1
|
Senftleben ML, Bajor A, Hirata E, Abrahamsson S, Brismar H. Fast volumetric multifocus structured illumination microscopy of subcellular dynamics in living cells. BIOMEDICAL OPTICS EXPRESS 2024; 15:2281-2292. [PMID: 38633103 PMCID: PMC11019691 DOI: 10.1364/boe.516261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
Studying the nanoscale dynamics of subcellular structures is possible with 2D structured illumination microscopy (SIM). The method allows for acquisition with improved resolution over typical widefield. For 3D samples, the acquisition speed is inherently limited by the need to acquire sequential two-dimensional planes to create a volume. Here, we present a development of multifocus SIM designed to provide high volumetric frame rate by using fast synchronized electro-optical components. We demonstrate the high volumetric imaging capacity of the microscope by recording the dynamics of microtubule and endoplasmatic reticulum in living cells at up to 2.3 super resolution volumes per second for a total volume of 30 × 30 × 1.8 µm3.
Collapse
Affiliation(s)
- Maximilian Lukas Senftleben
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Antone Bajor
- Baskin School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064, CA, USA
| | - Eduardo Hirata
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Sara Abrahamsson
- Baskin School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064, CA, USA
| | - Hjalmar Brismar
- Department of Applied Physics, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| |
Collapse
|
2
|
Liu Y, Liu Z, Hénault F, Ortiz A, Frain M, Feng Y. Fraunhofer diffraction at the two-dimensional quadratically distorted (QD) grating. OPTICS EXPRESS 2023; 31:43522-43534. [PMID: 38178446 DOI: 10.1364/oe.502016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
A two-dimensional (2D) mathematical model of quadratically distorted (QD) grating is established with the principles of Fraunhofer diffraction and Fourier optics. A discrete sampling method is applied for finding a numerical solution of the diffraction pattern of QD grating. An optimized working phase term, which determines the balanced energies and high efficiency of multi-plane images, can be obtained by the bisection algorithm. To confirm the analytical approach described above, the results have been compared with those obtained using a classical numerical model based on Fraunhofer diffraction theory and a fast Fourier transform (FFT) algorithm. The results show that our analytical approach allows the precise design of QD grating and improves the optical performance of simultaneous multi-plane imaging system. An optical setup based on our well-designed QD grating has been appended to the camera port of a commercial microscope, and some preliminary microscopy images have been successfully obtained. Further upgrade of our analytical model is in progress to improve the image quality and promote the applications.
Collapse
|
3
|
Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
Collapse
Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
4
|
Yamaguchi A, Wu R, McNulty P, Karagyozov D, Mihovilovic Skanata M, Gershow M. Multi-neuronal recording in unrestrained animals with all acousto-optic random-access line-scanning two-photon microscopy. Front Neurosci 2023; 17:1135457. [PMID: 37389365 PMCID: PMC10303936 DOI: 10.3389/fnins.2023.1135457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
To understand how neural activity encodes and coordinates behavior, it is desirable to record multi-neuronal activity in freely behaving animals. Imaging in unrestrained animals is challenging, especially for those, like larval Drosophila melanogaster, whose brains are deformed by body motion. A previously demonstrated two-photon tracking microscope recorded from individual neurons in freely crawling Drosophila larvae but faced limits in multi-neuronal recording. Here we demonstrate a new tracking microscope using acousto-optic deflectors (AODs) and an acoustic GRIN lens (TAG lens) to achieve axially resonant 2D random access scanning, sampling along arbitrarily located axial lines at a line rate of 70 kHz. With a tracking latency of 0.1 ms, this microscope recorded activities of various neurons in moving larval Drosophila CNS and VNC including premotor neurons, bilateral visual interneurons, and descending command neurons. This technique can be applied to the existing two-photon microscope to allow for fast 3D tracking and scanning.
Collapse
Affiliation(s)
- Akihiro Yamaguchi
- Department of Physics, New York University, New York, NY, United States
| | - Rui Wu
- Department of Physics, New York University, New York, NY, United States
| | - Paul McNulty
- Department of Physics, New York University, New York, NY, United States
| | - Doycho Karagyozov
- Department of Physics, New York University, New York, NY, United States
| | | | - Marc Gershow
- Department of Physics, New York University, New York, NY, United States
- Center for Neural Science, New York University, New York, NY, United States
- Neuroscience Institute, New York University, New York, NY, United States
| |
Collapse
|
5
|
Li H, Tan X, Jiao Q, Li Y, Liu S, Pei J, Zhang J, Zhang W, Xu L. Design and Study of a Reflector-Separated Light Dispersion-Compensated 3D Microscopy System. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23094516. [PMID: 37177720 PMCID: PMC10181646 DOI: 10.3390/s23094516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/01/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
The secondary-phase grating-based tomographic microscopy system, which is widely used in the biological and life sciences, can observe all the sample multilayer image information simultaneously because it has multifocal points. However, chromatic aberration exists in the grating diffraction, which seriously affects the observation of the image. To correct the chromatic aberration of the tomographic microscope system, this paper proposes a system that adopts blazed gratings and angle-variable reflectors as chromatic aberration correction devices according to the principle of dispersion compensation and Fourier phase-shift theory. A reflector-separated light dispersion-compensated 3D microscopy system is presented to achieve chromatic aberration correction while solving the problem of multilayer image overlap. The theoretical verification and optical design of the system were completed using ZEMAX software. The results show that the proposed system reduced the chromatic aberration of ordinary tomographic microscopy systems by more than 90%, retaining more wavelengths of light information. In addition, the system had a relatively wide range in the color difference compensation element installation position, reducing the difficulty of dispersion compensation element installation. Overall, the results indicate that the proposed system is effective in reducing chromatic aberration in grating diffraction.
