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Shimada K, Azuma K, Inada Y, Nakagawa K. Optical design of spectral filtering system in sequentially timed all-optical mapping photography for enhancing temporal resolution. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2025; 96:053703. [PMID: 40331838 DOI: 10.1063/5.0240730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 04/23/2025] [Indexed: 05/08/2025]
Abstract
Ultrafast imaging is crucial for understanding phenomena in the femtosecond to nanosecond time domains. Among ultrafast imaging techniques, sequentially timed all-optical mapping photography utilizing spectral filtering enables single-shot acquisition of ultrafast images with high spatial resolution and high quality. However, conventional designs based on Fourier optics struggle to achieve high temporal resolution while maintaining high pixel resolution, because the spatial-spectral dependence in this configuration makes laser wavelengths within each frame broad, resulting in longer exposure times. Here we propose an optical design that minimizes the bandwidth of laser wavelengths within each frame to achieve high temporal resolution by collimating the beam incident on the diffractive optical element. Numerical analysis showed that increasing the magnification of the imaging system before the diffractive optical element sufficiently narrows the bandwidth within each frame compared to the conventional designs. We experimentally demonstrated the effectiveness of the proposed configuration, achieving a bandwidth of 0.9 nm and a wavelength interval of 2.1 nm. These spectral properties enabled imaging with a 1.4 ps frame interval and an exposure time of 0.8 ps, which is 40% of the exposure time in the conventional Fourier configuration with similar setup parameters. Furthermore, the proposed configuration maintained a high pixel resolution of 480 pixels × 480 pixels for each of the five frames and was successfully applied to visualize laser ablation of glass. This article presents a highly spatiotemporally resolved imaging method for the detailed analysis of ultrafast phenomena such as laser ablation, shockwaves, and electric discharges.
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Affiliation(s)
- Keitaro Shimada
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kohei Azuma
- Department of Precision Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuki Inada
- Electronics and Information Sciences, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama-City, Saitama 338-8570, Japan
| | - Keiichi Nakagawa
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Precision Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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2
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Tanaka R, Shimada K, Ishijima A, Kobayashi E, Mikami H, Sakuma I, Nakagawa K. Compact, widely tunable ultrashort burst pulse generator using four mirrors. OPTICS LETTERS 2025; 50:2906-2909. [PMID: 40310797 DOI: 10.1364/ol.557473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Accepted: 04/13/2025] [Indexed: 05/03/2025]
Abstract
Ultrashort burst laser pulses serve as powerful tools for precise laser processing, broadband ultrafast spectroscopy, and high-speed laser-scanning microscopy. However, the performance of conventional burst pulse generators is limited by constraints in the pulse time interval variability, pulse energy variability, pulse number variability, and overall system complexity. Here, we present a compact burst pulse generator that offers a broad tuning range for pulse time intervals, along with control over the number of pulses and pulse energies within the burst. It consists of four mirrors, two of which are parallel to each other, and outputs pulses that are equally spaced both temporally and spatially. We demonstrated the generation of a burst laser pulse by shaping a single ultrashort laser pulse into six pulses with time intervals ranging from femtoseconds to nanoseconds. The pulse time intervals and energies were consistent with theoretical results.
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3
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Sala F, Paiè P, Candeo A, Ceccarelli F, Osellame R, Bassi A, Bragheri F. Femtosecond laser microfabrication of a fully-integrated optofluidic device for 3D imaging flow cytometry. Sci Rep 2025; 15:11950. [PMID: 40200036 PMCID: PMC11978988 DOI: 10.1038/s41598-025-93118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 03/04/2025] [Indexed: 04/10/2025] Open
Abstract
In recent years imaging flow cytometry (IFC) is gaining increasing attention as it combines the characteristics of conventional flow cytometry with optical microscopy techniques, allowing for high-throughput, multi-parameter screening of single cell populations. In the field of biology, the always increasing demand for high content morphological and spatial information led to the development of systems for volumetric imaging. However, current 3D IFC systems are often limited by the incompatibility with available microfluidic devices or by instrumental complexity that might lead to optical misalignment or mechanical instabilities in day-by-day operation. To this end, here we demonstrate the importance of advancing the laser fabrication technique by reporting on a fully integrated optofluidic platform composed of a borosilicate glass chip encompassing reconfigurable integrated photonic circuits for patterned light generation, bonded to a fused silica glass chip incorporating cylindrical hollow lenses, for light-sheet illumination, perfectly aligned to a microchannel where the sample under investigation flows. The system is capable of high-resolution imaging flow cytometry by implementing structured light sheet microscopy in a heterogeneously integrated platform with unprecedented stability. All the components are realized by femtosecond laser irradiation followed by chemical etching. The extreme level of integration permitted by the advanced optimization of the laser fabrication technique allowed the reduction of the assembled components and the absence of moving parts, thus ensuring durable alignment as well as mechanical and thermal stability both in short and long-term operation of the device, for the automated fluorescence signal acquisition during the sample flow.
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Affiliation(s)
- Federico Sala
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
| | - Petra Paiè
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
| | - Alessia Candeo
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
| | - Francesco Ceccarelli
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
| | - Roberto Osellame
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
| | - Andrea Bassi
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy
| | - Francesca Bragheri
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Piazza Leonardo da Vinci, 32, Milan, 20133, Italy.
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Venugopal Menon N, Lee J, Tang T, Lim CT. Microfluidics for morpholomics and spatial omics applications. LAB ON A CHIP 2025; 25:752-763. [PMID: 39865877 DOI: 10.1039/d4lc00869c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Creative designs, precise fluidic manipulation, and automation have supported the development of microfluidics for single-cell applications. Together with the advancements in detection technologies and artificial intelligence (AI), microfluidic-assisted platforms have been increasingly used for new modalities of single-cell investigations and in spatial omics applications. This review explores the use of microfluidic technologies for morpholomics and spatial omics with a focus on single-cell and tissue characterization. We emphasize how various fluid dynamic principles and unique design integrations enable highly precise fluid manipulation, enhancing sample handling in morpholomics. Additionally, we examine the use of microfluidics-assisted spatial barcoding with micrometer resolutions for the spatial profiling of tissue specimens. Finally, we discuss how microfluidics can serve as a bridge for integrating multiple unique fields in omics research and outline key challenges that these technologies may face in practical translation.
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Affiliation(s)
- Nishanth Venugopal Menon
- Mechanobiology Institute, National University of Singapore, Singapore, 117411 Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore
| | - Jeeyeon Lee
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore, 117599 Singapore
| | - Tao Tang
- Department of Biomedical Engineering, National University of Singapore, 117583, Singapore
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore, Singapore, 117411 Singapore
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore, 117599 Singapore
- Department of Biomedical Engineering, National University of Singapore, 117583, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore
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5
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Zhou J, Mei L, Yu M, Ma X, Hou D, Yin Z, Liu X, Ding Y, Yang K, Xiao R, Yuan X, Weng Y, Long M, Hu T, Hou J, Xu Y, Tao L, Mei S, Shen H, Yalikun Y, Zhou F, Wang L, Wang D, Liu S, Lei C. Imaging flow cytometry with a real-time throughput beyond 1,000,000 events per second. LIGHT, SCIENCE & APPLICATIONS 2025; 14:76. [PMID: 39924500 PMCID: PMC11808109 DOI: 10.1038/s41377-025-01754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 12/09/2024] [Accepted: 01/08/2025] [Indexed: 02/11/2025]
Abstract
Imaging flow cytometry (IFC) combines the imaging capabilities of microscopy with the high throughput of flow cytometry, offering a promising solution for high-precision and high-throughput cell analysis in fields such as biomedicine, green energy, and environmental monitoring. However, due to limitations in imaging framerate and real-time data processing, the real-time throughput of existing IFC systems has been restricted to approximately 1000-10,000 events per second (eps), which is insufficient for large-scale cell analysis. In this work, we demonstrate IFC with real-time throughput exceeding 1,000,000 eps by integrating optical time-stretch (OTS) imaging, microfluidic-based cell manipulation, and online image processing. Cells flowing at speeds up to 15 m/s are clearly imaged with a spatial resolution of 780 nm, and images of each individual cell are captured, stored, and analyzed. The capabilities and performance of our system are validated through the identification of malignancies in clinical colorectal samples. This work sets a new record for throughput in imaging flow cytometry, and we believe it has the potential to revolutionize cell analysis by enabling highly efficient, accurate, and intelligent measurement.
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Affiliation(s)
- Jiehua Zhou
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Liye Mei
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
- School of Computer Science, Hubei University of Technology, Wuhan, 430068, China
| | - Mingjie Yu
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiao Ma
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Dan Hou
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhuo Yin
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Xun Liu
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
- Division of Materials Science, Nara Institute of Science and Technology, Takayama-cho, 8916-5, Japan
| | - Yan Ding
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Kaining Yang
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Ruidong Xiao
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiandan Yuan
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
- School of Science, Hubei University of Technology, Wuhan, 430068, China
| | - Yueyun Weng
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengping Long
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
- Department of Pathology, Peking University Cancer Hospital, Beijing, 100142, China
| | - Taobo Hu
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
- Department of Breast Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jinxuan Hou
- Department of Thyroid and Breast Surgery, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yu Xu
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Liang Tao
- People's Hospital of Anshun City Guizhou Province, Anshun, 561000, China
| | - Sisi Mei
- People's Hospital of Anshun City Guizhou Province, Anshun, 561000, China
| | - Hui Shen
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yaxiaer Yalikun
- Division of Materials Science, Nara Institute of Science and Technology, Takayama-cho, 8916-5, Japan
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Liang Wang
- National Engineering Laboratory for Next Generation Internet Access System, School of Optics and Electronic Information, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Du Wang
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China.
| | - Sheng Liu
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China
| | - Cheng Lei
- The Institute of Technological Sciences, Wuhan University, Wuhan, 430072, China.
- Suzhou Institute of Wuhan University, Suzhou, 215000, China.
- Shenzhen Institute of Wuhan University, Shenzhen, 518057, China.
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Zhang J, Qiao W, Jin R, Li H, Gong H, Chen SC, Luo Q, Yuan J. Optical sectioning methods in three-dimensional bioimaging. LIGHT, SCIENCE & APPLICATIONS 2025; 14:11. [PMID: 39741128 DOI: 10.1038/s41377-024-01677-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 09/24/2024] [Accepted: 10/28/2024] [Indexed: 01/02/2025]
Abstract
In recent advancements in life sciences, optical microscopy has played a crucial role in acquiring high-quality three-dimensional structural and functional information. However, the quality of 3D images is often compromised due to the intense scattering effect in biological tissues, compounded by several issues such as limited spatiotemporal resolution, low signal-to-noise ratio, inadequate depth of penetration, and high phototoxicity. Although various optical sectioning techniques have been developed to address these challenges, each method adheres to distinct imaging principles for specific applications. As a result, the effective selection of suitable optical sectioning techniques across diverse imaging scenarios has become crucial yet challenging. This paper comprehensively overviews existing optical sectioning techniques and selection guidance under different imaging scenarios. Specifically, we categorize the microscope design based on the spatial relationship between the illumination and detection axis, i.e., on-axis and off-axis. This classification provides a unique perspective to compare the implementation and performances of various optical sectioning approaches. Lastly, we integrate selected optical sectioning methods on a custom-built off-axis imaging system and present a unique perspective for the future development of optical sectioning techniques.
