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Zheng J, Cole T, Zhang Y, Kim J, Tang SY. Exploiting machine learning for bestowing intelligence to microfluidics. Biosens Bioelectron 2021; 194:113666. [PMID: 34600338 DOI: 10.1016/j.bios.2021.113666] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 02/06/2023]
Abstract
Intelligent microfluidics is an emerging cross-discipline research area formed by combining microfluidics with machine learning. It uses the advantages of microfluidics, such as high throughput and controllability, and the powerful data processing capabilities of machine learning, resulting in improved systems in biotechnology and chemistry. Compared to traditional microfluidics using manual analysis methods, intelligent microfluidics needs less human intervention, and results in a more user-friendly experience with faster processing. There is a paucity of literature reviewing this burgeoning and highly promising cross-discipline. Therefore, we herein comprehensively and systematically summarize several aspects of microfluidic applications enabled by machine learning. We list the types of microfluidics used in intelligent microfluidic applications over the last five years, as well as the machine learning algorithms and the hardware used for training. We also present the most recent advances in key technologies, developments, challenges, and the emerging opportunities created by intelligent microfluidics.
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Affiliation(s)
- Jiahao Zheng
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tim Cole
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Yuxin Zhang
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jeeson Kim
- Department of Intelligent Mechatronics Engineering, Sejong University, Seoul, 05006, South Korea.
| | - Shi-Yang Tang
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Daga KR, Priyadarshani P, Larey AM, Rui K, Mortensen LJ, Marklein RA. Shape up before you ship out: morphology as a potential critical quality attribute for cellular therapies. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021. [DOI: 10.1016/j.cobme.2021.100352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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53
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Wang C, Ma Y, Pei Z, Song F, Zhong J, Wang Y, Yan X, Dai P, Jiang Y, Qiu J, Shi M, Wu X. Sheathless acoustic based flow cell sorter for enrichment of rare cells. Cytometry A 2021; 101:311-324. [PMID: 34806837 DOI: 10.1002/cyto.a.24521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/12/2022]
Abstract
Cell enrichment is a powerful tool in many kinds of cell research, especially in applications with low abundance cell types. In this work, we developed a microfluidic fluorescence activated cell sorting device that was able to perform on-demand, low loss cell detection, and sorting. The chip utilizes three-dimensional acoustic standing waves to position all cells in the same fluid velocity regime without sheath. When the cells pass through a laser interrogation region, the scattering and fluorescent signals are detected, translated and transported to software. The target cells are then identified by gating on the plots. Short bursts of standing acoustic waves are triggered by order from PC to sort target cells within predefined gating region. For very low abundance and rare labeled lymphocytes mixed with high concentration unlabeled white blood cells (WBCs), (1-100 labeled lymphocytes are diluted in 106 WBCs in 1 ml volume fluid), the device is able to remove more than 98% WBCs and recover labeled lymphocytes with efficiency of 80%. We further demonstrated that this device worked with real clinical samples by successfully isolating fetal nucleated red blood cells (FNRBCs) in the blood samples from pregnant women with male fetus. The obtained cells were sequenced and the expressions of (sex determining region Y) SRY genes were tested to determine fetal cell proportion. In genetic analysis, the proportion of fetal cells in the final picked sample is up to 40.64%. With this ability, the device proposed could be valuable for biomedical applications involving fetal cells, circulating tumor cells, and stem cells.
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Affiliation(s)
- Ce Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yuting Ma
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhiguo Pei
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Feifei Song
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Jinfeng Zhong
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yao Wang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Xintao Yan
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Pu Dai
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Yi Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai ninth people's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jianping Qiu
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Mengdie Shi
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Xiaodong Wu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
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Kleiber A, Kraus D, Henkel T, Fritzsche W. Review: tomographic imaging flow cytometry. LAB ON A CHIP 2021; 21:3655-3666. [PMID: 34514484 DOI: 10.1039/d1lc00533b] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Within the last decades, conventional flow cytometry (FC) has evolved as a powerful measurement method in clinical diagnostics, biology, life sciences and healthcare. Imaging flow cytometry (IFC) extends the power of traditional FC by adding high resolution optical and spectroscopic information. However, the conventional IFC only provides a 2D projection of a 3D object. To overcome this limitation, tomographic imaging flow cytometry (tIFC) was developed to access 3D information about the target particles. The goal of tIFC is to visualize surfaces and internal structures in a holistic way. This review article gives an overview of the past and current developments in tIFC.