Collapse
Affiliation(s)
- Hui Li
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Tan
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
| | - Qingbin Jiao
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
| | - Yuhang Li
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Liu
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Pei
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahang Zhang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Xu
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 130033, China
| |
Collapse
|
6
|
Amin MJ, Zhao T, Yang H, Shaevitz JW. Multicolor multifocal 3D microscopy using in-situ optimization of a spatial light modulator. Sci Rep 2022; 12:16343. [PMID: 36175472 PMCID: PMC9522655 DOI: 10.1038/s41598-022-20664-z] [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: 02/03/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Multifocal microscopy enables high-speed three-dimensional (3D) volume imaging by using a multifocal grating in the emission path. This grating is typically designed to afford a uniform illumination of multifocal subimages for a single emission wavelength. Using the same grating for multicolor imaging results in non-uniform subimage intensities in emission wavelengths for which the grating is not designed. This has restricted multifocal microscopy applications for samples having multicolored fluorophores. In this paper, we present a multicolor multifocal microscope implementation which uses a Spatial Light Modulator (SLM) as a single multifocal grating to realize near-uniform multifocal subimage intensities across multiple wavelength emission bands. Using real-time control of an in-situ-optimized SLM implemented as a multifocal grating, we demonstrate multicolor multifocal 3D imaging over three emission bands by imaging multicolored particles as well as Escherichia coli (E. coli) interacting with human liver cancer cells, at [Formula: see text] multicolor 3D volumes per second acquisition speed. Our multicolor multifocal method is adaptable across SLM hardware, emission wavelength band locations and number of emission bands, making it particularly suited for researchers investigating fast processes occurring across a volume where multiple species are involved.
Collapse
Affiliation(s)
- M Junaid Amin
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Department of Physics, Princeton University, Princeton, NJ, 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Tian Zhao
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
| | - Joshua W Shaevitz
- Department of Physics, Princeton University, Princeton, NJ, 08544, USA. .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| |
Collapse
|
7
|
Flexible Multiplane Structured Illumination Microscope with a Four-Camera Detector. PHOTONICS 2022; 9. [PMID: 35966275 PMCID: PMC9373035 DOI: 10.3390/photonics9070501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Fluorescence microscopy provides an unparalleled tool for imaging biological samples. However, producing high-quality volumetric images quickly and without excessive complexity remains a challenge. Here, we demonstrate a four-camera structured illumination microscope (SIM) capable of simultaneously imaging multiple focal planes, allowing for the capture of 3D fluorescent images without any axial movement of the sample. This setup allows for the acquisition of many different 3D imaging modes, including 3D time lapses, high-axial-resolution 3D images, and large 3D mosaics. We imaged mitochondrial motions in live cells, neuronal structure in Drosophila larvae, and imaged up to 130 µm deep into mouse brain tissue. After SIM processing, the resolution measured using one of the four cameras improved from 357 nm to 253 nm when using a 30×/1.05 NA objective.
Collapse
|
8
|
Lin A, Witvliet D, Hernandez-Nunez L, Linderman SW, Samuel ADT, Venkatachalam V. Imaging whole-brain activity to understand behavior. NATURE REVIEWS. PHYSICS 2022; 4:292-305. [PMID: 37409001 PMCID: PMC10320740 DOI: 10.1038/s42254-022-00430-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 07/07/2023]
Abstract
The brain evolved to produce behaviors that help an animal inhabit the natural world. During natural behaviors, the brain is engaged in many levels of activity from the detection of sensory inputs to decision-making to motor planning and execution. To date, most brain studies have focused on small numbers of neurons that interact in limited circuits. This allows analyzing individual computations or steps of neural processing. During behavior, however, brain activity must integrate multiple circuits in different brain regions. The activities of different brain regions are not isolated, but may be contingent on one another. Coordinated and concurrent activity within and across brain areas is organized by (1) sensory information from the environment, (2) the animal's internal behavioral state, and (3) recurrent networks of synaptic and non-synaptic connectivity. Whole-brain recording with cellular resolution provides a new opportunity to dissect the neural basis of behavior, but whole-brain activity is also mutually contingent on behavior itself. This is especially true for natural behaviors like navigation, mating, or hunting, which require dynamic interaction between the animal, its environment, and other animals. In such behaviors, the sensory experience of an unrestrained animal is actively shaped by its movements and decisions. Many of the signaling and feedback pathways that an animal uses to guide behavior only occur in freely moving animals. Recent technological advances have enabled whole-brain recording in small behaving animals including nematodes, flies, and zebrafish. These whole-brain experiments capture neural activity with cellular resolution spanning sensory, decision-making, and motor circuits, and thereby demand new theoretical approaches that integrate brain dynamics with behavioral dynamics. Here, we review the experimental and theoretical methods that are being employed to understand animal behavior and whole-brain activity, and the opportunities for physics to contribute to this emerging field of systems neuroscience.