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Affiliation(s)
- Jing Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Innovation Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Qiao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Innovation Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Jin
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Innovation Institute, Huazhong University of Science and Technology, Wuhan, China
| | - Hongjin Li
- Hong Kong Center for Cerebro-Cardiovascular Health Engineering, N.T, Hong Kong, China
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Innovation Institute, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, Suzhou, China
| | - Shih-Chi Chen
- Hong Kong Center for Cerebro-Cardiovascular Health Engineering, N.T, Hong Kong, China.
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.
- MoE Key Laboratory for Biomedical Photonics, Innovation Institute, Huazhong University of Science and Technology, Wuhan, China.
- HUST-Suzhou Institute for Brainsmatics, Suzhou, China.
- School of Biomedical Engineering, Hainan University, Haikou, China.
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.
- MoE Key Laboratory for Biomedical Photonics, Innovation Institute, Huazhong University of Science and Technology, Wuhan, China.
- HUST-Suzhou Institute for Brainsmatics, Suzhou, China.
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7
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Nguyen TN, Shalaby RA, Lee E, Kim SS, Ro Kim Y, Kim S, Je HS, Kwon HS, Chung E. Ultrafast optical imaging techniques for exploring rapid neuronal dynamics. NEUROPHOTONICS 2025; 12:S14608. [PMID: 40017464 PMCID: PMC11867703 DOI: 10.1117/1.nph.12.s1.s14608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Revised: 01/20/2025] [Accepted: 01/27/2025] [Indexed: 03/01/2025]
Abstract
Optical neuroimaging has significantly advanced our understanding of brain function, particularly through techniques such as two-photon microscopy, which captures three-dimensional brain structures with sub-cellular resolution. However, traditional methods struggle to record fast, complex neuronal interactions in real time, which are crucial for understanding brain networks and developing treatments for neurological diseases such as Alzheimer's, Parkinson's, and chronic pain. Recent advancements in ultrafast imaging technologies, including kilohertz two-photon microscopy, light field microscopy, and event-based imaging, are pushing the boundaries of temporal resolution in neuroimaging. These techniques enable the capture of rapid neural events with unprecedented speed and detail. This review examines the principles, applications, and limitations of these technologies, highlighting their potential to revolutionize neuroimaging and improve the diagnose and treatment of neurological disorders. Despite challenges such as photodamage risks and spatial resolution trade-offs, integrating these approaches promises to enhance our understanding of brain function and drive future breakthroughs in neuroscience and medicine. Continued interdisciplinary collaboration is essential to fully leverage these innovations for advancements in both basic and clinical neuroscience.
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Affiliation(s)
- Tien Nhat Nguyen
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Reham A. Shalaby
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Eunbin Lee
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Sang Seong Kim
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Young Ro Kim
- Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts United States
- Harvard Medical School, Department of Radiology, Boston, Massachusetts, United States
| | - Seonghoon Kim
- Tsinghua University, Institute for Brain and Cognitive Sciences, Beijing, China
- Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou, China
| | - Hyunsoo Shawn Je
- Duke-NUS Medical School, Program in Neuroscience and Behavioral Disorders, Singapore
| | - Hyuk-Sang Kwon
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Euiheon Chung
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
- Gwangju Institute of Science and Technology, AI Graduate School, Gwangju, Republic of Korea
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8
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Yao J, Guo Z, Qi D, Xu S, Lin W, Cheng L, Jin C, He Y, Xu N, Pan Z, Mao J, Yao Y, Deng L, Shen Y, Zhao H, Sun Z, Zhang S. Discrete Illumination-Based Compressed Ultrafast Photography for High-Fidelity Dynamic Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2403854. [PMID: 39120051 PMCID: PMC11538675 DOI: 10.1002/advs.202403854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/03/2024] [Indexed: 08/10/2024]
Abstract
Compressed ultrafast photography (CUP) can capture irreversible or difficult-to-repeat dynamic scenes at the imaging speed of more than one billion frames per second, which is obtained by compressive sensing-based image reconstruction from a compressed 2D image through the discretization of detector pixels. However, an excessively high data compression ratio in CUP severely degrades the image reconstruction quality, thereby restricting its ability to observe ultrafast dynamic scenes with complex spatial structures. To address this issue, a discrete illumination-based CUP (DI-CUP) with high fidelity is reported. In DI-CUP, the dynamic scenes are loaded into an ultrashort laser pulse train with controllable sub-pulse number and time interval, thus the data compression ratio, as well as the overlap between adjacent frames, is greatly decreased and flexibly controlled through the discretization of dynamic scenes based on laser pulse train illumination, and high-fidelity image reconstruction can be realized within the same observation time window. Furthermore, the superior performance of DI-CUP is verified by observing femtosecond laser-induced ablation dynamics and plasma channel evolution, which are hardly resolved in the spatial structures using conventional CUP. It is anticipated that DI-CUP will be widely and dependably used in the real-time observations of various ultrafast dynamics.
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Affiliation(s)
- Jiali Yao
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
- Present address:
College of ScienceShanghai Institute of TechnologyShanghai201418China
| | - Zihan Guo
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Dalong Qi
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Shiyu Xu
- North Night Vision Technology Co. LtdKunming650217China
| | - Wenzhang Lin
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Long Cheng
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Chengzhi Jin
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Yu He
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Ning Xu
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Zhen Pan
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Jiayi Mao
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Yunhua Yao
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Lianzhong Deng
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Yuecheng Shen
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Heng Zhao
- North Night Vision Technology Co. LtdKunming650217China
| | - Zhenrong Sun
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
| | - Shian Zhang
- State Key Laboratory of Precision SpectroscopySchool of Physics and Electronic ScienceEast China Normal UniversityShanghai200241China
- Collaborative Innovation Center of Extreme OpticsShanxi UniversityTaiyuan030006China
- Joint Research Center of Light Manipulation Science and Photonic Integrated Chip of East China Normal University and Shandong Normal UniversityEast China Normal UniversityShanghai200241China
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9
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Lo MCK, Siu DMD, Lee KCM, Wong JSJ, Yeung MCF, Hsin MKY, Ho JCM, Tsia KK. Information-Distilled Generative Label-Free Morphological Profiling Encodes Cellular Heterogeneity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307591. [PMID: 38864546 PMCID: PMC11304271 DOI: 10.1002/advs.202307591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/17/2024] [Indexed: 06/13/2024]
Abstract
Image-based cytometry faces challenges due to technical variations arising from different experimental batches and conditions, such as differences in instrument configurations or image acquisition protocols, impeding genuine biological interpretation of cell morphology. Existing solutions, often necessitating extensive pre-existing data knowledge or control samples across batches, have proved limited, especially with complex cell image data. To overcome this, "Cyto-Morphology Adversarial Distillation" (CytoMAD), a self-supervised multi-task learning strategy that distills biologically relevant cellular morphological information from batch variations, is introduced to enable integrated analysis across multiple data batches without complex data assumptions or extensive manual annotation. Unique to CytoMAD is its "morphology distillation", symbiotically paired with deep-learning image-contrast translation-offering additional interpretable insights into label-free cell morphology. The versatile efficacy of CytoMAD is demonstrated in augmenting the power of biophysical imaging cytometry. It allows integrated label-free classification of human lung cancer cell types and accurately recapitulates their progressive drug responses, even when trained without the drug concentration information. CytoMAD also allows joint analysis of tumor biophysical cellular heterogeneity, linked to epithelial-mesenchymal plasticity, that standard fluorescence markers overlook. CytoMAD can substantiate the wide adoption of biophysical cytometry for cost-effective diagnosis and screening.
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Affiliation(s)
- Michelle C. K. Lo
- Department of Electrical and Electronic EngineeringThe University of Hong KongHong Kong000000Hong Kong
- Advanced Biomedical Instrumentation CentreHong Kong Science Park, New TerritoriesHong Kong000000Hong Kong
| | - Dickson M. D. Siu
- Department of Electrical and Electronic EngineeringThe University of Hong KongHong Kong000000Hong Kong
- Advanced Biomedical Instrumentation CentreHong Kong Science Park, New TerritoriesHong Kong000000Hong Kong
| | - Kelvin C. M. Lee
- Department of Electrical and Electronic EngineeringThe University of Hong KongHong Kong000000Hong Kong
- Advanced Biomedical Instrumentation CentreHong Kong Science Park, New TerritoriesHong Kong000000Hong Kong
| | - Justin S. J. Wong
- Conzeb LimitedHong Kong Science Park, New TerritoriesHong Kong000000Hong Kong
| | - Maximus C. F. Yeung
- Department of Pathology, Li Ka Shing Faculty of MedicineThe University of Hong KongPokfulam RoadHong Kong000000Hong Kong
| | - Michael K. Y. Hsin
- Department of Surgery, Li Ka Shing Faculty of MedicineThe University of Hong KongPokfulam RoadHong Kong000000Hong Kong
| | - James C. M. Ho
- Department of Medicine, Li Ka Shing Faculty of MedicineThe University of Hong KongPokfulam RoadHong Kong000000Hong Kong
| | - Kevin K. Tsia
- Department of Electrical and Electronic EngineeringThe University of Hong KongHong Kong000000Hong Kong
- Advanced Biomedical Instrumentation CentreHong Kong Science Park, New TerritoriesHong Kong000000Hong Kong
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10
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Kawai A, Horisaki R, Ideguchi T. Compressive time-stretch spectroscopy with pulse-by-pulse intensity modulation. OPTICS LETTERS 2024; 49:3468-3471. [PMID: 38875647 DOI: 10.1364/ol.522440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/20/2024] [Indexed: 06/16/2024]
Abstract
The photonic time-stretch technique is a single-pulse broadband spectroscopy method enabled by dispersive Fourier transformation. This technique enables an extremely high spectrum acquisition rate, determined by the repetition rates of femtosecond mode-locked lasers, which are typically in the range of tens of MHz. However, achieving this high spectrum acquisition rate necessitates a compromise in either the spectral resolution or the spectral bandwidth to prevent overlaps between adjacent stretched pulses. In this study, we introduce a method that overcomes this limitation by incorporating compressive sensing with pulse-by-pulse amplitude modulation, enabling the decomposition of excessively stretched, overlapping pulses. Through numerical evaluations of optofluidic microparticle flow analysis and high-speed gas-phase molecular spectroscopy, we demonstrate the efficacy of our noise-resilient algorithm, showcasing a severalfold increase in the spectrum acquisition rate without compromising resolution and bandwidth.