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Affiliation(s)
- Andreas Kleiber
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Daniel Kraus
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Thomas Henkel
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
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Wang Y, Wang X, Pan T, Li B, Chu J. Label-free single-cell isolation enabled by microfluidic impact printing and real-time cellular recognition. LAB ON A CHIP 2021; 21:3695-3706. [PMID: 34581393 DOI: 10.1039/d1lc00326g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Analysis of cellular components at the single-cell level is important to reveal cellular heterogeneity. However, current technologies to isolate individual cells are either label-based or have low performance. Here, we present a novel technique by integrating real-time cellular recognition and microfluidic impact printing (MIP) to isolate single cells with high efficiency and high throughput in a label-free manner. Specifically, morphological characteristics of polystyrene beads and cells, computed by an efficient image processing algorithm, are utilized as selection criteria to identify target objects. Subsequently, each detected single-cell object in the suspension is ejected from the microfluidic channel by impact force. It has been demonstrated that the single-cell isolating system has the ability to encapsulate polystyrene beads in droplets with an efficiency of 95%, while for HeLa cells, this has been experimentally measured as 90.3%. Single-cell droplet arrays are generated at a throughput of 2 Hz and 96.6% of the cells remain alive after isolation. This technology has significant potential in various emerging applications, including single-cell omics, tissue engineering, and cell-line development.
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Affiliation(s)
- Yiming Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiaojie Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Tingrui Pan
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Baoqing Li
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jiaru Chu
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, 230027, China
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56
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Yuan D, Yadav S, Ta HT, Fallahi H, An H, Kashaninejad N, Ooi CH, Nguyen NT, Zhang J. Investigation of viscoelastic focusing of particles and cells in a zigzag microchannel. Electrophoresis 2021; 42:2230-2237. [PMID: 34396540 DOI: 10.1002/elps.202100126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/26/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022]
Abstract
Microfluidic particle focusing has been a vital prerequisite step in sample preparation for downstream particle separation, counting, detection, or analysis, and has attracted broad applications in biomedical and chemical areas. Besides all the active and passive focusing methods in Newtonian fluids, particle focusing in viscoelastic fluids has been attracting increasing interest because of its advantages induced by intrinsic fluid property. However, to achieve a well-defined focusing position, there is a need to extend channel lengths when focusing micrometer-sized or sub-microsized particles, which would result in the size increase of the microfluidic devices. This work investigated the sheathless viscoelastic focusing of particles and cells in a zigzag microfluidic channel. Benefit from the zigzag structure of the channel, the channel length and the footprint of the device can be reduced without sacrificing the focusing performance. In this work, the viscoelastic focusing, including the focusing of 10 μm polystyrene particles, 5 μm polystyrene particles, 5 μm magnetic particles, white blood cells (WBCs), red blood cells (RBCs), and cancer cells, were all demonstrated. Moreover, magnetophoretic separation of magnetic and nonmagnetic particles after viscoelastic pre-focusing was shown. This focusing technique has the potential to be used in a range of biomedical applications.
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Affiliation(s)
- Dan Yuan
- Centre for Regional and Rural Futures, Deakin University, Geelong, Victoria, 3216, Australia
| | - Sharda Yadav
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
| | - Hang T Ta
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
| | - Hedieh Fallahi
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
| | - Hongjie An
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
| | - Navid Kashaninejad
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
| | - Chin Hong Ooi
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
| | - Jun Zhang
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland, 4111, Australia
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57
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Vargas-Ordaz EJ, Gorelick S, York HM, Liu B, Halls ML, Arumugam S, Neild A, de Marco A, Cadarso VJ. Three-dimensional imaging on a chip using optofluidics light-sheet fluorescence microscopy. LAB ON A CHIP 2021; 21:2945-2954. [PMID: 34124739 DOI: 10.1039/d1lc00098e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Volumetric, sub-micron to micron level resolution imaging is necessary to assay phenotypes or characteristics at the sub-cellular/organelle scale. However, three-dimensional fluorescence imaging of cells is typically low throughput or compromises on the achievable resolution in space and time. Here, we capitalise on the flow control capabilities of microfluidics and combine it with microoptics to integrate light-sheet based imaging directly into a microfluidic chip. Our optofluidic system flows suspended cells through a sub-micrometer thick light-sheet formed using micro-optical components that are cast directly in polydimethylsiloxane (PDMS). This design ensures accurate alignment, drift-free operation, and easy integration with conventional microfluidics, while providing sufficient spatial resolution, optical sectioning and volumetric data acquisition. We demonstrate imaging rates of 120 ms per cell at sub-μm resolution, that allow extraction of complex cellular phenotypes, exemplified by imaging of cell clusters, receptor distribution, and the analysis of endosomal size changes.