Collapse
Affiliation(s)
- Albert Lin
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- Center for the Physics of Biological Function, Princeton University, Princeton, NJ, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Daniel Witvliet
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Luis Hernandez-Nunez
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Scott W Linderman
- Department of Statistics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Aravinthan D T Samuel
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Vivek Venkatachalam
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| |
Collapse
|
9
|
Yang L, Ma Z, Liu S, Jiao Q, Zhang J, Zhang W, Pei J, Li H, Li Y, Zou Y, Xu Y, Tan X. Study of the Off-Axis Fresnel Zone Plate of a Microscopic Tomographic Aberration. SENSORS 2022; 22:s22031113. [PMID: 35161858 PMCID: PMC8838344 DOI: 10.3390/s22031113] [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] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 12/04/2022]
Abstract
A tomographic microscopy system can achieve instantaneous three-dimensional imaging, and this type of microscopy system has been widely used in the study of biological samples; however, existing chromatographic microscopes based on off-axis Fresnel zone plates have degraded image quality due to geometric aberrations such as spherical aberration, coma aberration, and image scattering. This issue hinders the further development of chromatographic microscopy systems. In this paper, we propose a method for the design of an off-axis Fresnel zone plate with the elimination of aberrations based on double exposure point holographic surface interference. The aberration coefficient model of the optical path function was used to solve the optimal recording parameters, and the principle of the aberration elimination tomography microscopic optical path was verified. The simulation and experimental verification were carried out utilizing a Seidel coefficient, average gradient, and signal-to-noise ratio. First, the aberration coefficient model of the optical path function was used to solve the optimal recording parameters. Then, the laminar mi-coroscopy optical system was constructed for the verification of the principle. Finally, the simulation calculation results and the experimental results were verified by comparing the Seidel coefficient, average gradient, and signal-to-noise ratio of the microscopic optical system before and after the aberration elimination. The results show that for the diffractive light at the orders 0 and ±1, the spherical aberration W040 decreases by 62–70%, the coma aberration W131 decreases by 96–98%, the image dispersion W222 decreases by 71–82%, and the field curvature W220 decreases by 96–96%, the average gradient increases by 2.8%, and the signal-to-noise ratio increases by 18%.
Collapse
Affiliation(s)
- Lin Yang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenyu Ma
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
| | - Siqi Liu
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbin Jiao
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
| | - Jiahang Zhang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Pei
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhang Li
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yubo Zou
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxing Xu
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Tan
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Beijing 100049, China; (L.Y.); (Z.M.); (S.L.); (Q.J.); (J.Z.); (W.Z.); (J.P.); (H.L.); (Y.L.); (Y.Z.); (Y.X.)
- Center of Materials Science and Optoelectronics Engineering, Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| |
Collapse
|
10
|
Durst ME, Yurak S, Moscatelli J, Linhares I, Vargas R. Remote Focusing in a Temporal Focusing Microscope. OSA CONTINUUM 2021; 4:2757-2770. [PMID: 35531308 PMCID: PMC9075704 DOI: 10.1364/osac.443116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
In a temporal focusing microscope, dispersion can remotely shift the temporal focal plane axially, but only a single depth can be in focus at a time on a fixed camera. In this paper, we demonstrate remote focusing in a temporal focusing microscope. Dispersion tuning with an electrically tunable lens (ETL) in a 4 f pulse shaper scans the excitation plane axially, and another ETL in the detection path keeps the shifted excitation plane in focus on the camera. Image stacks formed using two ETLs versus a traditional stage scan are equivalent.
Collapse
|
11
|
Gregor I, Butkevich E, Enderlein J, Mojiri S. Instant three-color multiplane fluorescence microscopy. BIOPHYSICAL REPORTS 2021; 1:100001. [PMID: 36425311 PMCID: PMC9680778 DOI: 10.1016/j.bpr.2021.100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/22/2021] [Indexed: 06/16/2023]
Abstract
One of the most widely used microscopy techniques in biology and medicine is fluorescence microscopy, offering high specificity in labeling as well as maximal sensitivity. For live-cell imaging, the ideal fluorescence microscope should offer high spatial resolution, fast image acquisition, three-dimensional sectioning, and multicolor detection. However, most existing fluorescence microscopes have to compromise between these different requirements. Here, we present a multiplane, multicolor wide-field microscope that uses a dedicated beam splitter for recording volumetric data in eight focal planes and for three emission colors with frame rates of hundreds of volumes per second. We demonstrate the efficiency and performance of our system by three-dimensional imaging of multiply labeled fixed and living cells. The use of commercially available components makes our proposed microscope straightforward for implementation, thus promising for widely used applications.