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11
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Mandracchia B, Zheng C, Rajendran S, Liu W, Forghani P, Xu C, Jia S. High-speed optical imaging with sCMOS pixel reassignment. Nat Commun 2024; 15:4598. [PMID: 38816394 PMCID: PMC11139943 DOI: 10.1038/s41467-024-48987-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Fluorescence microscopy has undergone rapid advancements, offering unprecedented visualization of biological events and shedding light on the intricate mechanisms governing living organisms. However, the exploration of rapid biological dynamics still poses a significant challenge due to the limitations of current digital camera architectures and the inherent compromise between imaging speed and other capabilities. Here, we introduce sHAPR, a high-speed acquisition technique that leverages the operating principles of sCMOS cameras to capture fast cellular and subcellular processes. sHAPR harnesses custom fiber optics to convert microscopy images into one-dimensional recordings, enabling acquisition at the maximum camera readout rate, typically between 25 and 250 kHz. We have demonstrated the utility of sHAPR with a variety of phantom and dynamic systems, including high-throughput flow cytometry, cardiomyocyte contraction, and neuronal calcium waves, using a standard epi-fluorescence microscope. sHAPR is highly adaptable and can be integrated into existing microscopy systems without requiring extensive platform modifications. This method pushes the boundaries of current fluorescence imaging capabilities, opening up new avenues for investigating high-speed biological phenomena.
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Affiliation(s)
- Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- E.T.S.I. Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Suraj Rajendran
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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12
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Lu W, Zhu Z, Willenberg B, Pupeikis J, Phillips CR, Keller U, Chen SC. Scan-less 3D microscopy based on spatiotemporal encoding on a single-cavity dual-comb laser. OPTICS LETTERS 2024; 49:1766-1769. [PMID: 38560858 DOI: 10.1364/ol.507661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Dual-comb microscopy enables high-speed and high-precision optical sampling by simultaneously extracting both amplitude and phase information from the interference signals with frequency division multiplexing. In this Letter, we introduce a spatiotemporal encoding approach for dual-comb microscopy that overcomes previous limitations such as mechanical scanning, low sampling efficiency, and system complexity. By employing free-space angular-chirp-enhanced delay (FACED) and a low-noise single-cavity dual-comb laser, we achieve scan-less 3D imaging with nanometer precision and a 3D distance-imaging rate of 330 Hz, restricted only by the repetition rate difference of the dual-comb laser. Specifically, the FACED unit linearly arranges the laser beam into an array. A grating subsequently disperses this array transversely into lines, facilitating ultrafast spectroscopic applications that are 1-2 orders of magnitude quicker than traditional dual-comb methods. This spatiotemporal encoding also eases the stringent conditions on various dual-comb laser parameters, such as repetition rates, coherence, and stability. Through carefully designed experiments, we demonstrate that our scan-less system can measure 3D profiles of microfabricated structures at a rate of 7 million pixels per second. Our method significantly enhances measurement speed while maintaining high precision, using a compact light source. This advancement has the potential for broad applications, including phase imaging, surface topography, distance ranging, and spectroscopy.
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13
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Kume D, Kozawa Y, Kawakami R, Ishii H, Watakabe Y, Uesugi Y, Imamura T, Nemoto T, Sato S. Graded arc beam in light needle microscopy for axially resolved, rapid volumetric imaging without nonlinear processes. OPTICS EXPRESS 2024; 32:7289-7306. [PMID: 38439413 DOI: 10.1364/oe.516437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
High-speed three-dimensional (3D) imaging is essential for revealing the structure and functions of biological specimens. Confocal laser scanning microscopy has been widely employed for this purpose. However, it requires a time-consuming image-stacking procedure. As a solution, we previously developed light needle microscopy using a Bessel beam with a wavefront-engineered approach [Biomed. Opt. Express13, 1702 (2022)10.1364/BOE.449329]. However, this method applies only to multiphoton excitation microscopy because of the requirement to reduce the sidelobes of the Bessel beam. Here, we introduce a beam that produces a needle spot while eluding the intractable artifacts due to the sidelobes. This beam can be adopted even in one-photon excitation fluorescence 3D imaging. The proposed method can achieve real-time, rapid 3D observation of 200-nm particles in water at a rate of over 50 volumes per second. In addition, fine structures, such as the spines of neurons in fixed mouse brain tissue, can be visualized in 3D from a single raster scan of the needle spot. The proposed method can be applied to various modalities in biological imaging, enabling rapid 3D image acquisition.
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14
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Saiki T, Shimada K, Ishijima A, Song H, Qi X, Okamoto Y, Mizushima A, Mita Y, Hosobata T, Takeda M, Morita S, Kushibiki K, Ozaki S, Motohara K, Yamagata Y, Tsukamoto A, Kannari F, Sakuma I, Inada Y, Nakagawa K. Single-shot optical imaging with spectrum circuit bridging timescales in high-speed photography. SCIENCE ADVANCES 2023; 9:eadj8608. [PMID: 38117881 PMCID: PMC10732534 DOI: 10.1126/sciadv.adj8608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Single-shot optical imaging based on ultrashort lasers has revealed nonrepetitive processes in subnanosecond timescales beyond the recording range of conventional high-speed cameras. However, nanosecond photography without sacrificing short exposure time and image quality is still missing because of the gap in recordable timescales between ultrafast optical imaging and high-speed electronic cameras. Here, we demonstrate nanosecond photography and ultrawide time-range high-speed photography using a spectrum circuit that produces interval-tunable pulse trains while keeping short pulse durations. We capture a shock wave propagating through a biological cell with a 1.5-ns frame interval and 44-ps exposure time while suppressing image blur. Furthermore, we observe femtosecond laser processing over multiple timescales (25-ps, 2.0-ns, and 1-ms frame intervals), showing that the plasma generated at the picosecond timescale affects subsequent shock wave formation at the nanosecond timescale. Our technique contributes to accumulating data of various fast processes for analysis and to analyzing multi-timescale phenomena as a series of physical processes.
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Affiliation(s)
- Takao Saiki
- Department of Precision Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Keitaro Shimada
- Department of Bioengineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Ayumu Ishijima
- PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Medical Device Development and Regulation Research Center, The University of Tokyo, Tokyo 113-8656, Japan
| | - Hang Song
- Department of Bioengineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Xinyi Qi
- Department of Bioengineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yuki Okamoto
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, Ibaraki 305-8564, Japan
| | - Ayako Mizushima
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yoshio Mita
- Department of Electrical and Electronic Engineering, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takuya Hosobata
- RIKEN Centre for Advanced Photonics (RAP), RIKEN, Saitama 351-0198, Japan
| | - Masahiro Takeda
- RIKEN Centre for Advanced Photonics (RAP), RIKEN, Saitama 351-0198, Japan
| | - Shinya Morita
- School of Engineering, Tokyo Denki University, Tokyo 120-8551, Japan
| | - Kosuke Kushibiki
- Institute of Astronomy, The University of Tokyo, Tokyo 181-0015, Japan
| | - Shinobu Ozaki
- National Astronomical Observatory of Japan (NAOJ), Tokyo 181-8588, Japan
| | - Kentaro Motohara
- Institute of Astronomy, The University of Tokyo, Tokyo 181-0015, Japan
- National Astronomical Observatory of Japan (NAOJ), Tokyo 181-8588, Japan
| | - Yutaka Yamagata
- RIKEN Centre for Advanced Photonics (RAP), RIKEN, Saitama 351-0198, Japan
| | - Akira Tsukamoto
- Department of Applied Physics, National Defense Academy of Japan, Kanagawa 239-8686, Japan
| | - Fumihiko Kannari
- Department of Electronics and Electrical Engineering, Keio University, Kanagawa 223-8522, Japan
| | - Ichiro Sakuma
- Department of Precision Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Department of Bioengineering, The University of Tokyo, Tokyo 113-8656, Japan
- Medical Device Development and Regulation Research Center, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yuki Inada
- PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Electronics and Information Sciences, Saitama University, Saitama 338-8570, Japan
| | - Keiichi Nakagawa
- Department of Precision Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Department of Bioengineering, The University of Tokyo, Tokyo 113-8656, Japan
- PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
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15
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Park J, Bai B, Ryu D, Liu T, Lee C, Luo Y, Lee MJ, Huang L, Shin J, Zhang Y, Ryu D, Li Y, Kim G, Min HS, Ozcan A, Park Y. Artificial intelligence-enabled quantitative phase imaging methods for life sciences. Nat Methods 2023; 20:1645-1660. [PMID: 37872244 DOI: 10.1038/s41592-023-02041-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/11/2023] [Indexed: 10/25/2023]
Abstract
Quantitative phase imaging, integrated with artificial intelligence, allows for the rapid and label-free investigation of the physiology and pathology of biological systems. This review presents the principles of various two-dimensional and three-dimensional label-free phase imaging techniques that exploit refractive index as an intrinsic optical imaging contrast. In particular, we discuss artificial intelligence-based analysis methodologies for biomedical studies including image enhancement, segmentation of cellular or subcellular structures, classification of types of biological samples and image translation to furnish subcellular and histochemical information from label-free phase images. We also discuss the advantages and challenges of artificial intelligence-enabled quantitative phase imaging analyses, summarize recent notable applications in the life sciences, and cover the potential of this field for basic and industrial research in the life sciences.
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Affiliation(s)
- Juyeon Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | - Bijie Bai
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - DongHun Ryu
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tairan Liu
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chungha Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | - Yi Luo
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mahn Jae Lee
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeongwon Shin
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Yijie Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Yuzhu Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Geon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | | | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA.
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA, USA.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea.
- Tomocube, Daejeon, Republic of Korea.
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16
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Pozzi P, Candeo A, Paiè P, Bragheri F, Bassi A. Artificial intelligence in imaging flow cytometry. FRONTIERS IN BIOINFORMATICS 2023; 3:1229052. [PMID: 37877042 PMCID: PMC10593470 DOI: 10.3389/fbinf.2023.1229052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Affiliation(s)
- Paolo Pozzi
- Department of Physics, Politecnico di Milano, Milano, Italy
| | - Alessia Candeo
- Department of Physics, Politecnico di Milano, Milano, Italy
| | - Petra Paiè
- Department of Physics, Politecnico di Milano, Milano, Italy
| | - Francesca Bragheri
- Institute for Photonics and Nanotechnologies, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Andrea Bassi
- Department of Physics, Politecnico di Milano, Milano, Italy
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17
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Hayashi M, Ohnuki S, Tsai Y, Kondo N, Zhou Y, Zhang H, Ishii NT, Ding T, Herbig M, Isozaki A, Ohya Y, Goda K. Is AI essential? Examining the need for deep learning in image-activated sorting of Saccharomyces cerevisiae. LAB ON A CHIP 2023; 23:4232-4244. [PMID: 37650583 DOI: 10.1039/d3lc00556a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Artificial intelligence (AI) has become a focal point across a multitude of societal sectors, with science not being an exception. Particularly in the life sciences, imaging flow cytometry has increasingly integrated AI for automated management and categorization of extensive cell image data. However, the necessity of AI over traditional classification methods when extending imaging flow cytometry to include cell sorting remains uncertain, primarily due to the time constraints between image acquisition and sorting actuation. AI-enabled image-activated cell sorting (IACS) methods remain substantially limited, even as recent advancements in IACS have found success while largely relying on traditional feature gating strategies. Here we assess the necessity of AI for image classification in IACS by contrasting the performance of feature gating, classical machine learning (ML), and deep learning (DL) with convolutional neural networks (CNNs) in the differentiation of Saccharomyces cerevisiae mutant images. We show that classical ML could only yield a 2.8-fold enhancement in target enrichment capability, albeit at the cost of a 13.7-fold increase in processing time. Conversely, a CNN could offer an 11.0-fold improvement in enrichment capability at an 11.5-fold increase in processing time. We further executed IACS on mixed mutant populations and quantified target strain enrichment via downstream DNA sequencing to substantiate the applicability of DL for the proposed study. Our findings validate the feasibility and value of employing DL in IACS for morphology-based genetic screening of S. cerevisiae, encouraging its incorporation in future advancements of similar technologies.
