great promise for providing new insights. This review outlines the technical advantages of STED microscopy for imaging in live brain tissue, and highlights key neurobiological findings brought about by the technique.
Collapse
Affiliation(s)
- Stefano Calovi
- Laboratory of Molecular Pharmacology, Institute of Experimental Medicine, Budapest, Hungary; János Szentágothai Doctoral School, Semmelweis University, Budapest, Hungary; Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Federico N Soria
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jan Tønnesen
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain.
| |
Collapse
|
21
|
In Situ 3D-Imaging of the Inner Ear Synapses with a Cochlear Implant. Life (Basel) 2021; 11:life11040301. [PMID: 33915846 PMCID: PMC8066088 DOI: 10.3390/life11040301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/27/2021] [Accepted: 03/28/2021] [Indexed: 11/17/2022] Open
Abstract
In recent years sensorineural hearing loss was found to affect not exclusively, nor at first, the sensory cells of the inner ear. The sensory cells' synapses and subsequent neurites are initially damaged. Auditory synaptopathies also play an important role in cochlear implant (CI) care, as they can lead to a loss of physiological hearing in patients with residual hearing. These auditory synaptopathies and in general the cascades of hearing pathologies have been in the focus of research in recent years with the aim to develop more targeted and individually tailored therapeutics. In the current study, a method to examine implanted inner ears of guinea pigs was developed to examine the synapse level. For this purpose, the cochlea is made transparent and scanned with the implant in situ using confocal laser scanning microscopy. Three different preparation methods were compared to enable both an overview image of the cochlea for assessing the CI position and images of the synapses on the same specimen. The best results were achieved by dissection of the bony capsule of the cochlea.
Collapse
|
22
|
Yang X, Annaert W. The Nanoscopic Organization of Synapse Structures: A Common Basis for Cell Communication. MEMBRANES 2021; 11:248. [PMID: 33808285 PMCID: PMC8065904 DOI: 10.3390/membranes11040248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 11/16/2022]
Abstract
Synapse structures, including neuronal and immunological synapses, can be seen as the plasma membrane contact sites between two individual cells where information is transmitted from one cell to the other. The distance between the two plasma membranes is only a few tens of nanometers, but these areas are densely populated with functionally different proteins, including adhesion proteins, receptors, and transporters. The narrow space between the two plasma membranes has been a barrier for resolving the synaptic architecture due to the diffraction limit in conventional microscopy (~250 nm). Various advanced super-resolution microscopy techniques, such as stimulated emission depletion (STED), structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM), bypass the diffraction limit and provide a sub-diffraction-limit resolving power, ranging from 10 to 100 nm. The studies using super-resolution microscopy have revealed unprecedented details of the nanoscopic organization and dynamics of synaptic molecules. In general, most synaptic proteins appear to be heterogeneously distributed and form nanodomains at the membranes. These nanodomains are dynamic functional units, playing important roles in mediating signal transmission through synapses. Herein, we discuss our current knowledge on the super-resolution nanoscopic architecture of synapses and their functional implications, with a particular focus on the neuronal synapses and immune synapses.
Collapse
Affiliation(s)
| | - Wim Annaert
- VIB Center for Brain and Disease Research and KU Leuven, Department of Neurosciences, Gasthuisberg, B-3000 Leuven, Belgium;
| |
Collapse
|
23
|
Chu LA, Chang SW, Tang WC, Tseng YT, Chen P, Chen BC. 5D superresolution imaging for a live cell nucleus. Curr Opin Genet Dev 2020; 67:77-83. [PMID: 33383256 DOI: 10.1016/j.gde.2020.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022]
Abstract
With a spatial resolution breaking the diffraction limit of light, superresolution imaging allows the visualization of detailed structures of organelles such as mitochondria, cytoskeleton, nucleus, and so on. With multi-dimensional imaging (x, y, z, t, λ), namely, multi-color 3D live imaging enables us fully understand the function of the cell. It is necessary to analyze structural changes or molecular interactions across a large volume in 3D with different labelled targets. To achieve this goal, scientists recently have expanded the original 2D superresolution microscopic tools into 3D imaging techniques. In this review, we will discuss recent development in superresolution microscopy for live imaging with minimal phototoxicity. We will focus our discussion on the cell nucleus where the genetic materials are stored and processed. Machine learning algorism will be introduced to improve the axial resolution of superresolution imaging.