Collapse
Affiliation(s)
| | | | - Jörg Enderlein
- III. Institute of Physics – Biophysics
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells,” Georg-August-University, Göttingen, Germany
| | | |
Collapse
|
12
|
Mojiri S, Isbaner S, Mühle S, Jang H, Bae AJ, Gregor I, Gholami A, Enderlein J. Rapid multi-plane phase-contrast microscopy reveals torsional dynamics in flagellar motion. BIOMEDICAL OPTICS EXPRESS 2021; 12:3169-3180. [PMID: 34221652 PMCID: PMC8221972 DOI: 10.1364/boe.419099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 05/23/2023]
Abstract
High speed volumetric optical microscopy is an important tool for observing rapid processes in living cells or for real-time tracking of sub-cellular components. However, the 3D imaging capability often comes at the price of a high technical complexity of the imaging system and/or the requirement of demanding image analysis. Here, we propose a combination of conventional phase-contrast imaging with a customized multi-plane beam-splitter for enabling simultaneous acquisition of images in eight different focal planes. Our method is technically straightforward and does not require complex post-processing image analysis. We apply our multi-plane phase-contrast microscope to the real-time observation of the fast motion of reactivated Chlamydomonas axonemes with sub-µm spatial and 4 ms temporal resolution. Our system allows us to observe not only bending but also the three-dimensional torsional dynamics of these micro-swimmers.
Collapse
Affiliation(s)
- Soheil Mojiri
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Sebastian Isbaner
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Steffen Mühle
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Hongje Jang
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Albert Johann Bae
- Max-Planck-Institute for
Dynamics and Self-Organization, 37077 Göttingen,
Germany
| | - Ingo Gregor
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| | - Azam Gholami
- Max-Planck-Institute for
Dynamics and Self-Organization, 37077 Göttingen,
Germany
- Cluster of Excellence “Multiscale
Bioimaging: from Molecular Machines to Networks of Excitable
Cells” (MBExC),
Georg-August-University, 37077
Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics –
Biophysics, Georg-August-University, 37077
Göttingen, Germany
| |
Collapse
|
13
|
He K, Wang X, Wang ZW, Yi H, Scherer NF, Katsaggelos AK, Cossairt O. Snapshot multifocal light field microscopy. OPTICS EXPRESS 2020; 28:12108-12120. [PMID: 32403711 DOI: 10.1364/oe.390719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Light field microscopy (LFM) is an emerging technology for high-speed wide-field 3D imaging by capturing 4D light field of 3D volumes. However, its 3D imaging capability comes at a cost of lateral resolution. In addition, the lateral resolution is not uniform across depth in the light field dconvolution reconstructions. To address these problems, here, we propose a snapshot multifocal light field microscopy (MFLFM) imaging method. The underlying concept of the MFLFM is to collect multiple focal shifted light fields simultaneously. We show that by focal stacking those focal shifted light fields, the depth-of-field (DOF) of the LFM can be further improved but without sacrificing the lateral resolution. Also, if all differently focused light fields are utilized together in the deconvolution, the MFLFM could achieve a high and uniform lateral resolution within a larger DOF. We present a house-built MFLFM system by placing a diffractive optical element at the Fourier plane of a conventional LFM. The optical performance of the MFLFM are analyzed and given. Both simulations and proof-of-principle experimental results are provided to demonstrate the effectiveness and benefits of the MFLFM. We believe that the proposed snapshot MFLFM has potential to enable high-speed and high resolution 3D imaging applications.
Collapse
|
14
|
Luo Y, Mengu D, Yardimci NT, Rivenson Y, Veli M, Jarrahi M, Ozcan A. Design of task-specific optical systems using broadband diffractive neural networks. LIGHT, SCIENCE & APPLICATIONS 2019; 8:112. [PMID: 31814969 PMCID: PMC6885516 DOI: 10.1038/s41377-019-0223-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 05/08/2023]
Abstract
Deep learning has been transformative in many fields, motivating the emergence of various optical computing architectures. Diffractive optical network is a recently introduced optical computing framework that merges wave optics with deep-learning methods to design optical neural networks. Diffraction-based all-optical object recognition systems, designed through this framework and fabricated by 3D printing, have been reported to recognize hand-written digits and fashion products, demonstrating all-optical inference and generalization to sub-classes of data. These previous diffractive approaches employed monochromatic coherent light as the illumination source. Here, we report a broadband diffractive optical neural network design that simultaneously processes a continuum of wavelengths generated by a temporally incoherent broadband source to all-optically perform a specific task learned using deep learning. We experimentally validated the success of this broadband diffractive neural network architecture by designing, fabricating and testing seven different multi-layer, diffractive optical systems that transform the optical wavefront generated by a broadband THz pulse to realize (1) a series of tuneable, single-passband and dual-passband spectral filters and (2) spatially controlled wavelength de-multiplexing. Merging the native or engineered dispersion of various material systems with a deep-learning-based design strategy, broadband diffractive neural networks help us engineer the light-matter interaction in 3D, diverging from intuitive and analytical design methods to create task-specific optical components that can all-optically perform deterministic tasks or statistical inference for optical machine learning.