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Affiliation(s)
- Erick J Vargas-Ordaz
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia. and Centre to Impact Antimicrobial Resistance - Sustainable Solutions, Monash University, Clayton, 3800, Victoria, Australia
| | - Sergey Gorelick
- Department of Biochemistry and Molecular Biology, Monash University, 3800 Clayton, Victoria, Australia. and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia
| | - Harrison M York
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia and European Molecular Biology Laboratory (EMBL) Australia, Monash University, 3800 Clayton, Victoria, Australia and Department of Anatomy and Developmental Biology, Monash University, 3800 Clayton, Victoria, Australia
| | - Bonan Liu
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Senthil Arumugam
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia and European Molecular Biology Laboratory (EMBL) Australia, Monash University, 3800 Clayton, Victoria, Australia and Department of Anatomy and Developmental Biology, Monash University, 3800 Clayton, Victoria, Australia
| | - Adrian Neild
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, 3800 Clayton, Victoria, Australia. and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 3800 Clayton, Victoria, Australia
| | - Victor J Cadarso
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia. and Centre to Impact Antimicrobial Resistance - Sustainable Solutions, Monash University, Clayton, 3800, Victoria, Australia and The Melbourne Centre for Nanofabrication, Victorian Node - Australian National Fabrication Facility, Clayton, Victoria 3800, Australia
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58
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Tang T, Liu X, Kiya R, Shen Y, Yuan Y, Zhang T, Suzuki K, Tanaka Y, Li M, Hosokawa Y, Yalikun Y. Microscopic impedance cytometry for quantifying single cell shape. Biosens Bioelectron 2021; 193:113521. [PMID: 34380102 DOI: 10.1016/j.bios.2021.113521] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/22/2021] [Accepted: 07/15/2021] [Indexed: 02/02/2023]
Abstract
In this work, we investigated the ability of impedance flow cytometry to measure the shape of single cells/particles. We found that the impedance pulses triggered by micro-objects that are asymmetric in morphology show a tilting trend, and there is no such a tilting trend for symmetric ones. Therefore, we proposed a new metric, tilt index, to quantify the tilt level of the impedance pulses. Through simulation, we found that the value of tilt index tends to be zero for perfectly symmetrical objects, while the value is greater than zero for asymmetrical ones. Also, this metric was found to be independent on the trajectories (i.e., lateral, and z-direction shift) of the target micro-object. In experiments, we adopted a home-made lock-in amplifier and performed experiments on 10 μm polystyrene beads and Euglena gracilis (E. gracilis) cells with varying shapes. The experimental results coincided with the simulation results and demonstrated that the new metric (tilt index) enables the impedance cytometry to characterize the shape single cells/particles without microscopy or other optical setups.
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Affiliation(s)
- Tao Tang
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho Ikoma, Nara, 630-0192, Japan
| | - Xun Liu
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho Ikoma, Nara, 630-0192, Japan
| | - Ryota Kiya
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho Ikoma, Nara, 630-0192, Japan
| | - Yigang Shen
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yapeng Yuan
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Tianlong Zhang
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho Ikoma, Nara, 630-0192, Japan; School of Engineering, Macquarie University, Sydney, 2109, Australia
| | | | - Yo Tanaka
- Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Ming Li
- School of Engineering, Macquarie University, Sydney, 2109, Australia
| | - Yoichiroh Hosokawa
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho Ikoma, Nara, 630-0192, Japan
| | - Yaxiaer Yalikun
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho Ikoma, Nara, 630-0192, Japan; Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.
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59
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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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60
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Li M, Liu H, Zhuang S, Goda K. Droplet flow cytometry for single-cell analysis. RSC Adv 2021; 11:20944-20960. [PMID: 35479393 PMCID: PMC9034116 DOI: 10.1039/d1ra02636d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/06/2021] [Indexed: 01/22/2023] Open
Abstract
The interrogation of single cells has revolutionised biology and medicine by providing crucial unparalleled insights into cell-to-cell heterogeneity. Flow cytometry (including fluorescence-activated cell sorting) is one of the most versatile and high-throughput approaches for single-cell analysis by detecting multiple fluorescence parameters of individual cells in aqueous suspension as they flow past through a focus of excitation lasers. However, this approach relies on the expression of cell surface and intracellular biomarkers, which inevitably lacks spatial and temporal phenotypes and activities of cells, such as secreted proteins, extracellular metabolite production, and proliferation. Droplet microfluidics has recently emerged as a powerful tool for the encapsulation and manipulation of thousands to millions of individual cells within pico-litre microdroplets. Integrating flow cytometry with microdroplet architectures surrounded by aqueous solutions (e.g., water-in-oil-in-water (W/O/W) double emulsion and hydrogel droplets) opens avenues for new cellular assays linking cell phenotypes to genotypes at the single-cell level. In this review, we discuss the capabilities and applications of droplet flow cytometry (DFC). This unique technique uses standard commercially available flow cytometry instruments to characterise or select individual microdroplets containing single cells of interest. We explore current challenges associated with DFC and present our visions for future development.
