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García-Vázquez FA. Artificial intelligence and porcine breeding. Anim Reprod Sci 2024:107538. [PMID: 38926001 DOI: 10.1016/j.anireprosci.2024.107538] [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: 03/29/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Livestock management is evolving into a new era, characterized by the analysis of vast quantities of data (Big Data) collected from both traditional breeding methods and new technologies such as sensors, automated monitoring system, and advanced analytics. Artificial intelligence (A-In), which refers to the capability of machines to mimic human intelligence, including subfields like machine learning and deep learning, is playing a pivotal role in this transformation. A wide array of A-In techniques, successfully employed in various industrial and scientific contexts, are now being integrated into mainstream livestock management practices. In the case of swine breeding, while traditional methods have yielded considerable success, the increasing amount of information requires the adoption of new technologies such as A-In to drive productivity, enhance animal welfare, and reduce environmental impact. Current findings suggest that these techniques have the potential to match or exceed the performance of traditional methods, often being more scalable in terms of efficiency and sustainability within the breeding industry. This review provides insights into the application of A-In in porcine breeding, from the perspectives of both sows (including welfare and reproductive management) and boars (including semen quality and health), and explores new approaches which are already being applied in other species.
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Affiliation(s)
- Francisco A García-Vázquez
- Departamento de Fisiología, Facultad de Veterinaria, Campus de Excelencia Mare Nostrum, Universidad de Murcia, Murcia 30100, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.
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2
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Wheeler MB, Rabel RAC, Rubessa M, Popescu G. Label-free, high-throughput holographic imaging to evaluate mammalian gametes and embryos†. Biol Reprod 2024; 110:1125-1134. [PMID: 38733568 PMCID: PMC11180620 DOI: 10.1093/biolre/ioae057] [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: 11/07/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 05/13/2024] Open
Abstract
Assisted reproduction is one of the significant tools to treat human infertility. Morphological assessment is the primary method to determine sperm and embryo viability during in vitro fertilization cycles. It has the advantage of being a quick, convenient, and inexpensive means of assessment. However, visual observation is of limited predictive value for early embryo morphology. It has led many to search for other imaging tools to assess the reproductive potential of a given embryo. The limitations of visual assessment apply to both humans and animals. One recent innovation in assisted reproduction technology imaging is interferometric phase microscopy, also known as holographic microscopy. Interferometric phase microscopy/quantitative phase imaging is the next likely progression of analytical microscopes for the assisted reproduction laboratory. The interferometric phase microscopy system analyzes waves produced by the light as it passes through the specimen observed. The microscope collects the light waves produced and uses the algorithm to create a hologram of the specimen. Recently, interferometric phase microscopy has been combined with quantitative phase imaging, which joins phase contrast microscopy with holographic microscopy. These microscopes collect light waves produced and use the algorithm to create a hologram of the specimen. Unlike other systems, interferometric phase microscopy can provide a quantitative digital image, and it can make 2D and 3D images of the samples. This review summarizes some newer and more promising quantitative phase imaging microscopy systems for evaluating gametes and embryos. Studies clearly show that quantitative phase imaging is superior to bright field microscopy-based evaluation methods when evaluating sperm and oocytes prior to IVF and embryos prior to transfer. However, further assessment of these systems for efficacy, reproducibility, cost-effectiveness, and embryo/gamete safety must take place before they are widely adopted.
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Affiliation(s)
- Matthew B Wheeler
- Department of Animal Sciences University of Illinois at Urbana-Champaign, Champaign, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - R A Chanaka Rabel
- Department of Animal Sciences University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Marcello Rubessa
- Department of Animal Sciences University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Gabriel Popescu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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3
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Goswami N, Anastasio MA, Popescu G. Quantitative phase imaging techniques for measuring scattering properties of cells and tissues: a review-part I. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:S22713. [PMID: 39026612 PMCID: PMC11257415 DOI: 10.1117/1.jbo.29.s2.s22713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 07/20/2024]
Abstract
Significance Quantitative phase imaging (QPI) techniques offer intrinsic information about the sample of interest in a label-free, noninvasive manner and have an enormous potential for wide biomedical applications with negligible perturbations to the natural state of the sample in vitro. Aim We aim to present an in-depth review of the scattering formulation of light-matter interactions as applied to biological samples such as cells and tissues, discuss the relevant quantitative phase measurement techniques, and present a summary of various reported applications. Approach We start with scattering theory and scattering properties of biological samples followed by an exploration of various microscopy configurations for 2D QPI for measurement of structure and dynamics. Results We reviewed 157 publications and presented a range of QPI techniques and discussed suitable applications for each. We also presented the theoretical frameworks for phase reconstruction associated with the discussed techniques and highlighted their domains of validity. Conclusions We provide detailed theoretical as well as system-level information for a wide range of QPI techniques. Our study can serve as a guideline for new researchers looking for an exhaustive literature review of QPI methods and relevant applications.