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Affiliation(s)
- Mika Hayashi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Yating Tsai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Yuqi Zhou
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Hongqian Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Natsumi Tiffany Ishii
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Tianben Ding
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Maik Herbig
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Mechanical Engineering, College of Science and Engineering, Ritsumeikan University, Shiga 525-8577, Japan.
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan 430072, China
- CYBO, Tokyo 135-0064, Japan
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18
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Yang Q, Wang Y, Yu C, Wang F, Guo M, Zhang L, Shao C, Wang M, Shen H, Qi Y, Hu L. High ytterbium concentration Yb/Al/P/Ce co-doped silica fiber for 1-µm ultra-short cavity fiber laser application. OPTICS EXPRESS 2023; 31:33741-33752. [PMID: 37859147 DOI: 10.1364/oe.500051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/02/2023] [Indexed: 10/21/2023]
Abstract
We demonstrate a high ytterbium concentration Yb/Al/P/Ce co-doped silica fiber by conventional modified chemical vapor deposition (MCVD) technology and solution doping process. The fiber has a Yb concentration of about 2.5 wt%, and the corresponding core absorption coefficient is measured to be ∼1400 dB/m at 976 nm. The gain coefficient was measured to be approximately 1.0 dB/cm. It is found that the Yb/Al/P/Ce co-doped silica shows a lower photodarkening-induced equilibrium loss of 52 dB/m at 633 nm than the Yb/Al/P co-doped silica fiber of 117 dB/m. Using the heavily Yb3+-doped silica fiber, a compact and robust ultrashort cavity single-frequency fiber laser was achieved with a maximum output power of 75 mW and a linewidth of 14 kHz. Furthermore, a compact passively mode-locked fiber laser (MLFL) with a repetition rate of 1.23 GHz was also proposed using our developed Yb-doped fiber. The laser properties of the proposed lasers were systematically investigated, demonstrating the superior performance of this fiber in terms of photodarkening resistance and ultrashort-cavity laser application. Furthermore, utilizing an all-fiber structure based on silica-based fiber offers the significant advantage of high stability and reliability.
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19
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Guo Y, Wang L, Luo Z, Zhu Y, Gao X, Weng X, Wang Y, Yan W, Qu J. Dynamic Volumetric Imaging of Mouse Cerebral Blood Vessels In Vivo with an Ultralong Anti-Diffracting Beam. Molecules 2023; 28:4936. [PMID: 37446598 DOI: 10.3390/molecules28134936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Volumetric imaging of a mouse brain in vivo with one-photon and two-photon ultralong anti-diffracting (UAD) beam illumination was performed. The three-dimensional (3D) structure of blood vessels in the mouse brain were mapped to a two-dimensional (2D) image. The speed of volumetric imaging was significantly improved due to the long focal length of the UAD beam. Comparing one-photon and two-photon UAD beam volumetric imaging, we found that the imaging depth of two-photon volumetric imaging (80 μm) is better than that of one-photon volumetric imaging (60 μm), and the signal-to-background ratio (SBR) of two-photon volumetric imaging is two times that of one-photon volumetric imaging. Therefore, we used two-photon UAD volumetric imaging to perform dynamic volumetric imaging of mouse brain blood vessels in vivo, and obtained the blood flow velocity.
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Affiliation(s)
- Yong Guo
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Luwei Wang
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Ziyi Luo
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Yinru Zhu
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Xinwei Gao
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Xiaoyu Weng
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Yiping Wang
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Wei Yan
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
| | - Junle Qu
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, China
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20
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Whiteley I, Song C, Howe GA, Knöpfel T, Rowlands CJ. DIRECT, a low-cost system for high-speed, low-noise imaging of fluorescent bio-samples. BIOMEDICAL OPTICS EXPRESS 2023; 14:2565-2575. [PMID: 37342684 PMCID: PMC10278627 DOI: 10.1364/boe.486507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 06/23/2023]
Abstract
A targeted imaging system has been developed for applications requiring recording from stationary samples at high spatiotemporal resolutions. It works by illuminating regions of interest in rapid sequence, and recording the signal from the whole field of view onto a single photodetector. It can be implemented at low cost on an existing microscope without compromising existing functionality. The system is characterized in terms of speed, spatial resolution, and tissue penetration depth, before being used to record individual action potentials from ASAP-3 expressing neurons in an ex vivo mouse brain slice preparation.
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Affiliation(s)
- Isabell Whiteley
- Department of Bioengineering, Imperial College London, London, UK
- Centre for Neurotechnology, Imperial College London, London, UK
| | - Chenchen Song
- Department of Brain Sciences, Imperial College London, London, UK
| | - Glenn A. Howe
- Department of Bioengineering, Imperial College London, London, UK
| | - Thomas Knöpfel
- Centre for Neurotechnology, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
- Department of Physics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Christopher J. Rowlands
- Department of Bioengineering, Imperial College London, London, UK
- Centre for Neurotechnology, Imperial College London, London, UK
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21
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Zhang T, Guo B, Jiang L, Zhu T, Hua Y, Zhan N, Yao H. Single-Shot Multi-Frame Imaging of Femtosecond Laser-Induced Plasma Propagation. MATERIALS (BASEL, SWITZERLAND) 2023; 16:3264. [PMID: 37110099 PMCID: PMC10142422 DOI: 10.3390/ma16083264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
Single-shot ultrafast multi-frame imaging technology plays a crucial role in the observation of laser-induced plasma. However, there are many challenges in the application of laser processing, such as technology fusion and imaging stability. To provide a stable and reliable observation method, we propose an ultrafast single-shot multi-frame imaging technology based on wavelength polarization multiplexing. Through the frequency doubling and birefringence effects of the BBO and the quartz crystal, the 800 nm femtosecond laser pulse was frequency doubled to 400 nm, and a sequence of probe sub-pulses with dual-wavelength and different polarization was generated. The coaxial propagation and framing imaging of multi-frequency pulses provided stable imaging quality and clarity, as well as high temporal/spatial resolution (200 fs and 228 lp/mm). In the experiments involving femtosecond laser-induced plasma propagation, the probe sub-pulses measured their time intervals by capturing the same results. Specifically, the measured time intervals were 200 fs between the same color pulses and 1 ps between the adjacent different. Finally, based on the obtained system time resolution, we observed and revealed the evolution mechanism of femtosecond laser-induced air plasma filaments, the multifilament propagation of femtosecond laser in fused silica, and the influence mechanism of air ionization on laser-induced shock waves.
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Affiliation(s)
- Tianyong Zhang
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China; (T.Z.); (B.G.); (T.Z.); (Y.H.); (N.Z.); (H.Y.)
| | - Baoshan Guo
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China; (T.Z.); (B.G.); (T.Z.); (Y.H.); (N.Z.); (H.Y.)
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314000, China
| | - Lan Jiang
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China; (T.Z.); (B.G.); (T.Z.); (Y.H.); (N.Z.); (H.Y.)
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314000, China
- Beijing Institute of Technology Chongqing Innovation Center, Chongqing 401120, China
| | - Tong Zhu
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China; (T.Z.); (B.G.); (T.Z.); (Y.H.); (N.Z.); (H.Y.)
| | - Yanhong Hua
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China; (T.Z.); (B.G.); (T.Z.); (Y.H.); (N.Z.); (H.Y.)
| | - Ningwei Zhan
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China; (T.Z.); (B.G.); (T.Z.); (Y.H.); (N.Z.); (H.Y.)
| | - Huan Yao
- Laser Micro/Nano Fabrication Laboratory, School of Mechanical Engineering, Beijing Institute of Technology, Beijing 100081, China; (T.Z.); (B.G.); (T.Z.); (Y.H.); (N.Z.); (H.Y.)
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22
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Tsai HF, Podder S, Chen PY. Microsystem Advances through Integration with Artificial Intelligence. MICROMACHINES 2023; 14:826. [PMID: 37421059 PMCID: PMC10141994 DOI: 10.3390/mi14040826] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 07/09/2023]
Abstract
Microfluidics is a rapidly growing discipline that involves studying and manipulating fluids at reduced length scale and volume, typically on the scale of micro- or nanoliters. Under the reduced length scale and larger surface-to-volume ratio, advantages of low reagent consumption, faster reaction kinetics, and more compact systems are evident in microfluidics. However, miniaturization of microfluidic chips and systems introduces challenges of stricter tolerances in designing and controlling them for interdisciplinary applications. Recent advances in artificial intelligence (AI) have brought innovation to microfluidics from design, simulation, automation, and optimization to bioanalysis and data analytics. In microfluidics, the Navier-Stokes equations, which are partial differential equations describing viscous fluid motion that in complete form are known to not have a general analytical solution, can be simplified and have fair performance through numerical approximation due to low inertia and laminar flow. Approximation using neural networks trained by rules of physical knowledge introduces a new possibility to predict the physicochemical nature. The combination of microfluidics and automation can produce large amounts of data, where features and patterns that are difficult to discern by a human can be extracted by machine learning. Therefore, integration with AI introduces the potential to revolutionize the microfluidic workflow by enabling the precision control and automation of data analysis. Deployment of smart microfluidics may be tremendously beneficial in various applications in the future, including high-throughput drug discovery, rapid point-of-care-testing (POCT), and personalized medicine. In this review, we summarize key microfluidic advances integrated with AI and discuss the outlook and possibilities of combining AI and microfluidics.
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Affiliation(s)
- Hsieh-Fu Tsai
- Department of Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan;
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, Keelung City 204, Taiwan
- Center for Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan
| | - Soumyajit Podder
- Department of Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan;
| | - Pin-Yuan Chen
- Department of Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan;
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, Keelung City 204, Taiwan
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23
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Li R, Wang S, Lyu J, Chen K, Sun X, Huang J, Sun P, Liang S, Li M, Yang M, Liu H, Zeng S, Chen X, Li L, Jia H, Zhou Z. Ten-kilohertz two-photon microscopy imaging of single-cell dendritic activity and hemodynamics in vivo. NEUROPHOTONICS 2023; 10:025006. [PMID: 37152357 PMCID: PMC10156610 DOI: 10.1117/1.nph.10.2.025006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023]
Abstract
Significance The studying of rapid neuronal signaling across large spatial scales in intact, living brains requires both high temporal resolution and versatility of the measurement device. Aim We introduce a high-speed two-photon microscope based on a custom-built acousto-optic deflector (AOD). This microscope has a maximum line scan frequency of 400 kHz and a maximum frame rate of 10,000 frames per second (fps) at 250 × 40 pixels . For stepwise magnification from population view to subcellular view with high spatial and temporal resolution, we combined the AOD with resonance-galvo (RS) scanning. Approach With this combinatorial device that supports both large-view navigation and small-view high-speed imaging, we measured dendritic calcium propagation velocity and the velocity of single red blood cells (RBCs). Results We measured dendritic calcium propagation velocity ( 80 / 62.5 - 116.7 μ m / ms ) in OGB-1-labeled single cortical neurons in mice in vivo. To benchmark the spatial precision and detection sensitivity of measurement in vivo, we also visualized the trajectories of single RBCs and found that their movement speed follows Poiseuille's law of laminar flow. Conclusions This proof-of-concept methodological development shows that the combination of AOD and RS scanning two-photon microscopy provides both versatility and precision for quantitative analysis of single neuronal activities and hemodynamics in vivo.