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Affiliation(s)
- Ming Li
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
- Biomolecular Discovery Research Centre, Macquarie University Sydney NSW 2109 Australia
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University Sydney NSW 2109 Australia
| | - Siyuan Zhuang
- School of Engineering, Macquarie University Sydney NSW 2109 Australia
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo Tokyo 113-0033 Japan
- Institute of Technological Sciences, Wuhan University 430072 Hubei PR China
- Department of Bioengineering, University of California Los Angeles CA 90095 USA
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Del Giudice F, D'Avino G, Maffettone PL. Microfluidic formation of crystal-like structures. LAB ON A CHIP 2021; 21:2069-2094. [PMID: 34002182 DOI: 10.1039/d1lc00144b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Crystal-like structures find application in several fields ranging from biomedical engineering to material science. For instance, droplet crystals are critical for high throughput assays and material synthesis, while particle crystals are important for particles and cell encapsulation, Drop-seq technologies, and single-cell analysis. Formation of crystal-like structures relies entirely on the possibility of manipulating with great accuracy the micrometer-size objects forming the crystal. In this context, microfluidic devices offer versatile tools for the precise manipulation of droplets and particles, thus enabling fabrication of crystal-like structures that form due to hydrodynamic interactions among droplets or particles. In this review, we aim at providing an holistic representation of crystal-like structure formation mediated by hydrodynamic interactions in microfluidic devices. We also discuss the physical origin of these hydrodynamic interactions and their relation to parameters such as device geometry, fluid properties, and flow conditions.
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Affiliation(s)
- Francesco Del Giudice
- System and Process Engineering Centre, College of Engineering, Fabian Way, Swansea, SA1 8EN, UK.
| | - Gaetano D'Avino
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Universitá degli Studi di Napoli Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Pier Luca Maffettone
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Universitá degli Studi di Napoli Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
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62
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Stanley J, Hui H, Erber W, Clynick B, Fuller K. Analysis of human chromosomes by imaging flow cytometry. CYTOMETRY PART B-CLINICAL CYTOMETRY 2021; 100:541-553. [PMID: 34033226 DOI: 10.1002/cyto.b.22023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/18/2021] [Accepted: 05/14/2021] [Indexed: 12/29/2022]
Abstract
Chromosomal analysis is traditionally performed by karyotyping on metaphase spreads, or by fluorescent in situ hybridization (FISH) on interphase cells or metaphase spreads. Flow cytometry was introduced as a new method to analyze chromosomes number (ploidy) and structure (telomere length) in the 1970s with data interpretation largely based on fluorescence intensity. This technology has had little uptake for human cytogenetic applications primarily due to analytical challenges. The introduction of imaging flow cytometry, with the addition of digital images to standard multi-parametric flow cytometry quantitative tools, has added a new dimension. The ability to visualize the chromosomes and FISH signals overcomes the inherent difficulties when the data is restricted to fluorescence intensity. This field is now moving forward with methods being developed to assess chromosome number and structure in whole cells (normal and malignant) in suspension. A recent advance has been the inclusion of immunophenotyping such that antigen expression can be used to identify specific cells of interest for specific chromosomes and their abnormalities. This capability has been illustrated in blood cancers, such as chronic lymphocytic leukemia and plasma cell myeloma. The high sensitivity and specificity achievable highlights the potential imaging flow cytometry has for cytogenomic applications (i.e., diagnosis and disease monitoring). This review introduces and describes the development, current status, and applications of imaging flow cytometry for chromosomal analysis of human chromosomes.
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Affiliation(s)
- Jason Stanley
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Henry Hui
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Wendy Erber
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia.,PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Britt Clynick
- Institute for Respiratory Health, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | - Kathy Fuller
- Translational Cancer Pathology Laboratory, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
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63
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Rodrigues MA, Probst CE, Zayats A, Davidson B, Riedel M, Li Y, Venkatachalam V. The in vitro micronucleus assay using imaging flow cytometry and deep learning. NPJ Syst Biol Appl 2021; 7:20. [PMID: 34006858 PMCID: PMC8131758 DOI: 10.1038/s41540-021-00179-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/16/2021] [Indexed: 02/07/2023] Open
Abstract
The in vitro micronucleus (MN) assay is a well-established assay for quantification of DNA damage, and is required by regulatory bodies worldwide to screen chemicals for genetic toxicity. The MN assay is performed in two variations: scoring MN in cytokinesis-blocked binucleated cells or directly in unblocked mononucleated cells. Several methods have been developed to score the MN assay, including manual and automated microscopy, and conventional flow cytometry, each with advantages and limitations. Previously, we applied imaging flow cytometry (IFC) using the ImageStream® to develop a rapid and automated MN assay based on high throughput image capture and feature-based image analysis in the IDEAS® software. However, the analysis strategy required rigorous optimization across chemicals and cell lines. To overcome the complexity and rigidity of feature-based image analysis, in this study we used the Amnis® AI software to develop a deep-learning method based on convolutional neural networks to score IFC data in both the cytokinesis-blocked and unblocked versions of the MN assay. We show that the use of the Amnis AI software to score imagery acquired using the ImageStream® compares well to manual microscopy and outperforms IDEAS® feature-based analysis, facilitating full automation of the MN assay.