Collapse
Affiliation(s)
- Yi Luo
- Electrical and Computer Engineering Department, University of California, 420 Westwood Plaza, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Deniz Mengu
- Electrical and Computer Engineering Department, University of California, 420 Westwood Plaza, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Nezih T. Yardimci
- Electrical and Computer Engineering Department, University of California, 420 Westwood Plaza, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Yair Rivenson
- Electrical and Computer Engineering Department, University of California, 420 Westwood Plaza, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Muhammed Veli
- Electrical and Computer Engineering Department, University of California, 420 Westwood Plaza, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Mona Jarrahi
- Electrical and Computer Engineering Department, University of California, 420 Westwood Plaza, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, 420 Westwood Plaza, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095 USA
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| |
Collapse
|
15
|
Lin W, Wang D, Meng Y, Chen SC. Multi-focus microscope with HiLo algorithm for fast 3-D fluorescent imaging. PLoS One 2019; 14:e0222729. [PMID: 31539402 PMCID: PMC6754165 DOI: 10.1371/journal.pone.0222729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/05/2019] [Indexed: 12/29/2022] Open
Abstract
In this paper, we present a new multi-focus microscope (MFM) system based on a phase mask and HiLo algorithm, achieving high-speed (20 volumes per second), high-resolution, low-noise 3-D fluorescent imaging. During imaging, the emissions from the specimen at nine different depths are simultaneously modulated and focused to different regions on a single CCD chip, i.e., the CCD chip is subdivided into nine regions to record images from the different selected depths. Next, HiLo algorithm is applied to remove the background noises and to form clean 3-D images. To visualize larger volumes, the nine layers are scanned axially, realizing fast 3-D imaging. In the imaging experiments, a mouse kidney sample of ~ 60 × 60 × 16 μm3 is visualized with only 10 raw images, demonstrating substantially enhanced resolution and contrast as well as suppressed background noises. The new method will find important applications in 3-D fluorescent imaging, e.g., recording fast dynamic events at multiple depths in vivo.
Collapse
Affiliation(s)
- Wei Lin
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
- Institute of Modern Optics, Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Nankai University, Tianjin, China
| | - Dongping Wang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yunlong Meng
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Shih-Chi Chen
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
- * E-mail:
| |
Collapse
|
16
|
Cui Y, Hu D, Markillie LM, Chrisler WB, Gaffrey MJ, Ansong C, Sussel L, Orr G. Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells. Nucleic Acids Res 2019; 46:e7. [PMID: 29040675 PMCID: PMC5778465 DOI: 10.1093/nar/gkx874] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/02/2017] [Indexed: 12/17/2022] Open
Abstract
Quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.
Collapse
Affiliation(s)
- Yi Cui
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Dehong Hu
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Lye Meng Markillie
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - William B Chrisler
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Matthew J Gaffrey
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Charles Ansong
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| | - Lori Sussel
- The Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Galya Orr
- Earth and Biological Science Directorate, Pacific Northwest National laboratory, Richland, WA 99354, USA
| |
Collapse
|
17
|
Calarco JA, Samuel ADT. Imaging whole nervous systems: insights into behavior from worms to fish. Nat Methods 2019; 16:14-15. [PMID: 30573822 DOI: 10.1038/s41592-018-0276-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- John A Calarco
- Department of Cell and Systems Biology, Toronto, ON, Canada
| | - Aravinthan D T Samuel
- Center for Brain Science and Department of Physics, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
18
|
He K, Wang Z, Huang X, Wang X, Yoo S, Ruiz P, Gdor I, Selewa A, Ferrier NJ, Scherer N, Hereld M, Katsaggelos AK, Cossairt O. Computational multifocal microscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:6477-6496. [PMID: 31065444 PMCID: PMC6491004 DOI: 10.1364/boe.9.006477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/27/2023]
Abstract
Despite recent advances, high performance single-shot 3D microscopy remains an elusive task. By introducing designed diffractive optical elements (DOEs), one is capable of converting a microscope into a 3D "kaleidoscope," in which case the snapshot image consists of an array of tiles and each tile focuses on different depths. However, the acquired multifocal microscopic (MFM) image suffers from multiple sources of degradation, which prevents MFM from further applications. We propose a unifying computational framework which simplifies the imaging system and achieves 3D reconstruction via computation. Our optical configuration omits optical elements for correcting chromatic aberrations and redesigns the multifocal grating to enlarge the tracking area. Our proposed setup features only one single grating in addition to a regular microscope. The aberration correction, along with Poisson and background denoising, are incorporated in our deconvolution-based fully-automated algorithm, which requires no empirical parameter-tuning. In experiments, we achieve spatial resolutions of 0.35um (lateral) and 0.5um (axial), which are comparable to the resolution that can be achieved with confocal deconvolution microscopy. We demonstrate a 3D video of moving bacteria recorded at 25 frames per second using our proposed computational multifocal microscopy technique.