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Affiliation(s)
- Ruijie Li
- Guangxi University, Advanced Institute for Brain and Intelligence, School of Physical Science and Technology, Nanning, China
- Third Military Medical University, Brain Research Center, State Key Laboratory of Trauma, Burns, and Combined Injury, Chongqing, China
| | - Sibo Wang
- Chinese Academy of Sciences, Suzhou Institute of Biomedical Engineering and Technology, Brain Research Instrument Innovation Center, Suzhou, China
| | - Jing Lyu
- Chinese Academy of Sciences, Suzhou Institute of Biomedical Engineering and Technology, Brain Research Instrument Innovation Center, Suzhou, China
| | - Ke Chen
- Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Medical School, Chengdu, China
| | - Xiaxin Sun
- Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Medical School, Chengdu, China
| | - Junjie Huang
- Chongqing University, School of Medicine, Center for Neurointelligence, Chongqing, China
| | - Pei Sun
- Third Military Medical University, Brain Research Center, State Key Laboratory of Trauma, Burns, and Combined Injury, Chongqing, China
| | - Susu Liang
- Chongqing University, School of Medicine, Center for Neurointelligence, Chongqing, China
| | - Min Li
- Chinese Academy of Sciences, Suzhou Institute of Biomedical Engineering and Technology, Brain Research Instrument Innovation Center, Suzhou, China
| | - Mengke Yang
- Chinese Academy of Sciences, Suzhou Institute of Biomedical Engineering and Technology, Brain Research Instrument Innovation Center, Suzhou, China
| | - Hongbang Liu
- Guangxi University, Advanced Institute for Brain and Intelligence, School of Physical Science and Technology, Nanning, China
| | - Shaoqun Zeng
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
| | - Xiaowei Chen
- Third Military Medical University, Brain Research Center, State Key Laboratory of Trauma, Burns, and Combined Injury, Chongqing, China
- Chongqing Institute for Brain and Intelligence, Guangyang Bay Laboratory, Chongqing, China
| | - Longhui Li
- Chongqing University, School of Medicine, Center for Neurointelligence, Chongqing, China
| | - Hongbo Jia
- Guangxi University, Advanced Institute for Brain and Intelligence, School of Physical Science and Technology, Nanning, China
- Chinese Academy of Sciences, Suzhou Institute of Biomedical Engineering and Technology, Brain Research Instrument Innovation Center, Suzhou, China
- Leibniz Institute for Neurobiology, Magdeburg, Germany
- Technical University Munich, Institute of Neuroscience and the SyNergy Cluster, Munich, Germany
| | - Zhenqiao Zhou
- Chinese Academy of Sciences, Suzhou Institute of Biomedical Engineering and Technology, Brain Research Instrument Innovation Center, Suzhou, China
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24
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Běhal J, Pirone D, Sirico D, Bianco V, Mugnano M, Del Giudice D, Cavina B, Kurelac I, Memmolo P, Miccio L, Ferraro P. On monocytes and lymphocytes biolens clustering by in flow holographic microscopy. Cytometry A 2023; 103:251-259. [PMID: 36028475 DOI: 10.1002/cyto.a.24685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/09/2022]
Abstract
Live cells act as biological lenses and can be employed as real-world optical components in bio-hybrid systems. Imaging at nanoscale, optical tweezers, lithography and also photonic waveguiding are some of the already proven functionalities, boosted by the advantage that cells are fully biocompatible for intra-body applications. So far, various cell types have been studied for this purpose, such as red blood cells, bacterial cells, stem cells and yeast cells. White Blood Cells (WBCs) play a very important role in the regulation of the human body activities and are usually monitored for assessing its health. WBCs can be considered bio-lenses but, to the best of our knowledge, characterization of their optical properties have not been investigated yet. Here, we report for the first time an accurate study of two model classes of WBCs (i.e., monocytes and lymphocytes) by means of a digital holographic microscope coupled with a microfluidic system, assuming WBCs bio-lens characteristics. Thus, quantitative phase maps for many WBCs have been retrieved in flow-cytometry (FC) by achieving a significant statistical analysis to prove the enhancement in differentiation among sphere-like bio-lenses according to their sizes (i.e., diameter d) exploiting intensity parameters of the modulated light in proximity of the cell optical axis. We show that the measure of the low intensity area (S: I z < I th z ) in a fixed plane, is a feasible parameter for cell clustering, while achieving robustness against experimental misalignments and allowing to adjust the measurement sensitivity in post-processing. 2D scatterplots of the identified parameters (d-S) show better differentiation respect to the 1D case. The results show that the optical focusing properties of WBCs allow the clustering of the two populations by means of a mere morphological analysis, thus leading to the new concept of cell-optical-fingerprint avoiding fluorescent dyes. This perspective can open new routes in biomedical sciences, such as the chance to find optical-biomarkers at single cell level for label-free diagnosis.
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Affiliation(s)
- Jaromír Běhal
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
- Department of Optics, Palacký University, Olomouc, Czech Republic
| | - Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
- DIETI, Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", Naples, Italy
| | - Daniele Sirico
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
- Department of Chemical, Materials and Production Engineering of the University of Naples Federico II, Naples, Italy
| | - Vittorio Bianco
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
| | - Martina Mugnano
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
| | - Danila Del Giudice
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
- Department of Mathematics and Physics, University of Campania "L. Vanvitelli", Caserta, Italy
| | - Beatrice Cavina
- Department of Medical and Surgical Sciences (DIMEC), Centro di Studio e Ricerca sulle Neoplasie (CSR) Ginecologiche, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), Centro di Studio e Ricerca sulle Neoplasie (CSR) Ginecologiche, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Centre for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Pasquale Memmolo
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
| | - Lisa Miccio
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
| | - Pietro Ferraro
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Naples, Italy
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25
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Deng Y, Tay HM, Zhou Y, Fei X, Tang X, Nishikawa M, Yatomi Y, Hou HW, Xiao TH, Goda K. Studying the efficacy of antiplatelet drugs on atherosclerosis by optofluidic imaging on a chip. LAB ON A CHIP 2023; 23:410-420. [PMID: 36511820 DOI: 10.1039/d2lc00895e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Vascular stenosis caused by atherosclerosis instigates activation and aggregation of platelets, eventually resulting in thrombus formation. Although antiplatelet drugs are commonly used to inhibit platelet activation and aggregation, they unfortunately cannot prevent recurrent thrombotic events in patients with atherosclerosis. This is partially due to the limited understanding of the efficacy of antiplatelet drugs in the complex hemodynamic environment of vascular stenosis. Conventional methods for evaluating the efficacy of antiplatelet drugs under stenosis either fail to simulate the hemodynamic environment of vascular stenosis characterized by high shear stress and recirculatory flow or lack spatial resolution in their analytical techniques to statistically identify and characterize platelet aggregates. Here we propose and experimentally demonstrate a method comprising an in vitro 3D stenosis microfluidic chip and an optical time-stretch quantitative phase imaging system for studying the efficacy of antiplatelet drugs under stenosis. Our method simulates the atherogenic flow environment of vascular stenosis while enabling high-resolution and statistical analysis of platelet aggregates. Using our method, we distinguished the efficacy of three antiplatelet drugs, acetylsalicylic acid (ASA), cangrelor, and eptifibatide, for inhibiting platelet aggregation induced by stenosis. Specifically, ASA failed to inhibit stenosis-induced platelet aggregation, while eptifibatide and cangrelor showed high and moderate efficacy, respectively. Furthermore, we demonstrated that the drugs tested also differed in their efficacy for inhibiting platelet aggregation synergistically induced by stenosis and agonists (e.g., adenosine diphosphate, and collagen). Taken together, our method is an effective tool for investigating the efficacy of antiplatelet drugs under vascular stenosis, which could assist the development of optimal pharmacologic strategies for patients with atherosclerosis.
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Affiliation(s)
- Yunjie Deng
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.
| | - Hui Min Tay
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Yuqi Zhou
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.
| | - Xueer Fei
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.
| | - Xuke Tang
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.
| | - Masako Nishikawa
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, 113-0033, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, 113-0033, Japan
| | - Han Wei Hou
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 639798, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Ting-Hui Xiao
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.
- Institute of Technological Sciences, Wuhan University, Hubei, 430072, China
- Department of Bioengineering, University of California, Los Angeles, California, 90095, USA
- CYBO, Tokyo 101-0022, Japan
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26
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Xu D, Ding JB, Peng L. Depth random-access two-photon Bessel light-sheet imaging in brain tissue. OPTICS EXPRESS 2022; 30:26396-26406. [PMID: 36236832 PMCID: PMC9363024 DOI: 10.1364/oe.456871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 06/16/2023]
Abstract
Two-photon light-sheet fluorescence microscopy enables high-resolution imaging of neural activity in brain tissue at a high frame rate. Traditionally, light-sheet microscopy builds up a 3D stack by multiple depth scans with uniform spatial intervals, which substantially limits the volumetric imaging speed. Here, we introduce the depth random-access light-sheet microscopy, allowing rapid switching scanning depth for light-sheet imaging. With a low-cost electrically tunable lens and minimum modification of an existing two-photon light-sheet imaging instrument, we demonstrated fast random depth hopping light-sheet imaging at 100 frames per second in the live brain slice. Through depth random-access, calcium activities for an astrocyte were recorded on four user-selected detection planes at a refreshing rate of 25 Hz.
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Affiliation(s)
- Dongli Xu
- College of Optical Science, The University of Arizona, Tucson, AZ 85721, USA
- Department of Neurosurgery, Department of Neurology and Neurological Sciences, Wu-Tsai Neuroscience Institute, Stanford University, Stanford, CA 94305, USA
| | - Jun B. Ding
- Department of Neurosurgery, Department of Neurology and Neurological Sciences, Wu-Tsai Neuroscience Institute, Stanford University, Stanford, CA 94305, USA
| | - Leilei Peng
- College of Optical Science, The University of Arizona, Tucson, AZ 85721, USA
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27
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A FACED lift for cerebral blood flow imaging. Proc Natl Acad Sci U S A 2022; 119:e2207474119. [PMID: 35867770 PMCID: PMC9282448 DOI: 10.1073/pnas.2207474119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Ultrafast two-photon fluorescence imaging of cerebral blood circulation in the mouse brain in vivo. Proc Natl Acad Sci U S A 2022; 119:e2117346119. [PMID: 35648820 PMCID: PMC9191662 DOI: 10.1073/pnas.2117346119] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SignificanceCharacterizing blood flow by tracking individual red blood cells as they move through vessels is essential for understanding vascular function. With high spatial resolution, two-photon fluorescence microscopy is the method of choice for imaging blood flow at the cellular level. However, its application is limited to a low flow speed regimen in anesthetized animals by its slow focus scanning mechanism. Using an ultrafast scanning module, we demonstrated two-photon fluorescence imaging of blood flow at 1,000 two-dimensional frames and 1,000,000 one-dimensional line scans per second in the brains of awake mice. These ultrafast measurements enabled us to study hemodynamic and fluid mechanical regimens beyond the reach of conventional methods.