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Affiliation(s)
- Neha Goswami
- University of Illinois Urbana-Champaign, Department of Bioengineering, Urbana, Illinois, United States
| | - Mark A. Anastasio
- University of Illinois Urbana-Champaign, Department of Bioengineering, Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
| | - Gabriel Popescu
- University of Illinois Urbana-Champaign, Department of Bioengineering, Urbana, Illinois, United States
- University of Illinois Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
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4
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Pirone D, Bianco V, Miccio L, Memmolo P, Psaltis D, Ferraro P. Beyond fluorescence: advances in computational label-free full specificity in 3D quantitative phase microscopy. Curr Opin Biotechnol 2024; 85:103054. [PMID: 38142647 DOI: 10.1016/j.copbio.2023.103054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/26/2023]
Abstract
Despite remarkable progresses in quantitative phase imaging (QPI) microscopes, their wide acceptance is limited due to the lack of specificity compared with the well-established fluorescence microscopy. In fact, the absence of fluorescent tag prevents to identify subcellular structures in single cells, making challenging the interpretation of label-free 2D and 3D phase-contrast data. Great effort has been made by many groups worldwide to address and overcome such limitation. Different computational methods have been proposed and many more are currently under investigation to achieve label-free microscopic imaging at single-cell level to recognize and quantify different subcellular compartments. This route promises to bridge the gap between QPI and FM for real-world applications.
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Affiliation(s)
- Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Vittorio Bianco
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Lisa Miccio
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Pasquale Memmolo
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Demetri Psaltis
- EPFL, Ecole Polytechnique Fédérale de Lausanne, Optics Laboratory, CH-1015 Lausanne, Switzerland
| | - Pietro Ferraro
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
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5
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Wang K, Song L, Wang C, Ren Z, Zhao G, Dou J, Di J, Barbastathis G, Zhou R, Zhao J, Lam EY. On the use of deep learning for phase recovery. LIGHT, SCIENCE & APPLICATIONS 2024; 13:4. [PMID: 38161203 PMCID: PMC10758000 DOI: 10.1038/s41377-023-01340-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024]
Abstract
Phase recovery (PR) refers to calculating the phase of the light field from its intensity measurements. As exemplified from quantitative phase imaging and coherent diffraction imaging to adaptive optics, PR is essential for reconstructing the refractive index distribution or topography of an object and correcting the aberration of an imaging system. In recent years, deep learning (DL), often implemented through deep neural networks, has provided unprecedented support for computational imaging, leading to more efficient solutions for various PR problems. In this review, we first briefly introduce conventional methods for PR. Then, we review how DL provides support for PR from the following three stages, namely, pre-processing, in-processing, and post-processing. We also review how DL is used in phase image processing. Finally, we summarize the work in DL for PR and provide an outlook on how to better use DL to improve the reliability and efficiency of PR. Furthermore, we present a live-updating resource ( https://github.com/kqwang/phase-recovery ) for readers to learn more about PR.
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Affiliation(s)
- Kaiqiang Wang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong SAR, China.
- School of Physical Science and Technology, Northwestern Polytechnical University, Xi'an, China.
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Li Song
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Chutian Wang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Zhenbo Ren
- School of Physical Science and Technology, Northwestern Polytechnical University, Xi'an, China
| | - Guangyuan Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jiazhen Dou
- School of Information Engineering, Guangdong University of Technology, Guangzhou, China
| | - Jianglei Di
- School of Information Engineering, Guangdong University of Technology, Guangzhou, China
| | - George Barbastathis
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Renjie Zhou
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jianlin Zhao
- School of Physical Science and Technology, Northwestern Polytechnical University, Xi'an, China.
| | - Edmund Y Lam
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong SAR, China.