Collapse
Affiliation(s)
- Kuan He
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Zihao Wang
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Xiang Huang
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Xiaolei Wang
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
| | - Seunghwan Yoo
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Pablo Ruiz
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Itay Gdor
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
| | - Alan Selewa
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Nicola J. Ferrier
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Norbert Scherer
- Department of Chemistry, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
- James Franck Institute, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637,
USA
| | - Mark Hereld
- Mathematics and Computer Science, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439,
USA
| | - Aggelos K. Katsaggelos
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| | - Oliver Cossairt
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208,
USA
| |
Collapse
|
19
|
Attota RK. Fidelity test for through-focus or volumetric type of optical imaging methods. OPTICS EXPRESS 2018; 26:19100-19114. [PMID: 30114170 PMCID: PMC6159218 DOI: 10.1364/oe.26.019100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
Rapid increase in interest and applications of through-focus (TF) or volumetric type of optical imaging in biology and other areas has resulted in the development of several TF image collection methods. Achieving quantitative results from images requires standardization and optimization of image acquisition protocols. Several standardization protocols are available for conventional optical microscopy where a best-focus image is used, but to date, rigorous testing protocols do not exist for TF optical imaging. In this paper, we present a method to determine the fidelity of the TF optical data using the TF scanning optical microscopy images.
Collapse
Affiliation(s)
- Ravi Kiran Attota
- Engineering Physics Division, PML, NIST, Gaithersburg, MD 20899-8212, USA
| |
Collapse
|
20
|
Weisenburger S, Vaziri A. A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity. Annu Rev Neurosci 2018; 41:431-452. [PMID: 29709208 PMCID: PMC6037565 DOI: 10.1146/annurev-neuro-072116-031458] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and high resolution over a large area of the brain. Although the use of optical approaches by the neuroscience community has rapidly increased over the past two decades, most microscopy approaches are unable to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolutions. In this review, we survey the recent development in optical technologies for Ca2+ imaging in this regard and provide an overview of the strengths and limitations of each modality and its potential for scalability. We provide guidance from the perspective of a biological user driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.
Collapse
Affiliation(s)
- Siegfried Weisenburger
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
- Kavli Neural Systems Institute, The Rockefeller University, New York, New York 10065, USA
- Research Institute of Molecular Pathology, 1030 Vienna, Austria;
| |
Collapse
|
21
|
Attota RK. Through-focus or volumetric type of optical imaging methods: a review. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-10. [PMID: 29981229 PMCID: PMC6157599 DOI: 10.1117/1.jbo.23.7.070901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/11/2018] [Indexed: 05/04/2023]
Abstract
In recent years, the use of through-focus (TF) or volumetric type of optical imaging has gained momentum in several areas such as biological imaging, microscopy, adaptive optics, material processing, optical data storage, and optical inspection. We provide a review of basic TF optical methods highlighting their design, major unique characteristics, and application space.
Collapse
Affiliation(s)
- Ravi Kiran Attota
- Engineering Physics Division, PML, National Institute of Standards and Technology Gaithersburg, MD 20899, USA
| |
Collapse
|
22
|
Liao J, Wang Z, Zhang Z, Bian Z, Guo K, Nambiar A, Jiang Y, Jiang S, Zhong J, Choma M, Zheng G. Dual light-emitting diode-based multichannel microscopy for whole-slide multiplane, multispectral and phase imaging. JOURNAL OF BIOPHOTONICS 2018; 11:10.1002/jbio.201700075. [PMID: 28700137 PMCID: PMC5766431 DOI: 10.1002/jbio.201700075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/22/2017] [Accepted: 05/31/2017] [Indexed: 05/20/2023]
Abstract
We report the development of a multichannel microscopy for whole-slide multiplane, multispectral and phase imaging. We use trinocular heads to split the beam path into 6 independent channels and employ a camera array for parallel data acquisition, achieving a maximum data throughput of approximately 1 gigapixel per second. To perform single-frame rapid autofocusing, we place 2 near-infrared light-emitting diodes (LEDs) at the back focal plane of the condenser lens to illuminate the sample from 2 different incident angles. A hot mirror is used to direct the near-infrared light to an autofocusing camera. For multiplane whole-slide imaging (WSI), we acquire 6 different focal planes of a thick specimen simultaneously. For multispectral WSI, we relay the 6 independent image planes to the same focal position and simultaneously acquire information at 6 spectral bands. For whole-slide phase imaging, we acquire images at 3 focal positions simultaneously and use the transport-of-intensity equation to recover the phase information. We also provide an open-source design to further increase the number of channels from 6 to 15. The reported platform provides a simple solution for multiplexed fluorescence imaging and multimodal WSI. Acquiring an instant focal stack without z-scanning may also enable fast 3-dimensional dynamic tracking of various biological samples.
Collapse
Affiliation(s)
- Jun Liao
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Zhe Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Zibang Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, China
| | - Zichao Bian
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Kaikai Guo
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Aparna Nambiar
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Yutong Jiang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Shaowei Jiang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Jingang Zhong
- Department of Optoelectronic Engineering, Jinan University, Guangzhou 510632, China
| | - Michael Choma
- Department of Radiology & Biomedical Imaging, Biomedical Engineering, Applied Physics, and Pediatrics, Yale University, CT, 06520, USA
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| |
Collapse
|
23
|
Abrahamsson S, Blom H, Agostinho A, Jans DC, Jost A, Müller M, Nilsson L, Bernhem K, Lambert TJ, Heintzmann R, Brismar H. Multifocus structured illumination microscopy for fast volumetric super-resolution imaging. BIOMEDICAL OPTICS EXPRESS 2017; 8:4135-4140. [PMID: 28966852 PMCID: PMC5611928 DOI: 10.1364/boe.8.004135] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/04/2023]
Abstract
We here report for the first time the synergistic implementation of structured illumination microscopy (SIM) and multifocus microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in super-resolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.