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Affiliation(s)
| | | | - Artiom Zayats
- Amnis Flow Cytometry, Luminex Corporation, Seattle, WA, USA
| | - Bryan Davidson
- Amnis Flow Cytometry, Luminex Corporation, Seattle, WA, USA
| | - Michael Riedel
- Amnis Flow Cytometry, Luminex Corporation, Seattle, WA, USA
| | - Yang Li
- Amnis Flow Cytometry, Luminex Corporation, Seattle, WA, USA
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64
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Luo S, Shi Y, Chin LK, Zhang Y, Wen B, Sun Y, Nguyen BTT, Chierchia G, Talbot H, Bourouina T, Jiang X, Liu AQ. Rare bioparticle detection via deep metric learning. RSC Adv 2021; 11:17603-17610. [PMID: 35480202 PMCID: PMC9032704 DOI: 10.1039/d1ra02869c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Recent deep neural networks have shown superb performance in analyzing bioimages for disease diagnosis and bioparticle classification. Conventional deep neural networks use simple classifiers such as SoftMax to obtain highly accurate results. However, they have limitations in many practical applications that require both low false alarm rate and high recovery rate, e.g., rare bioparticle detection, in which the representative image data is hard to collect, the training data is imbalanced, and the input images in inference time could be different from the training images. Deep metric learning offers a better generatability by using distance information to model the similarity of the images and learning function maps from image pixels to a latent space, playing a vital role in rare object detection. In this paper, we propose a robust model based on a deep metric neural network for rare bioparticle (Cryptosporidium or Giardia) detection in drinking water. Experimental results showed that the deep metric neural network achieved a high accuracy of 99.86% in classification, 98.89% in precision rate, 99.16% in recall rate and zero false alarm rate. The reported model empowers imaging flow cytometry with capabilities of biomedical diagnosis, environmental monitoring, and other biosensing applications.
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Affiliation(s)
- Shaobo Luo
- ESYCOM, CNRS UMR 9007, Universite Gustave Eiffel, ESIEE Paris Noisy-le-Grand 93162 France .,Institute for Infocomm Research (I2R), Agency for Science, Technology and Research (ASTAR) 138668 Singapore
| | - Yuzhi Shi
- School of Electrical & Electronic Engineering, Nanyang Technological University 639798 Singapore
| | - Lip Ket Chin
- School of Electrical & Electronic Engineering, Nanyang Technological University 639798 Singapore .,Center for Systems Biology, Massachusetts General Hospital Massachusetts 02114 USA
| | - Yi Zhang
- School of Mechanical & Aerospace Engineering, Nanyang Technological University 639798 Singapore
| | - Bihan Wen
- School of Electrical & Electronic Engineering, Nanyang Technological University 639798 Singapore
| | - Ying Sun
- Institute for Infocomm Research (I2R), Agency for Science, Technology and Research (ASTAR) 138668 Singapore
| | - Binh T T Nguyen
- School of Electrical & Electronic Engineering, Nanyang Technological University 639798 Singapore
| | - Giovanni Chierchia
- ESYCOM, CNRS UMR 9007, Universite Gustave Eiffel, ESIEE Paris Noisy-le-Grand 93162 France
| | - Hugues Talbot
- CentraleSupelec, Universite Paris-Saclay Saint-Aubin 91190 France
| | - Tarik Bourouina
- ESYCOM, CNRS UMR 9007, Universite Gustave Eiffel, ESIEE Paris Noisy-le-Grand 93162 France
| | - Xudong Jiang
- School of Electrical & Electronic Engineering, Nanyang Technological University 639798 Singapore
| | - Ai-Qun Liu
- School of Electrical & Electronic Engineering, Nanyang Technological University 639798 Singapore .,Nanyang Environment and Water Research Institute, Nanyang Technological University 637141 Singapore
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65
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Lee K, Kim SE, Doh J, Kim K, Chung WK. User-friendly image-activated microfluidic cell sorting technique using an optimized, fast deep learning algorithm. LAB ON A CHIP 2021; 21:1798-1810. [PMID: 33734252 DOI: 10.1039/d0lc00747a] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Image-activated cell sorting is an essential biomedical research technique for understanding the unique characteristics of single cells. Deep learning algorithms can be used to extract hidden cell features from high-content image information to enable the discrimination of cell-to-cell differences in image-activated cell sorters. However, such systems are challenging to implement from a technical perspective due to the advanced imaging and sorting requirements and the long processing times of deep learning algorithms. Here, we introduce a user-friendly image-activated microfluidic sorting technique based on a fast deep learning model under the TensorRT framework to enable sorting decisions within 3 ms. The proposed sorter employs a significantly simplified operational procedure based on the use of a syringe connected to a piezoelectric actuator. The sorter has a 2.5 ms latency. The utility of the sorter was demonstrated through real-time sorting of fluorescent polystyrene beads and cells. The sorter achieved 98.0%, 95.1%, and 94.2% sorting purities for 15 μm and 10 μm beads, HL-60 and Jurkat cells, and HL-60 and K562 cells, respectively, with a throughput of up to 82.8 events per second (eps).