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29
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Touil M, Idlahcen S, Becheker R, Lebrun D, Rozé C, Hideur A, Godin T. Acousto-optically driven lensless single-shot ultrafast optical imaging. LIGHT, SCIENCE & APPLICATIONS 2022; 11:66. [PMID: 35318313 PMCID: PMC8940908 DOI: 10.1038/s41377-022-00759-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 05/02/2023]
Abstract
Driven by many applications in a wide span of scientific fields, a myriad of advanced ultrafast imaging techniques have emerged in the last decade, featuring record-high imaging speeds above a trillion-frame-per-second with long sequence depths. Although bringing remarkable insights into various ultrafast phenomena, their application out of a laboratory environment is however limited in most cases, either by the cost, complexity of the operation or by heavy data processing. We then report a versatile single-shot imaging technique combining sequentially timed all-optical mapping photography (STAMP) with acousto-optics programmable dispersive filtering (AOPDF) and digital in-line holography (DIH). On the one hand, a high degree of simplicity is reached through the AOPDF, which enables full control over the acquisition parameters via an electrically driven phase and amplitude spectro-temporal tailoring of the imaging pulses. Here, contrary to most single-shot techniques, the frame rate, exposure time, and frame intensities can be independently adjusted in a wide range of pulse durations and chirp values without resorting to complex shaping stages, making the system remarkably agile and user-friendly. On the other hand, the use of DIH, which does not require any reference beam, allows to achieve an even higher technical simplicity by allowing its lensless operation but also for reconstructing the object on a wide depth of field, contrary to classical techniques that only provide images in a single plane. The imaging speed of the system as well as its flexibility are demonstrated by visualizing ultrashort events on both the picosecond and nanosecond timescales. The virtues and limitations as well as the potential improvements of this on-demand ultrafast imaging method are critically discussed.
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Affiliation(s)
- Mohamed Touil
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Saïd Idlahcen
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Rezki Becheker
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Denis Lebrun
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Claude Rozé
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Ammar Hideur
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France
| | - Thomas Godin
- CORIA, CNRS UMR6614-Université de Rouen Normandie-INSA Rouen, 76800, Saint Etienne du Rouvray, France.
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30
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Kozawa Y, Nakamura T, Uesugi Y, Sato S. Wavefront engineered light needle microscopy for axially resolved rapid volumetric imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:1702-1717. [PMID: 35415006 PMCID: PMC8973193 DOI: 10.1364/boe.449329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Increasing the acquisition speed of three-dimensional volumetric images is important-particularly in biological imaging-to unveil the structural dynamics and functionalities of specimens in detail. In conventional laser scanning fluorescence microscopy, volumetric images are constructed from optical sectioning images sequentially acquired by changing the observation plane, limiting the acquisition speed. Here, we present a novel method to realize volumetric imaging from two-dimensional raster scanning of a light needle spot without sectioning, even in the traditional framework of laser scanning microscopy. Information from multiple axial planes is simultaneously captured using wavefront engineering for fluorescence signals, allowing us to readily survey the entire depth range while maintaining spatial resolution. This technique is applied to real-time and video-rate three-dimensional tracking of micrometer-sized particles, as well as the prompt visualization of thick fixed biological specimens, offering substantially faster volumetric imaging.
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Affiliation(s)
- Yuichi Kozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Tomoya Nakamura
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuuki Uesugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shunichi Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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31
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Light sheet based volume flow cytometry (VFC) for rapid volume reconstruction and parameter estimation on the go. Sci Rep 2022; 12:78. [PMID: 34997009 PMCID: PMC8741756 DOI: 10.1038/s41598-021-03902-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/06/2021] [Indexed: 11/08/2022] Open
Abstract
Optical imaging is paramount for disease diagnosis and to access its progression over time. The proposed optical flow imaging (VFC/iLIFE) is a powerful technique that adds new capabilities (3D volume visualization, organelle-level resolution, and multi-organelle screening) to the existing system. Unlike state-of-the-art point-illumination-based biomedical imaging techniques, the sheet-based VFC technique is capable of single-shot sectional visualization, high throughput interrogation, real-time parameter estimation, and instant volume reconstruction with organelle-level resolution of live specimens. The specimen flow system was realized on a multichannel (Y-type) microfluidic chip that enables visualization of organelle distribution in several cells in-parallel at a relatively high flow-rate (2000 nl/min). The calibration of VFC system requires the study of point emitters (fluorescent beads) at physiologically relevant flow-rates (500-2000 nl/min) for determining flow-induced optical aberration in the system point spread function (PSF). Subsequently, the recorded raw images and volumes were computationally deconvolved with flow-variant PSF to reconstruct the cell volume. High throughput investigation of the mitochondrial network in HeLa cancer cell was carried out at sub-cellular resolution in real-time and critical parameters (mitochondria count and size distribution, morphology, entropy, and cell strain statistics) were determined on-the-go. These parameters determine the physiological state of cells, and the changes over-time, revealing the metastatic progression of diseases. Overall, the developed VFC system enables real-time monitoring of sub-cellular organelle organization at a high-throughput with high-content capacity.
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32
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Xiao S, Davison I, Mertz J. Scan multiplier unit for ultrafast laser scanning beyond the inertia limit. OPTICA 2021; 8:1403-1404. [PMID: 37275678 PMCID: PMC10237152 DOI: 10.1364/optica.445254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 06/07/2023]
Abstract
A passive add-on greatly multiplies the sweep rate of any mechanical scanner while also enhancing throughput, enabling a single linear scanner to produce ultrafast 1D or 2D laser scans for general applications.
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Affiliation(s)
- Sheng Xiao
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA 02215, USA
| | - Ian Davison
- Department of Biology, Boston University, 24 Cummington Mall, Boston MA 02215, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA 02215, USA
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33
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Chattoraj S, Chakraborty A, Gupta A, Vishwakarma Y, Vishwakarma K, Aparajeeta J. Deep Phenotypic Cell Classification using Capsule Neural Network. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:4031-4036. [PMID: 34892115 DOI: 10.1109/embc46164.2021.9629862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent developments in ultra-high-throughput microscopy have created a new generation of cell classification methodologies focused solely on image-based cell phenotypes. These image-based analyses enable morphological profiling and screening of thousands or even millions of single cells at a fraction of the cost. They have been shown to demonstrate the statistical significance required for understanding the role of cell heterogeneity in diverse biologists. However, these single-cell analysis techniques are slow and require expensive genetic/epigenetic analysis. This treatise proposes an innovative DL system based on the newly created capsule networks (CapsNet) architecture. The proposed deep CapsNet model employs "Capsules" for high-level feature abstraction relevant to the cell category. Experiments demonstrate that our proposed system can accurately classify different types of cells based on phenotypic label-free bright-field images with over 98.06% accuracy and that deep CapsNet models outperform CNN models in the prior art.
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34
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Stassen SV, Yip GGK, Wong KKY, Ho JWK, Tsia KK. Generalized and scalable trajectory inference in single-cell omics data with VIA. Nat Commun 2021; 12:5528. [PMID: 34545085 PMCID: PMC8452770 DOI: 10.1038/s41467-021-25773-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/31/2021] [Indexed: 11/08/2022] Open
Abstract
Inferring cellular trajectories using a variety of omic data is a critical task in single-cell data science. However, accurate prediction of cell fates, and thereby biologically meaningful discovery, is challenged by the sheer size of single-cell data, the diversity of omic data types, and the complexity of their topologies. We present VIA, a scalable trajectory inference algorithm that overcomes these limitations by using lazy-teleporting random walks to accurately reconstruct complex cellular trajectories beyond tree-like pathways (e.g., cyclic or disconnected structures). We show that VIA robustly and efficiently unravels the fine-grained sub-trajectories in a 1.3-million-cell transcriptomic mouse atlas without losing the global connectivity at such a high cell count. We further apply VIA to discovering elusive lineages and less populous cell fates missed by other methods across a variety of data types, including single-cell proteomic, epigenomic, multi-omics datasets, and a new in-house single-cell morphological dataset.
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Affiliation(s)
- Shobana V Stassen
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Gwinky G K Yip
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kenneth K Y Wong
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Kevin K Tsia
- Department of Electrical & Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong.
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35
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High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy. Nat Methods 2021; 18:1103-1111. [PMID: 34462592 PMCID: PMC8958902 DOI: 10.1038/s41592-021-01239-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/09/2021] [Indexed: 02/07/2023]
Abstract
Two-photon microscopy has enabled high-resolution imaging of neuroactivity at depth within scattering brain tissue. However, its various realizations have not overcome the tradeoffs between speed and spatiotemporal sampling that would be necessary to enable mesoscale volumetric recording of neuroactivity at cellular resolution and speed compatible with resolving calcium transients. Here, we introduce light beads microscopy (LBM), a scalable and spatiotemporally optimal acquisition approach limited only by fluorescence lifetime, where a set of axially separated and temporally distinct foci record the entire axial imaging range near-simultaneously, enabling volumetric recording at 1.41 × 108 voxels per second. Using LBM, we demonstrate mesoscopic and volumetric imaging at multiple scales in the mouse cortex, including cellular-resolution recordings within ~3 × 5 × 0.5 mm volumes containing >200,000 neurons at ~5 Hz and recordings of populations of ~1 million neurons within ~5.4 × 6 × 0.5 mm volumes at ~2 Hz, as well as higher speed (9.6 Hz) subcellular-resolution volumetric recordings. LBM provides an opportunity for discovering the neurocomputations underlying cortex-wide encoding and processing of information in the mammalian brain.
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36
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Lai QTK, Yip GGK, Wu J, Wong JSJ, Lo MCK, Lee KCM, Le TTHD, So HKH, Ji N, Tsia KK. High-speed laser-scanning biological microscopy using FACED. Nat Protoc 2021; 16:4227-4264. [PMID: 34341580 DOI: 10.1038/s41596-021-00576-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/25/2021] [Indexed: 12/28/2022]
Abstract
Laser scanning is used in advanced biological microscopy to deliver superior imaging contrast, resolution and sensitivity. However, it is challenging to scale up the scanning speed required for interrogating a large and heterogeneous population of biological specimens or capturing highly dynamic biological processes at high spatiotemporal resolution. Bypassing the speed limitation of traditional mechanical methods, free-space angular-chirp-enhanced delay (FACED) is an all-optical, passive and reconfigurable laser-scanning approach that has been successfully applied in different microscopy modalities at an ultrafast line-scan rate of 1-80 MHz. Optimal FACED imaging performance requires optimized experimental design and implementation to enable specific high-speed applications. In this protocol, we aim to disseminate information allowing FACED to be applied to a broader range of imaging modalities. We provide (i) a comprehensive guide and design specifications for the FACED hardware; (ii) step-by-step optical implementations of the FACED module including the key custom components; and (iii) the overall image acquisition and reconstruction pipeline. We illustrate two practical imaging configurations: multimodal FACED imaging flow cytometry (bright-field, fluorescence and second-harmonic generation) and kHz 2D two-photon fluorescence microscopy. Users with basic experience in optical microscope operation and software engineering should be able to complete the setup of the FACED imaging hardware and software in ~2-3 months.