Collapse
Affiliation(s)
- Sara Abrahamsson
- Lulu and Anthony Wang Laboratory for Neural Circuits and Behavior, The Rockefeller University New York, NY 10021, USA
| | - Hans Blom
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Ana Agostinho
- Department of Cell- and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel C. Jans
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Aurelie Jost
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Germany
- Leibniz-Institute of Photonic Technology, Jena, Germany
| | - Marcel Müller
- Biomolecular Photonics, Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Linnea Nilsson
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Kristoffer Bernhem
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| | - Talley J. Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rainer Heintzmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Germany
- Leibniz-Institute of Photonic Technology, Jena, Germany
| | - Hjalmar Brismar
- Department of Applied Physics, KTH (Royal Institute of Technology), Science for Life Laboratory, Stockholm, Sweden
| |
Collapse
|
24
|
Highly efficient multicolor multifocus microscopy by optimal design of diffraction binary gratings. Sci Rep 2017; 7:5284. [PMID: 28706216 PMCID: PMC5509674 DOI: 10.1038/s41598-017-05531-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/30/2017] [Indexed: 11/08/2022] Open
Abstract
Multifocus microscopy (MFM) allows sensitive and fast three-dimensional imaging. It relies on the efficient design of diffraction phase gratings yielding homogeneous intensities in desired diffraction orders. Such performances are however guaranteed only for a specific wavelength. Here, we discuss a novel approach for designing binary phase gratings with dual color properties and improved diffraction efficiency for MFM. We simulate binary diffraction gratings with tunable phase shifts to explore its best diffraction performances. We report the design and fabrication of a binary array generator of 3 × 3 equal-intensity diffraction orders with 74% efficiency, 95% uniformity and dual color capability. The multicolor properties of this new design are highlighted by two-color MFM imaging. Finally, we discuss the basics of extending this approach to a variety of diffraction pattern designs.
Collapse
|
25
|
von Diezmann A, Shechtman Y, Moerner WE. Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking. Chem Rev 2017; 117:7244-7275. [PMID: 28151646 PMCID: PMC5471132 DOI: 10.1021/acs.chemrev.6b00629] [Citation(s) in RCA: 252] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information on single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems.
Collapse
Affiliation(s)
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| |
Collapse
|
26
|
Dean KM, Roudot P, Welf ES, Pohlkamp T, Garrelts G, Herz J, Fiolka R. Imaging Subcellular Dynamics with Fast and Light-Efficient Volumetrically Parallelized Microscopy. OPTICA 2017; 4:263-271. [PMID: 28944279 PMCID: PMC5609504 DOI: 10.1364/optica.4.000263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In fluorescence microscopy, the serial acquisition of 2D images to form a 3D volume limits the maximum imaging speed. This is particularly evident when imaging adherent cells in a light-sheet fluorescence microscopy format, as their elongated morphologies require ~200 image planes per image volume. Here, by illuminating the specimen with three light-sheets, each independently detected, we present a light-efficient, crosstalk free, and volumetrically parallelized 3D microscopy technique that is optimized for high-speed (up to 14 Hz) subcellular (300 nm lateral, 600 nm axial resolution) imaging of adherent cells. We demonstrate 3D imaging of intracellular processes, including cytoskeletal dynamics in single cell migration and collective wound healing for 1500 and 1000 time points, respectively. Further, we capture rapid biological processes, including trafficking of early endosomes with velocities exceeding 10 microns per second and calcium signaling in primary neurons.
Collapse
Affiliation(s)
- Kevin M. Dean
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Lyda Hill Department of Bioinformatics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Philippe Roudot
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Lyda Hill Department of Bioinformatics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Erik S. Welf
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Lyda Hill Department of Bioinformatics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Theresa Pohlkamp
- Department of Molecular Genetics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Gerard Garrelts
- Coleman Technologies. 5131 West Chester Pike, Newtown Square, Pennsylvania, United States of America
| | - Joachim Herz
- Department of Molecular Genetics. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
| | - Reto Fiolka
- Department of Cell Biology. UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas, United States of America
- Corresponding author:
| |
Collapse
|
27
|
Oudjedi L, Fiche JB, Abrahamsson S, Mazenq L, Lecestre A, Calmon PF, Cerf A, Nöllmann M. Astigmatic multifocus microscopy enables deep 3D super-resolved imaging. BIOMEDICAL OPTICS EXPRESS 2016; 7:2163-73. [PMID: 27375935 PMCID: PMC4918573 DOI: 10.1364/boe.7.002163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 05/15/2023]
Abstract
We have developed a 3D super-resolution microscopy method that enables deep imaging in cells. This technique relies on the effective combination of multifocus microscopy and astigmatic 3D single-molecule localization microscopy. We describe the optical system and the fabrication process of its key element, the multifocus grating. Then, two strategies for localizing emitters with our imaging method are presented and compared with a previously described deep 3D localization algorithm. Finally, we demonstrate the performance of the method by imaging the nuclear envelope of eukaryotic cells reaching a depth of field of ~4µm.