Collapse
Affiliation(s)
- Li-An Chu
- Department of Biomedical Engineering and Environmental Science, National Tsing Hua University, Hsinchu, 30013, Taiwan; Brain Research Center, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Ting Tseng
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Bi-Chang Chen
- Brain Research Center, National Tsing Hua University, Hsinchu, 30013, Taiwan; Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
24
|
Carrier M, Robert MÈ, González Ibáñez F, Desjardins M, Tremblay MÈ. Imaging the Neuroimmune Dynamics Across Space and Time. Front Neurosci 2020; 14:903. [PMID: 33071723 PMCID: PMC7539119 DOI: 10.3389/fnins.2020.00903] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
The immune system is essential for maintaining homeostasis, as well as promoting growth and healing throughout the brain and body. Considering that immune cells respond rapidly to changes in their microenvironment, they are very difficult to study without affecting their structure and function. The advancement of non-invasive imaging methods greatly contributed to elucidating the physiological roles performed by immune cells in the brain across stages of the lifespan and contexts of health and disease. For instance, techniques like two-photon in vivo microscopy were pivotal for studying microglial functional dynamics in the healthy brain. Through these observations, their interactions with neurons, astrocytes, blood vessels and synapses were uncovered. High-resolution electron microscopy with immunostaining and 3D-reconstruction, as well as super-resolution fluorescence microscopy, provided complementary insights by revealing microglial interventions at synapses (phagocytosis, trogocytosis, synaptic stripping, etc.). In addition, serial block-face scanning electron microscopy has provided the first 3D reconstruction of a microglial cell at nanoscale resolution. This review will discuss the technical toolbox that currently allows to study microglia and other immune cells in the brain, as well as introduce emerging methods that were developed and could be used to increase the spatial and temporal resolution of neuroimmune imaging. A special attention will also be placed on positron emission tomography and the development of selective functional radiotracers for microglia and peripheral macrophages, considering their strong potential for research translation between animals and humans, notably when paired with other imaging modalities such as magnetic resonance imaging.
Collapse
Affiliation(s)
- Micaël Carrier
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Marie-Ève Robert
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Fernando González Ibáñez
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
| | - Michèle Desjardins
- Axe Oncologie, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada.,Department of Physics, Physical Engineering and Optics, Université Laval, Québec City, QC, Canada
| | - Marie-Ève Tremblay
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada.,Department of Molecular Medicine, Université Laval, Québec City, QC, Canada.,Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| |
Collapse
|
25
|
Louis B, Camacho R, Bresolí-Obach R, Abakumov S, Vandaele J, Kudo T, Masuhara H, Scheblykin IG, Hofkens J, Rocha S. Fast-tracking of single emitters in large volumes with nanometer precision. OPTICS EXPRESS 2020; 28:28656-28671. [PMID: 32988132 DOI: 10.1364/oe.401557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Multifocal plane microscopy allows for capturing images at different focal planes simultaneously. Using a proprietary prism which splits the emitted light into paths of different lengths, images at 8 different focal depths were obtained, covering a volume of 50x50x4 µm3. The position of single emitters was retrieved using a phasor-based approach across the different imaging planes, with better than 10 nm precision in the axial direction. We validated the accuracy of this approach by tracking fluorescent beads in 3D to calculate water viscosity. The fast acquisition rate (>100 fps) also enabled us to follow the capturing of 0.2 µm fluorescent beads into an optical trap.