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Affiliation(s)
- Keondo Lee
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Seong-Eun Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Junsang Doh
- Department of Materials Science and Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Keehoon Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Wan Kyun Chung
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
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66
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Manz A, Lee AP, Wheeler AR. Lab on a Chip- past, present, and future. LAB ON A CHIP 2021; 21:1197-1198. [PMID: 33877233 DOI: 10.1039/d1lc90030g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We check in with past, present, and future Editors-in-Chief, including Andreas Manz (2001–2008), Abe Lee (2017–2020), and Aaron Wheeler (2021–), about the state of the field.
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Affiliation(s)
- Andreas Manz
- Korea Institute of Science and Technology Europe, Germany
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67
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Kasai Y, Leipe C, Saito M, Kitagawa H, Lauterbach S, Brauer A, Tarasov PE, Goslar T, Arai F, Sakuma S. Breakthrough in purification of fossil pollen for dating of sediments by a new large-particle on-chip sorter. SCIENCE ADVANCES 2021; 7:7/16/eabe7327. [PMID: 33853775 PMCID: PMC8046374 DOI: 10.1126/sciadv.abe7327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Particle sorting is a fundamental method in various fields of medical and biological research. However, existing sorting applications are not capable for high-throughput sorting of large-size (>100 micrometers) particles. Here, we present a novel on-chip sorting method using traveling vortices generated by on-demand microjet flows, which locally exceed laminar flow condition, allowing for high-throughput sorting (5 kilohertz) with a record-wide sorting area of 520 micrometers. Using an activation system based on fluorescence detection, the method successfully sorted 160-micrometer microbeads and purified fossil pollen (maximum dimension around 170 micrometers) from lake sediments. Radiocarbon dates of sorting-derived fossil pollen concentrates proved accurate, demonstrating the method's ability to enhance building chronologies for paleoenvironmental records from sedimentary archives. The method is capable to cover urgent needs for high-throughput large-particle sorting in genomics, metabolomics, and regenerative medicine and opens up new opportunities for the use of pollen and other microfossils in geochronology, paleoecology, and paleoclimatology.
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Affiliation(s)
- Y Kasai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan
| | - C Leipe
- Institute for Space-Earth Environmental Research, Nagoya University, Aichi 464-8603, Japan.
| | - M Saito
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan
| | - H Kitagawa
- Institute for Space-Earth Environmental Research, Nagoya University, Aichi 464-8603, Japan
| | - S Lauterbach
- Leibniz Laboratory for Radiometric Dating and Stable Isotope Research, Kiel University, Max-Eyth-Str. 11-13, 24118 Kiel, Germany
- Institute of Geosciences, Kiel University, Ludewig-Meyn-Str. 10, 24118 Kiel, Germany
| | - A Brauer
- GFZ German Research Centre for Geosciences, Section 4.3-Climate Dynamics and Landscape Evolution, Telegrafenberg, 14473 Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - P E Tarasov
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74-100, Building D, 12249 Berlin, Germany
| | - T Goslar
- Poznan Radiocarbon Laboratory, Foundation of the Adam Mickiewicz University, Rubiez 46, Poznan, Poland
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan, Poland
| | - F Arai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan
- Department of Mechanical Engineering, The University of Tokyo, Bunkyo-ku 113-8656, Japan
| | - S Sakuma
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Aichi 464-8603, Japan.