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Affiliation(s)
- Queenie T K Lai
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Gwinky G K Yip
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Jianglai Wu
- Department of Physics, University of California, Berkeley, Berkeley, CA, USA.,Chinese Institute for Brain Research, Beijing, China
| | - Justin S J Wong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Michelle C K Lo
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Kelvin C M Lee
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Tony T H D Le
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Hayden K H So
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Na Ji
- Department of Physics, University of California, Berkeley, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA. .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China. .,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin New Town, Hong Kong.
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37
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Xu M, Harmon J, Yuan D, Yan S, Lei C, Hiramatsu K, Zhou Y, Loo MH, Hasunuma T, Isozaki A, Goda K. Morphological Indicator for Directed Evolution of Euglena gracilis with a High Heavy Metal Removal Efficiency. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7880-7889. [PMID: 33913704 DOI: 10.1021/acs.est.0c05278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the past few decades, microalgae-based bioremediation methods for treating heavy metal (HM)-polluted wastewater have attracted much attention by virtue of their environment friendliness, cost efficiency, and sustainability. However, their HM removal efficiency is far from practical use. Directed evolution is expected to be effective for developing microalgae with a much higher HM removal efficiency, but there is no non-invasive or label-free indicator to identify them. Here, we present an intelligent cellular morphological indicator for identifying the HM removal efficiency of Euglena gracilis in a non-invasive and label-free manner. Specifically, we show a strong monotonic correlation (Spearman's ρ = -0.82, P = 2.1 × 10-5) between a morphological meta-feature recognized via our machine learning algorithms and the Cu2+ removal efficiency of 19 E. gracilis clones. Our findings firmly suggest that the morphology of E. gracilis cells can serve as an effective HM removal efficiency indicator and hence have great potential, when combined with a high-throughput image-activated cell sorter, for directed-evolution-based development of E. gracilis with an extremely high HM removal efficiency for practical wastewater treatment worldwide.
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Affiliation(s)
- Muzhen Xu
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jeffrey Harmon
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dan Yuan
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sheng Yan
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Cheng Lei
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Kotaro Hiramatsu
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Kanagawa Institute of Industrial Science and Technology, Ebina, Kanagawa 243-0435, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Yuqi Zhou
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mun Hong Loo
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Hyogo, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Hyogo, Kobe 657-8501, Japan
| | - Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Kanagawa Institute of Industrial Science and Technology, Ebina, Kanagawa 243-0435, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
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38
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Wang G, Shao L, Liu Y, Xu W, Xiao D, Liu S, Hu J, Zhao F, Shum P, Wang W, Zhou Y, Min R, Wang C. Low-cost compressive sensing imaging based on spectrum-encoded time-stretch structure. OPTICS EXPRESS 2021; 29:14931-14940. [PMID: 33985204 DOI: 10.1364/oe.421055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
A low-cost compressive sensing imaging (CSI) system based on spectrum-encoded time-stretch (SETS) structure involving cascaded Mach-Zehnder Interferometers (MZIs) for spectral domain random mixing (also known as the optical random pattern generator) is proposed and experimentally demonstrated. A proof-of-principle simulation and experiment is performed. A mode-locked laser with a repetition rate of 50MHz and low-cost cascaded MZIs as the key devices enable fast CSI system. Data compression ratio from 6% to 25% are obtained using proposed CSI based SETS system. The proposed design solves the big data issue in the traditional time-stretch system. It has great potential in fast dynamic phenomena with low-cost and easy-access components.
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39
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Lee KCM, Guck J, Goda K, Tsia KK. Toward deep biophysical cytometry: prospects and challenges. Trends Biotechnol 2021; 39:1249-1262. [PMID: 33895013 DOI: 10.1016/j.tibtech.2021.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022]
Abstract
The biophysical properties of cells reflect their identities, underpin their homeostatic state in health, and define the pathogenesis of disease. Recent leapfrogging advances in biophysical cytometry now give access to this information, which is obscured in molecular assays, with a discriminative power that was once inconceivable. However, biophysical cytometry should go 'deeper' in terms of exploiting the information-rich cellular biophysical content, generating a molecular knowledge base of cellular biophysical properties, and standardizing the protocols for wider dissemination. Overcoming these barriers, which requires concurrent innovations in microfluidics, optical imaging, and computer vision, could unleash the enormous potential of biophysical cytometry not only for gaining a new mechanistic understanding of biological systems but also for identifying new cost-effective biomarkers of disease.
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Affiliation(s)
- Kelvin C M Lee
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Jochen Guck
- Max Planck Institute for the Science of Light, and Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany; Department of Physics, Friedrich-Alexander Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan; Institute of Technological Sciences, Wuhan University, Hubei 430072, China; Department of Bioengineering, University of California, Los Angeles, California 90095, USA
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong.
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40
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Holzner G, Mateescu B, van Leeuwen D, Cereghetti G, Dechant R, Stavrakis S, deMello A. High-throughput multiparametric imaging flow cytometry: toward diffraction-limited sub-cellular detection and monitoring of sub-cellular processes. Cell Rep 2021; 34:108824. [PMID: 33691119 DOI: 10.1016/j.celrep.2021.108824] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/07/2020] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
We present a sheathless, microfluidic imaging flow cytometer that incorporates stroboscopic illumination for blur-free fluorescence detection at ultra-high analytical throughput. The imaging platform is capable of multiparametric fluorescence quantification and sub-cellular localization of these structures down to 500 nm with microscopy image quality. We demonstrate the efficacy of the approach through the analysis and localization of P-bodies and stress granules in yeast and human cells using fluorescence and bright-field detection at analytical throughputs in excess of 60,000 and 400,000 cells/s, respectively. Results highlight the utility of our imaging flow cytometer in directly investigating phase-separated compartments within cellular environments and screening rare events at the sub-cellular level for a range of diagnostic applications.
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Affiliation(s)
- Gregor Holzner
- Institute for Chemical & Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Bogdan Mateescu
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel van Leeuwen
- Department of Biology, ETH Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Gea Cereghetti
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Reinhard Dechant
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical & Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Andrew deMello
- Institute for Chemical & Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
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41
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Fan JL, Rivera JA, Sun W, Peterson J, Haeberle H, Rubin S, Ji N. High-speed volumetric two-photon fluorescence imaging of neurovascular dynamics. Nat Commun 2020; 11:6020. [PMID: 33243995 PMCID: PMC7693336 DOI: 10.1038/s41467-020-19851-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/13/2020] [Indexed: 02/02/2023] Open
Abstract
Understanding the structure and function of vasculature in the brain requires us to monitor distributed hemodynamics at high spatial and temporal resolution in three-dimensional (3D) volumes in vivo. Currently, a volumetric vasculature imaging method with sub-capillary spatial resolution and blood flow-resolving speed is lacking. Here, using two-photon laser scanning microscopy (TPLSM) with an axially extended Bessel focus, we capture volumetric hemodynamics in the awake mouse brain at a spatiotemporal resolution sufficient for measuring capillary size and blood flow. With Bessel TPLSM, the fluorescence signal of a vessel becomes proportional to its size, which enables convenient intensity-based analysis of vessel dilation and constriction dynamics in large volumes. We observe entrainment of vasodilation and vasoconstriction with pupil diameter and measure 3D blood flow at 99 volumes/second. Demonstrating high-throughput monitoring of hemodynamics in the awake brain, we expect Bessel TPLSM to make broad impacts on neurovasculature research.
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Affiliation(s)
- Jiang Lan Fan
- University of California, Berkeley, CA, USA.,University of California, San Francisco, CA, USA
| | - Jose A Rivera
- Department of Physics, University of California, Berkeley, CA, USA
| | - Wei Sun
- Thorlabs Imaging Systems, Sterling, VA, USA
| | | | | | - Sam Rubin
- Thorlabs Imaging Systems, Sterling, VA, USA.,LightPath Technologies Inc., Orlando, FL, USA
| | - Na Ji
- Department of Physics, University of California, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. .,Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA. .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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42
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Liang J, Wang P, Zhu L, Wang LV. Single-shot stereo-polarimetric compressed ultrafast photography for light-speed observation of high-dimensional optical transients with picosecond resolution. Nat Commun 2020; 11:5252. [PMID: 33067438 PMCID: PMC7567836 DOI: 10.1038/s41467-020-19065-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/16/2020] [Indexed: 12/27/2022] Open
Abstract
Simultaneous and efficient ultrafast recording of multiple photon tags contributes to high-dimensional optical imaging and characterization in numerous fields. Existing high-dimensional optical imaging techniques that record space and polarization cannot detect the photon's time of arrival owing to the limited speeds of the state-of-the-art electronic sensors. Here, we overcome this long-standing limitation by implementing stereo-polarimetric compressed ultrafast photography (SP-CUP) to record light-speed high-dimensional events in a single exposure. Synergizing compressed sensing and streak imaging with stereoscopy and polarimetry, SP-CUP enables video-recording of five photon tags (x, y, z: space; t: time of arrival; and ψ: angle of linear polarization) at 100 billion frames per second with a picosecond temporal resolution. We applied SP-CUP to the spatiotemporal characterization of linear polarization dynamics in early-stage plasma emission from laser-induced breakdown. This system also allowed three-dimensional ultrafast imaging of the linear polarization properties of a single ultrashort laser pulse propagating in a scattering medium.
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Affiliation(s)
- Jinyang Liang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 138-78, Pasadena, CA, 91125, USA
- Laboratory of Applied Computational Imaging, Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes, QC, J3X1S2, Canada
| | - Peng Wang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 138-78, Pasadena, CA, 91125, USA
| | - Liren Zhu
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 138-78, Pasadena, CA, 91125, USA
| | - Lihong V Wang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 138-78, Pasadena, CA, 91125, USA.
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43
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Weng Y, Mei L, Wu G, Chen S, Zhan B, Goda K, Liu S, Lei C. Analysis of signal detection configurations in optical time-stretch imaging. OPTICS EXPRESS 2020; 28:29272-29284. [PMID: 33114830 DOI: 10.1364/oe.403454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Optical time-stretch (OTS) imaging is effective for observing ultra-fast dynamic events in real time by virtue of its capability of acquiring images with high spatial resolution at high speed. In different implementations of OTS imaging, different configurations of its signal detection, i.e. fiber-coupled and free-space detection schemes, are employed. In this research, we quantitatively analyze and compare the two detection configurations of OTS imaging in terms of sensitivity and image quality with the USAF-1951 resolution chart and diamond films, respectively, providing a valuable guidance for the system design of OTS imaging in diverse fields.