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6
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Asada Y. Evolution of intracytoplasmic sperm injection: From initial challenges to wider applications. Reprod Med Biol 2024; 23:e12582. [PMID: 38803410 PMCID: PMC11129627 DOI: 10.1002/rmb2.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/18/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Background In vitro fertilization (IVF) has revolutionized infertility treatment. Nevertheless, male infertility requires more effective solutions. In 1992, the first-ever case of human birth via intracytoplasmic sperm injection (ICSI) was reported. ICSI involves microscopically injecting a sperm into an ovum. Successful ICSI has become a reliable therapy for couples facing infertility, a significant milestone. However, it has also introduced various challenges. This study also delves into ethical dilemmas arising from widespread ICSI use. Methods This review traces the history of ICSI, presenting pioneering attempts, first successful attempts, and critical reports on account of the initial skepticism toward the technology. The review also focuses on chronological progress until ICSI was recognized as effective and became widely applied. Main findings The review reveals that ICSI, although transformative, presents challenges. Successes include addressing male infertility and aiding fertilization. However, concerns arise regarding optimal sperm and embryo selection, genetic mutations, and long-term health implications. Ethical considerations surrounding ICSI's broad applications also surface. Conclusions Despite its success and effectiveness, ICSI is still evolving as a therapeutic method. By comprehensively evaluating the historical progress and the current status of ICSI and exploring its future prospects, this study highlights the importance of ICSI in infertility treatment.
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Ghayda RA, Cannarella R, Calogero AE, Shah R, Rambhatla A, Zohdy W, Kavoussi P, Avidor-Reiss T, Boitrelle F, Mostafa T, Saleh R, Toprak T, Birowo P, Salvio G, Calik G, Kuroda S, Kaiyal RS, Ziouziou I, Crafa A, Phuoc NHV, Russo GI, Durairajanayagam D, Al-Hashimi M, Hamoda TAAAM, Pinggera GM, Adriansjah R, Maldonado Rosas I, Arafa M, Chung E, Atmoko W, Rocco L, Lin H, Huyghe E, Kothari P, Solorzano Vazquez JF, Dimitriadis F, Garrido N, Homa S, Falcone M, Sabbaghian M, Kandil H, Ko E, Martinez M, Nguyen Q, Harraz AM, Serefoglu EC, Karthikeyan VS, Tien DMB, Jindal S, Micic S, Bellavia M, Alali H, Gherabi N, Lewis S, Park HJ, Simopoulou M, Sallam H, Ramirez L, Colpi G, Agarwal A. Artificial Intelligence in Andrology: From Semen Analysis to Image Diagnostics. World J Mens Health 2024; 42:39-61. [PMID: 37382282 PMCID: PMC10782130 DOI: 10.5534/wjmh.230050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/10/2023] [Accepted: 03/17/2023] [Indexed: 06/30/2023] Open
Abstract
Artificial intelligence (AI) in medicine has gained a lot of momentum in the last decades and has been applied to various fields of medicine. Advances in computer science, medical informatics, robotics, and the need for personalized medicine have facilitated the role of AI in modern healthcare. Similarly, as in other fields, AI applications, such as machine learning, artificial neural networks, and deep learning, have shown great potential in andrology and reproductive medicine. AI-based tools are poised to become valuable assets with abilities to support and aid in diagnosing and treating male infertility, and in improving the accuracy of patient care. These automated, AI-based predictions may offer consistency and efficiency in terms of time and cost in infertility research and clinical management. In andrology and reproductive medicine, AI has been used for objective sperm, oocyte, and embryo selection, prediction of surgical outcomes, cost-effective assessment, development of robotic surgery, and clinical decision-making systems. In the future, better integration and implementation of AI into medicine will undoubtedly lead to pioneering evidence-based breakthroughs and the reshaping of andrology and reproductive medicine.