Collapse
|
26
|
Wu YL, Tschanz A, Krupnik L, Ries J. Quantitative Data Analysis in Single-Molecule Localization Microscopy. Trends Cell Biol 2020; 30:837-851. [PMID: 32830013 DOI: 10.1016/j.tcb.2020.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022]
Abstract
Super-resolution microscopy, and specifically single-molecule localization microscopy (SMLM), is becoming a transformative technology for cell biology, as it allows the study of cellular structures with nanometer resolution. Here, we review a wide range of data analyses approaches for SMLM that extract quantitative information about the distribution, size, shape, spatial organization, and stoichiometry of macromolecular complexes to guide biological interpretation. We present a case study using the nuclear pore complex as an example that highlights the power of combining complementary approaches by identifying its symmetry, ringlike structure, and protein copy number. In face of recent technical and computational advances, this review serves as a guideline for selecting appropriate analysis tools and controls to exploit the potential of SMLM for a wide range of biological questions.
Collapse
Affiliation(s)
- Yu-Le Wu
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Aline Tschanz
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Leonard Krupnik
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Faculty of Chemistry and Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany.
| |
Collapse
|
27
|
Nosov G, Kahms M, Klingauf J. The Decade of Super-Resolution Microscopy of the Presynapse. Front Synaptic Neurosci 2020; 12:32. [PMID: 32848695 PMCID: PMC7433402 DOI: 10.3389/fnsyn.2020.00032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 07/21/2020] [Indexed: 01/05/2023] Open
Abstract
The presynaptic compartment of the chemical synapse is a small, yet extremely complex structure. Considering its size, most methods of optical microscopy are not able to resolve its nanoarchitecture and dynamics. Thus, its ultrastructure could only be studied by electron microscopy. In the last decade, new methods of optical superresolution microscopy have emerged allowing the study of cellular structures and processes at the nanometer scale. While this is a welcome addition to the experimental arsenal, it has necessitated careful analysis and interpretation to ensure the data obtained remains artifact-free. In this article we review the application of nanoscopic techniques to the study of the synapse and the progress made over the last decade with a particular focus on the presynapse. We find to our surprise that progress has been limited, calling for imaging techniques and probes that allow dense labeling, multiplexing, longer imaging times, higher temporal resolution, while at least maintaining the spatial resolution achieved thus far.
Collapse
Affiliation(s)
- Georgii Nosov
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany.,CIM-IMPRS Graduate Program in Münster, Münster, Germany
| | - Martin Kahms
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Jurgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| |
Collapse
|
28
|
Li W, He P, Yuan W, Yu Y. Efficiency-enhanced and sidelobe-suppressed super-oscillatory lenses for sub-diffraction-limit fluorescence imaging with ultralong working distance. NANOSCALE 2020; 12:7063-7071. [PMID: 32187246 DOI: 10.1039/c9nr10697a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Super-oscillatory lens (SOL) optical microscopy, behaving as a non-invasive and universal imaging technique, as well as being a simple post-processing procedure, may provide a potential application for sub-diffraction-limit fluorescence imaging. However, the low energy concentration, high-intensity sidelobes and micrometer-scale working distance of the reported planar SOLs impose unavoidable restrictions on the ground-state applications. Here, we demonstrate step-shaped SOLs based on the multiple-phase-modulated (MPM) method to improve the focusing efficiency. Two pivotal advantages are thus generated: (i) the fabrication complexity can be effectively reduced based on several conventional optical lithography steps; (ii) the focusing efficiency is much higher than that of the random MPM ones due to the efficient manipulation of the wavefronts, bringing about a stronger light concentration to the focal spot. Additionally, the ratio of the sidelobe intensity is flexibly tuned to meet the customized requirements, and a 2 mm-working-distance MPM SOL with the sidelobe intensity highly suppressed is finally exploited. For the first time, as far as we know, a SOL-based fluorescence microscopy without the pinhole filter to map the horizontal morphology of the dispersive fluorescent particles is established. Compared with the results achieved by the conventional wide-field microscopy, the sample details beating the diffraction limit can be reconstructed by simple imaging fusion. This research demonstrates the promising applications of SOLs for low-cost, simplified and highly customized sub-diffraction-limit fluorescence imaging systems free from photobleaching and an extremely short working distance.