Collapse
Affiliation(s)
- Laura Oudjedi
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Sara Abrahamsson
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Mazenq
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aurélie Lecestre
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Pierre-François Calmon
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Aline Cerf
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400 Toulouse, France
- Université de Toulouse, LAAS, F-31031 Toulouse, France
| | - Marcelo Nöllmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| |
Collapse
|
28
|
Davanco M, Yu L, Chen L, Luciani V, Liddle JA. Assessing fabrication tolerances for a multilevel 2D binary grating for 3D multifocus microscopy. OPTICS EXPRESS 2016; 24:9224-9236. [PMID: 27137539 DOI: 10.1364/oe.24.009224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We perform a comprehensive theoretical assessment of fabrication tolerances for a 2D eight-level binary phase grating that is the central element of a multi-focal plane 3D microscopy apparatus. The fabrication process encompasses a sequence of aligned lithography and etching steps with stringent requirements on layer-to-layer overlay, etch depth and etched sidewall slope, which we show are nonetheless achievable with state-of-the-art optical lithography and etching tools. We also perform broadband spectroscopic diffraction pattern measurements on a fabricated grating, and show how such measurements can be valuable in determining small fabrication errors in diffractive optical elements.
Collapse
|
29
|
Balram KC, Westly DA, Davanço M, Grutter KE, Li Q, Michels T, Ray CH, Yu L, Kasica RJ, Wallin CB, Gilbert IJ, Bryce BA, Simelgor G, Topolancik J, Lobontiu N, Liu Y, Neuzil P, Svatos V, Dill KA, Bertrand NA, Metzler MG, Lopez G, Czaplewski DA, Ocola L, Srinivasan KA, Stavis SM, Aksyuk VA, Liddle JA, Krylov S, Ilic BR. The Nanolithography Toolbox. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2016; 121:464-475. [PMID: 34434635 PMCID: PMC7339749 DOI: 10.6028/jres.121.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
This article introduces in archival form the Nanolithography Toolbox, a platform-independent software package for scripted lithography pattern layout generation. The Center for Nanoscale Science and Technology (CNST) at the National Institute of Standards and Technology (NIST) developed the Nanolithography Toolbox to help users of the CNST NanoFab design devices with complex curves and aggressive critical dimensions. Using parameterized shapes as building blocks, the Nanolithography Toolbox allows users to rapidly design and layout nanoscale devices of arbitrary complexity through scripting and programming. The Toolbox offers many parameterized shapes, including structure libraries for micro- and nanoelectromechanical systems (MEMS and NEMS) and nanophotonic devices. Furthermore, the Toolbox allows users to precisely define the number of vertices for each shape or create vectorized shapes using Bezier curves. Parameterized control allows users to design smooth curves with complex shapes. The Toolbox is applicable to a broad range of design tasks in the fabrication of microscale and nanoscale devices.
Collapse
Affiliation(s)
- Krishna C Balram
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
- University of Maryland, Maryland NanoCenter, College Park, MD 20740 USA
| | - Daron A Westly
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Marcelo Davanço
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Karen E Grutter
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Qing Li
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
- University of Maryland, Maryland NanoCenter, College Park, MD 20740 USA
| | - Thomas Michels
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Christopher H Ray
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Liya Yu
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Richard J Kasica
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Christopher B Wallin
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
- University of Maryland, Maryland NanoCenter, College Park, MD 20740 USA
| | - Ian J Gilbert
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
- University of Maryland, Maryland NanoCenter, College Park, MD 20740 USA
| | | | | | | | - Nicolae Lobontiu
- University of Alaska, Mechanical Engineering, Anchorage, AK 99508 USA
| | - Yuxiang Liu
- Worcester Polytechnic Institute, Mechanical Engineering, Worcester, MA 01609 USA
| | - Pavel Neuzil
- Brno University of Technology (BUT), Central European Institute of Technology (CEITEC), Technicka 3058/10, CZ-616 00 Brno, Czech Republic
- Department of Microsystems, Northwestern Polytechnical University, Xi'an, P.R. China
| | - Vojtech Svatos
- Brno University of Technology (BUT), Central European Institute of Technology (CEITEC), Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Kristen A Dill
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Neal A Bertrand
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Meredith G Metzler
- Quattrone Nanofabrication Facility, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Gerald Lopez
- Quattrone Nanofabrication Facility, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - David A Czaplewski
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Leonidas Ocola
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL 60439 USA
| | | | - Samuel M Stavis
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Vladimir A Aksyuk
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Slava Krylov
- Tel Aviv University, School of Mechanical Engineering, Ramat Aviv 69978 Tel Aviv, Israel
| | - B Robert Ilic
- National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| |
Collapse
|