- Department of Mechanical Engineering, Kyushu University, Fukuoka 819-0395, Japan
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68
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Rodin AS, Gogoshin G, Hilliard S, Wang L, Egelston C, Rockne RC, Chao J, Lee PP. Dissecting Response to Cancer Immunotherapy by Applying Bayesian Network Analysis to Flow Cytometry Data. Int J Mol Sci 2021; 22:ijms22052316. [PMID: 33652558 PMCID: PMC7956201 DOI: 10.3390/ijms22052316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer immunotherapy, specifically immune checkpoint blockade, has been found to be effective in the treatment of metastatic cancers. However, only a subset of patients achieve clinical responses. Elucidating pretreatment biomarkers predictive of sustained clinical response is a major research priority. Another research priority is evaluating changes in the immune system before and after treatment in responders vs. nonresponders. Our group has been studying immune networks as an accurate reflection of the global immune state. Flow cytometry (FACS, fluorescence-activated cell sorting) data characterizing immune cell panels in peripheral blood mononuclear cells (PBMC) from gastroesophageal adenocarcinoma (GEA) patients were used to analyze changes in immune networks in this setting. Here, we describe a novel computational pipeline to perform secondary analyses of FACS data using systems biology/machine learning techniques and concepts. The pipeline is centered around comparative Bayesian network analyses of immune networks and is capable of detecting strong signals that conventional methods (such as FlowJo manual gating) might miss. Future studies are planned to validate and follow up the immune biomarkers (and combinations/interactions thereof) associated with clinical responses identified with this computational pipeline.
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Affiliation(s)
- Andrei S. Rodin
- City of Hope National Medical Center, Department of Computational and Quantitative Medicine, Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, USA; (G.G.); (S.H.); (R.C.R.)
- Correspondence: (A.S.R.); (P.P.L.)
| | - Grigoriy Gogoshin
- City of Hope National Medical Center, Department of Computational and Quantitative Medicine, Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, USA; (G.G.); (S.H.); (R.C.R.)
| | - Seth Hilliard
- City of Hope National Medical Center, Department of Computational and Quantitative Medicine, Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, USA; (G.G.); (S.H.); (R.C.R.)
| | - Lei Wang
- City of Hope National Medical Center, Department of Immuno-Oncology, Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, USA; (L.W.); (C.E.)
| | - Colt Egelston
- City of Hope National Medical Center, Department of Immuno-Oncology, Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, USA; (L.W.); (C.E.)
| | - Russell C. Rockne
- City of Hope National Medical Center, Department of Computational and Quantitative Medicine, Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, USA; (G.G.); (S.H.); (R.C.R.)
| | - Joseph Chao
- City of Hope National Medical Center, Department of Medical Oncology & Therapeutics Research, 1500 East Duarte Road, Duarte, CA 91010, USA;
| | - Peter P. Lee
- City of Hope National Medical Center, Department of Immuno-Oncology, Beckman Research Institute, 1500 East Duarte Road, Duarte, CA 91010, USA; (L.W.); (C.E.)
- Correspondence: (A.S.R.); (P.P.L.)
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69
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Mandracchia B, Son J, Jia S. Super-resolution optofluidic scanning microscopy. LAB ON A CHIP 2021; 21:489-493. [PMID: 33325966 PMCID: PMC8024922 DOI: 10.1039/d0lc00889c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Optofluidics enables visualizing diverse anatomical and functional traits of single-cell specimens with new degrees of imaging capabilities. However, the current optofluidic microscopy systems suffer from either low resolution to reveal subcellular details or incompatibility with general microfluidic devices or operations. Here, we report optofluidic scanning microscopy (OSM) for super-resolution, live-cell imaging. The system exploits multi-focal excitation using the innate fluidic motion of the specimens, allowing for minimal instrumental complexity and full compatibility with various microfluidic configurations. The results present effective resolution doubling, optical sectioning and contrast enhancement. We anticipate the OSM system to offer a promising super-resolution optofluidic paradigm for miniaturization and different levels of integration at the chip scale.
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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.
| | - Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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70
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Luo S, Nguyen KT, Nguyen BTT, Feng S, Shi Y, Elsayed A, Zhang Y, Zhou X, Wen B, Chierchia G, Talbot H, Bourouina T, Jiang X, Liu AQ. Deep learning-enabled imaging flow cytometry for high-speed Cryptosporidium and Giardia detection. Cytometry A 2021; 99:1123-1133. [PMID: 33550703 DOI: 10.1002/cyto.a.24321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/19/2022]
Abstract
Imaging flow cytometry has become a popular technology for bioparticle image analysis because of its capability of capturing thousands of images per second. Nevertheless, the vast number of images generated by imaging flow cytometry imposes great challenges for data analysis especially when the species have similar morphologies. In this work, we report a deep learning-enabled high-throughput system for predicting Cryptosporidium and Giardia in drinking water. This system combines imaging flow cytometry and an efficient artificial neural network called MCellNet, which achieves a classification accuracy >99.6%. The system can detect Cryptosporidium and Giardia with a sensitivity of 97.37% and a specificity of 99.95%. The high-speed analysis reaches 346 frames per second, outperforming the state-of-the-art deep learning algorithm MobileNetV2 in speed (251 frames per second) with a comparable classification accuracy. The reported system empowers rapid, accurate, and high throughput bioparticle detection in clinical diagnostics, environmental monitoring and other potential biosensing applications.