Collapse
Affiliation(s)
- Wenli Li
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Room 2501, No.45, Gaoxin South 9th Road, Nanshan District, Guangdong, Shenzhen 518057, China
| | | | | | | |
Collapse
|
29
|
Epigenetic Regulation of Notch Signaling During Drosophila Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1218:59-75. [PMID: 32060871 DOI: 10.1007/978-3-030-34436-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Notch signaling exerts multiple important functions in various developmental processes, including cell differentiation and cell proliferation, while mis-regulation of this pathway results in a variety of complex diseases, such as cancer and developmental defects. The simplicity of the Notch pathway in Drosophila melanogaster, in combination with the availability of powerful genetics, makes this an attractive model for studying the fundamental mechanisms of how Notch signaling is regulated and how it functions in various cellular contexts. Recently, increasing evidence for epigenetic control of Notch signaling reveals the intimate link between epigenetic regulators and Notch signaling pathway. In this chapter, we summarize the research advances of Notch and CAF-1 in Drosophila development and the epigenetic regulation mechanisms of Notch signaling activity by CAF-1 as well as other epigenetic modification machineries, which enables Notch to orchestrate different biological inputs and outputs in specific cellular contexts.
Collapse
|
30
|
Whole-cell imaging of plasma membrane receptors by 3D lattice light-sheet dSTORM. Nat Commun 2020; 11:887. [PMID: 32060305 PMCID: PMC7021797 DOI: 10.1038/s41467-020-14731-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 01/30/2020] [Indexed: 11/08/2022] Open
Abstract
The molecular organization of receptors in the plasma membrane of cells is paramount for their functionality. We combined lattice light-sheet (LLS) microscopy with three-dimensional (3D) single-molecule localization microscopy (dSTORM) and single-particle tracking to quantify the expression and distribution, and mobility of CD56 receptors on whole fixed and living cells, finding that CD56 accumulated at cell-cell interfaces. For comparison, we investigated two other receptors, CD2 and CD45, which showed different expression levels and distributions in the plasma membrane. Overall, 3D-LLS-dSTORM enabled imaging and single-particle tracking of plasma membrane receptors with single-molecule sensitivity unperturbed by surface effects. Our results demonstrate that receptor distribution and mobility are largely unaffected by contact to the coverslip but the measured localization densities are in general lower at the basal plasma membrane due to partial limited accessibility for antibodies.
Collapse
|
31
|
Miao Y, Zhao Y, Ma H, Jiang M, Lin J, Jin P. Design of diffractive optical element projector for a pseudorandom dot array by an improved encoding method. APPLIED OPTICS 2019; 58:G169-G176. [PMID: 31873500 DOI: 10.1364/ao.58.00g169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
Here we achieved the structured light patterns of a pseudorandom dot array by a single diffractive optical element. The dot array can be applied to achieve three-dimensional imaging. First, the pseudorandom dot array was generated by the proposed improved encoding methods, which are an improved formula-method-based encoding algorithm and an improved enumeration-method-based encoding algorithm. Second, diffractive optical elements were designed as dot projectors to generate pseudorandom dots by the Gerchberg-Saxton algorithm. Pseudorandom dot arrays with different sizes were generated to validate the proposed encoding methods. A pseudorandom dot array with a maximal size of 713×449 was experimentally achieved. By analyzing the intensity distribution of the projecting pattern, the projected dots have a unique window of 7×7, and the dot array is distortion free. The proposed encoding methods, optimization algorithm, and applied fabrication technology have potential applications in three-dimensional imaging, three-dimensional sensing, shape measurement, and deformation measurement with high decoding speed.