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44
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Nemoto H, Suzuki T, Kannari F. Single-shot ultrafast burst imaging using an integral field spectroscope with a microlens array. OPTICS LETTERS 2020; 45:5004-5007. [PMID: 32932438 DOI: 10.1364/ol.398036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
To fully utilize the functions of a center-wavelength-sweeping pulse train generated by a free-space angular-chirp-enhanced delay optical layout for a probe laser pulse in sequentially timed all-optical mapping photography (STAMP), we introduced an integral field spectroscopy (IFS) method using a microlens array (MLA) to produce hyperspectral images, referring to the technique as lens array (LA)-STAMP. Compared with the previous STAMP utilizing spectral filtering where a bandpass filter generated hyperspectral images, LA-STAMP achieved much higher optical throughput. In a prototype setup, we used a 60×60 MLA and demonstrated single-shot burst imaging of a femtosecond laser-induced ablation process on a glass surface with 300 ps frame intervals in a 1.8 ns time window. Each frame image was constructed by assembling spectrally dispersed 36×36 monochromatic segments distributed by each lenslet on 5×5 pixels of a CCD camera. The spatial resolution was ∼4.4µm, which was determined by the MLA's pitch and the magnification of the microscope lens. We limited the number of frames to seven in this prototype setup, although it can be scaled to ∼24 with a spatial resolution of ∼1µm by designing IFS with a fine pitch MLA.
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45
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Isozaki A, Harmon J, Zhou Y, Li S, Nakagawa Y, Hayashi M, Mikami H, Lei C, Goda K. AI on a chip. LAB ON A CHIP 2020; 20:3074-3090. [PMID: 32644061 DOI: 10.1039/d0lc00521e] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Artificial intelligence (AI) has dramatically changed the landscape of science, industry, defence, and medicine in the last several years. Supported by considerably enhanced computational power and cloud storage, the field of AI has shifted from mostly theoretical studies in the discipline of computer science to diverse real-life applications such as drug design, material discovery, speech recognition, self-driving cars, advertising, finance, medical imaging, and astronomical observation, where AI-produced outcomes have been proven to be comparable or even superior to the performance of human experts. In these applications, what is essentially important for the development of AI is the data needed for machine learning. Despite its prominent importance, the very first process of the AI development, namely data collection and data preparation, is typically the most laborious task and is often a limiting factor of constructing functional AI algorithms. Lab-on-a-chip technology, in particular microfluidics, is a powerful platform for both the construction and implementation of AI in a large-scale, cost-effective, high-throughput, automated, and multiplexed manner, thereby overcoming the above bottleneck. On this platform, high-throughput imaging is a critical tool as it can generate high-content information (e.g., size, shape, structure, composition, interaction) of objects on a large scale. High-throughput imaging can also be paired with sorting and DNA/RNA sequencing to conduct a massive survey of phenotype-genotype relations whose data is too complex to analyze with traditional computational tools, but is analyzable with the power of AI. In addition to its function as a data provider, lab-on-a-chip technology can also be employed to implement the developed AI for accurate identification, characterization, classification, and prediction of objects in mixed, heterogeneous, or unknown samples. In this review article, motivated by the excellent synergy between AI and lab-on-a-chip technology, we outline fundamental elements, recent advances, future challenges, and emerging opportunities of AI with lab-on-a-chip technology or "AI on a chip" for short.
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Affiliation(s)
- Akihiro Isozaki
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan. and Kanagawa Institute of Industrial Science and Technology, Kanagawa 213-0012, Japan
| | - Jeffrey Harmon
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan.
| | - Yuqi Zhou
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan.
| | - Shuai Li
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan. and The Cambridge Centre for Data-Driven Discovery, Cambridge University, Cambridge CB3 0WA, UK
| | - Yuta Nakagawa
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan.
| | - Mika Hayashi
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan.
| | - Hideharu Mikami
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan.
| | - Cheng Lei
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan. and Institute of Technological Sciences, Wuhan University, Hubei 430072, China
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan. and Institute of Technological Sciences, Wuhan University, Hubei 430072, China and Department of Bioengineering, University of California, Los Angeles, California 90095, USA
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Nemoto H, Suzuki T, Kannari F. Extension of time window into nanoseconds in single-shot ultrafast burst imaging by spectrally sweeping pulses. APPLIED OPTICS 2020; 59:5210-5215. [PMID: 32543540 DOI: 10.1364/ao.392676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
We achieved single-shot 2D-burst imaging with a ∼22ps temporal resolution in a nanosecond time window using sequentially timed all-optical mapping photography with a spectral filtering (SF-STAMP) scheme, where a single snapshot of spectral images measured with a linear frequency chirped laser pulse forms time-resolved snapshots. We combined a pulse-stretching scheme of a free-space angular-chirp-enhanced delay (FACED) composed of a pair of tilted mirrors and a 4f-system. With a 4f-FACED system, we generated collinearly propagating burst laser pulses with a different center wavelength and a tunable time interval and demonstrated single-shot burst imaging with a 303 ps interval in a 1.5 ns time window by an SF-STAMP with spectrally sweeping probe pulses.
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47
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Zhao W, Guo Y, Yang S, Chen M, Chen H. Fast intelligent cell phenotyping for high-throughput optofluidic time-stretch microscopy based on the XGBoost algorithm. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-12. [PMID: 32495539 PMCID: PMC7267411 DOI: 10.1117/1.jbo.25.6.066001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
SIGNIFICANCE The use of optofluidic time-stretch flow cytometry enables extreme-throughput cell imaging but suffers from the difficulties of capturing and processing a large amount of data. As significant amounts of continuous image data are generated, the images require identification with high speed. AIM We present an intelligent cell phenotyping framework for high-throughput optofluidic time-stretch microscopy based on the XGBoost algorithm, which is able to classify obtained cell images rapidly and accurately. The applied image recognition consists of density-based spatial clustering of applications with noise outlier detection, histograms of oriented gradients combining gray histogram fused feature, and XGBoost classification. APPROACH We tested the ability of this framework against other previously proposed or commonly used algorithms to phenotype two groups of cell images. We quantified their performances with measures of classification ability and computational complexity based on AUC and test runtime. The tested cell image datasets were acquired from high-throughput imaging of over 20,000 drug-treated and untreated cells with an optofluidic time-stretch microscope. RESULTS The framework we built beats other methods with an accuracy of over 97% and a classification frequency of 3000 cells / s. In addition, we determined the optimal structure of training sets according to model performances under different training set components. CONCLUSIONS The proposed XGBoost-based framework acts as a promising solution to processing large flow image data. This work provides a foundation for future cell sorting and clinical practice of high-throughput imaging cytometers.
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Affiliation(s)
- Wanyue Zhao
- Tsinghua University, Beijing National Research Center for Information Science and Technology, Department of Electronic Engineering, Beijing, China
| | - Yingxue Guo
- Tsinghua University, Beijing National Research Center for Information Science and Technology, Department of Electronic Engineering, Beijing, China
| | - Sigang Yang
- Tsinghua University, Beijing National Research Center for Information Science and Technology, Department of Electronic Engineering, Beijing, China
| | - Minghua Chen
- Tsinghua University, Beijing National Research Center for Information Science and Technology, Department of Electronic Engineering, Beijing, China
| | - Hongwei Chen
- Tsinghua University, Beijing National Research Center for Information Science and Technology, Department of Electronic Engineering, Beijing, China
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48
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Eastman AE, Guo S. The palette of techniques for cell cycle analysis. FEBS Lett 2020; 594:10.1002/1873-3468.13842. [PMID: 32441778 PMCID: PMC9261528 DOI: 10.1002/1873-3468.13842] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022]
Abstract
The cell division cycle is the generational period of cellular growth and propagation. Cell cycle progression needs to be highly regulated to preserve genomic fidelity while increasing cell number. In multicellular organisms, the cell cycle must also coordinate with cell fate specification during development and tissue homeostasis. Altered cell cycle dynamics play a central role also in a number of pathophysiological processes. Thus, extensive effort has been made to define the biochemical machineries that execute the cell cycle and their regulation, as well as implementing more sensitive and accurate cell cycle measurements. Here, we review the available techniques for cell cycle analysis, revisiting the assumptions behind conventional population-based measurements and discussing new tools to better address cell cycle heterogeneity in the single-cell era. We weigh the strengths, weaknesses, and trade-offs of methods designed to measure temporal aspects of the cell cycle. Finally, we discuss emerging techniques for capturing cell cycle speed at single-cell resolution in live animals.
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Affiliation(s)
- Anna E Eastman
- Department of Cell Biology and Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Shangqin Guo
- Department of Cell Biology and Yale Stem Cell Center, Yale University, New Haven, CT, USA
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49
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Jing JC, Wei X, Wang LV. Spatio-temporal-spectral imaging of non-repeatable dissipative soliton dynamics. Nat Commun 2020; 11:2059. [PMID: 32345966 PMCID: PMC7189376 DOI: 10.1038/s41467-020-15900-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/23/2020] [Indexed: 11/29/2022] Open
Abstract
Dissipative solitons (DSs) are multi-dimensionally localized waves that arise from complex dynamical balances in far-from-equilibrium nonlinear systems and widely exist in physics, chemistry and biology. Real-time observations of DS dynamics across many dimensions thus have a broad impact on unveiling various nonlinear complexities in different fields. However, these observations are challenging as DS transitions are stochastic, non-repeatable and often strongly coupled across spatio-temporal-spectral (STS) domains. Here we report multi-dimensional (space xy + discrete time t + wavelength λ) DS dynamics imaged by STS compressed ultrafast photography, enabling imaging at up to trillions of frames per second. Various transient and random phenomena of multimode DSs are revealed, highlighting the importance of real-time multi-dimensional observation without the need for event repetition in decomposing the complexities of DSs. Due to three-dimensional, stochastic and non-repeatable transitions of dissipative solitons, it is challenging to monitor their full dynamics. Here, the authors resolve the dynamics by wavelength and along two spatial dimensions with up to trillions of frames per second using compressed ultrafast photography.
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Affiliation(s)
- Joseph C Jing
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 138-78, Pasadena, CA, 91125, USA
| | - Xiaoming Wei
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 138-78, Pasadena, CA, 91125, USA. .,School of Physics and Optoelectronics; State Key Laboratory of Luminescent Materials and Devices; Guangdong Engineering Technology Research and Development Center of Special Optical Fiber Materials and Devices; Guangdong Provincial Key Laboratory of Fiber Laser Materials and Applied Techniques, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, China.
| | - Lihong V Wang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 138-78, Pasadena, CA, 91125, USA.
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50
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Liu Y, Wu J, Wen X, Lin W, Wang W, Guan X, Qiao T, Guo Y, Wang W, Wei X, Yang Z. >100 W GHz femtosecond burst mode all-fiber laser system at 1.0 µm. OPTICS EXPRESS 2020; 28:13414-13422. [PMID: 32403816 DOI: 10.1364/oe.391515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
In this work, we report a >100 W femtosecond (fs) burst mode all-fiber laser system at 1.0 µm that operates at an intra-burst repetition rate of up to 1.2 GHz. This fiber laser system provides the highest output power that has been reported so far for GHz fs fiber lasers, to the best of our knowledge. In addition to the superior output power, this fiber laser system also shows a promising overall figure of merit, specifically in terms of pulse width (473 fs), long-term reliability (<0.67% power fluctuation) and system compactness (all-fiber configuration). We anticipate that this all-fiber laser system can be a promising ultrafast laser source for these applications requiring fs pulses with both high average power and high repetition rate, such as micromachining, bioimaging and frequency metrology.
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