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Affiliation(s)
- Shaobo Luo
- ESIEE, Universite Paris-Est, Noisy-le-Grand Cedex, France.,Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Kim Truc Nguyen
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore, Singapore.,School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Binh T T Nguyen
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Shilun Feng
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore, Singapore.,School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yuzhi Shi
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ahmed Elsayed
- ESIEE, Universite Paris-Est, Noisy-le-Grand Cedex, France
| | - Yi Zhang
- School of Mechanical & Aerospace Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhou
- Research Centre of Environmental and Health Sensing Technology, School of Environment, Tsinghua University, Beijing, China
| | - Bihan Wen
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Hugues Talbot
- CentraleSupelec, Universite Paris-Saclay, Saint-Aubin, France
| | | | - Xudong Jiang
- School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ai Qun Liu
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore, Singapore.,School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore, Singapore
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71
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Zhou Y, Isozaki A, Yasumoto A, Xiao TH, Yatomi Y, Lei C, Goda K. Intelligent Platelet Morphometry. Trends Biotechnol 2021; 39:978-989. [PMID: 33509656 DOI: 10.1016/j.tibtech.2020.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022]
Abstract
Technological advances in image-based platelet analysis or platelet morphometry are critical for a better understanding of the structure and function of platelets in biological research as well as for the development of better clinical strategies in medical practice. Recently, the advent of high-throughput optical imaging and deep learning has boosted platelet morphometry to the next level by providing a new set of capabilities beyond what is achievable with traditional platelet morphometry, shedding light on the unexplored domain of platelet analysis. This Opinion article introduces emerging opportunities in 'intelligent' platelet morphometry, which are expected to pave the way for a new class of diagnostics, pharmacometrics, and therapeutics.
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Affiliation(s)
- Yuqi Zhou
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiro Isozaki
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan; Kanagawa Institute of Industrial Science and Technology, Kanagawa 213-0012, Japan
| | - Atsushi Yasumoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan; Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo 060-8648, Japan
| | - Ting-Hui Xiao
- Department of Chemistry, 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
| | - Cheng Lei
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan; Institute of Technological Sciences, Wuhan University, Hubei 430072, China
| | - 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, Los Angeles, CA 90095, USA.
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72
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LaBelle CA, Massaro A, Cortés-Llanos B, Sims CE, Allbritton NL. Image-Based Live Cell Sorting. Trends Biotechnol 2020; 39:613-623. [PMID: 33190968 DOI: 10.1016/j.tibtech.2020.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022]
Abstract
Technologies capable of cell separation based on cell images provide powerful tools enabling cell selection criteria that rely on spatially or temporally varying properties. Image-based cell sorting (IBCS) systems utilize microfluidic or microarray platforms, each having unique characteristics and applications. The advent of IBCS marks a new paradigm in which cell phenotype and behavior can be explored with high resolution and tied to cellular physiological and omics data, providing a deeper understanding of single-cell physiology and the creation of cell lines with unique properties. Cell sorting guided by high-content image information has far-reaching implications in biomedical research, clinical medicine, and pharmaceutical development.
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Affiliation(s)
- Cody A LaBelle
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, and North Carolina State University, Raleigh, NC, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Angelo Massaro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Christopher E Sims
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
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73
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Berlanda SF, Breitfeld M, Dietsche CL, Dittrich PS. Recent Advances in Microfluidic Technology for Bioanalysis and Diagnostics. Anal Chem 2020; 93:311-331. [DOI: 10.1021/acs.analchem.0c04366] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon F. Berlanda
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Maximilian Breitfeld
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Claudius L. Dietsche
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
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74
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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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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: 15.0] [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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Abil Z, Danelon C. Roadmap to Building a Cell: An Evolutionary Approach. Front Bioeng Biotechnol 2020; 8:927. [PMID: 32974299 PMCID: PMC7466671 DOI: 10.3389/fbioe.2020.00927] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022] Open
Abstract
Laboratory synthesis of an elementary biological cell from isolated components may aid in understanding of the fundamental principles of life and will provide a platform for a range of bioengineering and medical applications. In essence, building a cell consists in the integration of cellular modules into system's level functionalities satisfying a definition of life. To achieve this goal, we propose in this perspective to undertake a semi-rational, system's level evolutionary approach. The strategy would require iterative cycles of genetic integration of functional modules, diversification of hereditary information, compartmentalized gene expression, selection/screening, and possibly, assistance from open-ended evolution. We explore the underlying challenges to each of these steps and discuss possible solutions toward the bottom-up construction of an artificial living cell.
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Affiliation(s)
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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