Collapse
|
32
|
Rapid single-wavelength lightsheet localization microscopy for clarified tissue. Nat Commun 2019; 10:4762. [PMID: 31628310 PMCID: PMC6800451 DOI: 10.1038/s41467-019-12715-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 09/27/2019] [Indexed: 02/02/2023] Open
Abstract
Optical super-resolution microscopy allows nanoscale imaging of protein molecules in intact biological tissues. However, it is still challenging to perform large volume super-resolution imaging for entire animal organs. Here we develop a single-wavelength Bessel lightsheet method, optimized for refractive-index matching with clarified specimens to overcome the aberrations encountered in imaging thick tissues. Using spontaneous blinking fluorophores to label proteins of interest, we resolve the morphology of most, if not all, dopaminergic neurons in the whole adult brain (3.64 × 107 µm3) of Drosophila melanogaster at the nanometer scale with high imaging speed (436 µm3 per second) for localization. Quantitative single-molecule localization reveals the subcellular distribution of a monoamine transporter protein in the axons of a single, identified serotonergic Dorsal Paired Medial (DPM) neuron. Large datasets are obtained from imaging one brain per day to provide a robust statistical analysis of these imaging data.
Collapse
|
33
|
Single-molecule localization to study cytoskeletal structures, membrane complexes, and mechanosensors. Biophys Rev 2019; 11:745-756. [PMID: 31529362 DOI: 10.1007/s12551-019-00595-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/03/2019] [Indexed: 12/21/2022] Open
Abstract
In the last decades, a promising breakthrough in fluorescence imaging was represented by the advent of super-resolution microscopy (SRM). Super-resolution techniques recently became a popular method to study sub-cellular structures, providing a successful approach to observe cytoskeletal and focal adhesion proteins. Among the SR techniques, single-molecule localization microscopy plays a significant role due to its ability to unveil structures and molecular organizations in biological systems. Furthermore, since they provide information at the molecular level, these techniques are increasingly being used to study the stoichiometry and interaction between several membrane channel proteins and their accessory subunits. The aim of this review is to describe the single-molecule localization-based techniques and their applications relevant to cytoskeletal structures and membrane complexes in order to provide as future prospective an overall picture of their correlation with the mechanosensor channel expression and activity.
Collapse
|
34
|
Chen CY, Liu YT, Lu CH, Lee PY, Tsai YC, Wu JS, Chen P, Chen BC. The Applications of Lattice Light-sheet Microscopy for Functional Volumetric Imaging of Hippocampal Neurons in a Three-Dimensional Culture System. MICROMACHINES 2019; 10:E599. [PMID: 31514427 PMCID: PMC6780203 DOI: 10.3390/mi10090599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/07/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
Abstract
The characterization of individual cells in three-dimensions (3D) with very high spatiotemporal resolution is crucial for the development of organs-on-chips, in which 3D cell cultures are integrated with microfluidic systems. In this study, we report the applications of lattice light-sheet microscopy (LLSM) for monitoring neuronal activity in three-dimensional cell culture. We first established a 3D environment for culturing primary hippocampal neurons by applying a scaffold-based 3D tissue engineering technique. Fully differentiated and mature hippocampal neurons were observed in our system. With LLSM, we were able to monitor the behavior of individual cells in a 3D cell culture, which was very difficult under a conventional microscope due to strong light scattering from thick samples. We demonstrated that our system could study the membrane voltage and intracellular calcium dynamics at subcellular resolution in 3D under both chemical and electrical stimulation. From the volumetric images, it was found that the voltage indicators mainly resided in the cytosol instead of the membrane, which cannot be distinguished using conventional microscopy. Neuronal volumetric images were sheet scanned along the axial direction and recorded at a laser exposure of 6 ms, which covered an area up to 4800 μm2, with an image pixel size of 0.102 μm. When we analyzed the time-lapse volumetric images, we could quantify the voltage responses in different neurites in 3D extensions.
Collapse
Affiliation(s)
- Chin-Yi Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Po-Yi Lee
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yun-Chi Tsai
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Jyun-Sian Wu
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan.
| |
Collapse
|