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Affiliation(s)
- Ramy Abou Ghayda
- Urology Institute, University Hospitals, Case Western Reserve University, Cleveland, OH, USA
| | - Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- Glickman Urological & Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Aldo E. Calogero
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rupin Shah
- Department of Urology, Lilavati Hospital and Research Centre, Mumbai, India
| | - Amarnath Rambhatla
- Department of Urology, Henry Ford Health System, Vattikuti Urology Institute, Detroit, MI, USA
| | - Wael Zohdy
- Andrology and STDs, Cairo University, Cairo, Egypt
| | - Parviz Kavoussi
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Tomer Avidor-Reiss
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA
- Department of Urology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Florence Boitrelle
- Reproductive Biology, Fertility Preservation, Andrology, CECOS, Poissy Hospital, Poissy, France
- Department of Biology, Reproduction, Epigenetics, Environment, and Development, Paris Saclay University, UVSQ, INRAE, BREED, Paris, France
| | - Taymour Mostafa
- Andrology, Sexology & STIs Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Ramadan Saleh
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Tuncay Toprak
- Department of Urology, Fatih Sultan Mehmet Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Ponco Birowo
- Department of Urology, Dr. Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Gianmaria Salvio
- Department of Endocrinology, Polytechnic University of Marche, Ancona, Italy
| | - Gokhan Calik
- Department of Urology, Istanbul Medipol University, Istanbul, Turkey
| | - Shinnosuke Kuroda
- Glickman Urological & Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Department of Urology, Reproduction Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Raneen Sawaid Kaiyal
- Glickman Urological & Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Imad Ziouziou
- Department of Urology, College of Medicine and Pharmacy, Ibn Zohr University, Agadir, Morocco
| | - Andrea Crafa
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Nguyen Ho Vinh Phuoc
- Department of Andrology, Binh Dan Hospital, Ho Chi Minh City, Vietnam
- Department of Urology and Andrology, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | | | - Damayanthi Durairajanayagam
- Department of Physiology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Manaf Al-Hashimi
- Department of Urology, Burjeel Hospital, Abu Dhabi, United Arab Emirates (UAE)
- Khalifa University, College of Medicine and Health Science, Abu Dhabi, United Arab Emirates (UAE)
| | - Taha Abo-Almagd Abdel-Meguid Hamoda
- Department of Urology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Urology, Faculty of Medicine, Minia University, El-Minia, Egypt
| | | | - Ricky Adriansjah
- Department of Urology, Hasan Sadikin General Hospital, Universitas Padjadjaran, Banding, Indonesia
| | | | - Mohamed Arafa
- Department of Urology, Hamad Medical Corporation, Doha, Qatar
- Department of Urology, Weill Cornell Medical-Qatar, Doha, Qatar
| | - Eric Chung
- Department of Urology, Princess Alexandra Hospital, University of Queensland, Brisbane QLD, Australia
| | - Widi Atmoko
- Department of Urology, Dr. Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Lucia Rocco
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Peking University, Beijing, China
| | - Eric Huyghe
- Department of Urology and Andrology, University Hospital of Toulouse, Toulouse, France
| | - Priyank Kothari
- Department of Urology, B.Y.L. Nair Charitable Hospital, Topiwala National Medical College, Mumbai, India
| | | | - Fotios Dimitriadis
- Department of Urology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nicolas Garrido
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Sheryl Homa
- Department of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Marco Falcone
- Department of Urology, Molinette Hospital, A.O.U. Città della Salute e della Scienza, University of Turin, Torino, Italy
| | - Marjan Sabbaghian
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | | | - Edmund Ko
- Department of Urology, Loma Linda University Health, Loma Linda, CA, USA
| | - Marlon Martinez
- Section of Urology, Department of Surgery, University of Santo Tomas Hospital, Manila, Philippines
| | - Quang Nguyen
- Section of Urology, Department of Surgery, University of Santo Tomas Hospital, Manila, Philippines
- Center for Andrology and Sexual Medicine, Viet Duc University Hospital, Hanoi, Vietnam
- Department of Urology, Andrology and Sexual Medicine, University of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Ahmed M. Harraz
- Urology and Nephrology Center, Mansoura University, Mansoura, Egypt
- Department of Surgery, Urology Unit, Farwaniya Hospital, Farwaniya, Kuwait
- Department of Urology, Sabah Al Ahmad Urology Center, Kuwait City, Kuwait
| | - Ege Can Serefoglu
- Department of Urology, Biruni University School of Medicine, Istanbul, Turkey
| | | | - Dung Mai Ba Tien
- Department of Andrology, Binh Dan Hospital, Ho Chi Minh City, Vietnam
| | - Sunil Jindal
- Department of Andrology and Reproductive Medicine, Jindal Hospital, Meerut, India
| | - Sava Micic
- Department of Andrology, Uromedica Polyclinic, Belgrade, Serbia
| | - Marina Bellavia
- Andrology and IVF Center, Next Fertility Procrea, Lugano, Switzerland
| | - Hamed Alali
- King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Nazim Gherabi
- Andrology Committee of the Algerian Association of Urology, Algiers, Algeria
| | - Sheena Lewis
- Examen Lab Ltd., Northern Ireland, United Kingdom
| | - Hyun Jun Park
- Department of Urology, Pusan National University School of Medicine, Busan, Korea
- Medical Research Institute of Pusan National University Hospital, Busan, Korea
| | - Mara Simopoulou
- Department of Experimental Physiology, School of Health Sciences, Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Hassan Sallam
- Alexandria University Faculty of Medicine, Alexandria, Egypt
| | - Liliana Ramirez
- IVF Laboratory, CITMER Reproductive Medicine, Mexico City, Mexico
| | - Giovanni Colpi
- Andrology and IVF Center, Next Fertility Procrea, Lugano, Switzerland
| | - Ashok Agarwal
- Global Andrology Forum, Moreland Hills, OH, USA
- Cleveland Clinic, Cleveland, OH, USA
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8
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Astratov VN, Sahel YB, Eldar YC, Huang L, Ozcan A, Zheludev N, Zhao J, Burns Z, Liu Z, Narimanov E, Goswami N, Popescu G, Pfitzner E, Kukura P, Hsiao YT, Hsieh CL, Abbey B, Diaspro A, LeGratiet A, Bianchini P, Shaked NT, Simon B, Verrier N, Debailleul M, Haeberlé O, Wang S, Liu M, Bai Y, Cheng JX, Kariman BS, Fujita K, Sinvani M, Zalevsky Z, Li X, Huang GJ, Chu SW, Tzang O, Hershkovitz D, Cheshnovsky O, Huttunen MJ, Stanciu SG, Smolyaninova VN, Smolyaninov II, Leonhardt U, Sahebdivan S, Wang Z, Luk’yanchuk B, Wu L, Maslov AV, Jin B, Simovski CR, Perrin S, Montgomery P, Lecler S. Roadmap on Label-Free Super-Resolution Imaging. LASER & PHOTONICS REVIEWS 2023; 17:2200029. [PMID: 38883699 PMCID: PMC11178318 DOI: 10.1002/lpor.202200029] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 06/18/2024]
Abstract
Label-free super-resolution (LFSR) imaging relies on light-scattering processes in nanoscale objects without a need for fluorescent (FL) staining required in super-resolved FL microscopy. The objectives of this Roadmap are to present a comprehensive vision of the developments, the state-of-the-art in this field, and to discuss the resolution boundaries and hurdles which need to be overcome to break the classical diffraction limit of the LFSR imaging. The scope of this Roadmap spans from the advanced interference detection techniques, where the diffraction-limited lateral resolution is combined with unsurpassed axial and temporal resolution, to techniques with true lateral super-resolution capability which are based on understanding resolution as an information science problem, on using novel structured illumination, near-field scanning, and nonlinear optics approaches, and on designing superlenses based on nanoplasmonics, metamaterials, transformation optics, and microsphere-assisted approaches. To this end, this Roadmap brings under the same umbrella researchers from the physics and biomedical optics communities in which such studies have often been developing separately. The ultimate intent of this paper is to create a vision for the current and future developments of LFSR imaging based on its physical mechanisms and to create a great opening for the series of articles in this field.
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Affiliation(s)
- Vasily N. Astratov
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223-0001, USA
| | - Yair Ben Sahel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yonina C. Eldar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, California 90095, USA
- Bioengineering Department, University of California, Los Angeles, California 90095, USA
- California Nano Systems Institute (CNSI), University of California, Los Angeles, California 90095, USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, California 90095, USA
- Bioengineering Department, University of California, Los Angeles, California 90095, USA
- California Nano Systems Institute (CNSI), University of California, Los Angeles, California 90095, USA
- David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Nikolay Zheludev
- Optoelectronics Research Centre, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Disruptive Photonic Technologies, The Photonics Institute, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Junxiang Zhao
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zachary Burns
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Zhaowei Liu
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Material Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Evgenii Narimanov
- School of Electrical Engineering, and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - Neha Goswami
- Quantitative Light Imaging Laboratory, Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Gabriel Popescu
- Quantitative Light Imaging Laboratory, Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - Emanuel Pfitzner
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Philipp Kukura
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Yi-Teng Hsiao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica 1, Roosevelt Rd. Sec. 4, Taipei 10617 Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica 1, Roosevelt Rd. Sec. 4, Taipei 10617 Taiwan
| | - Brian Abbey
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia
| | - Alberto Diaspro
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Aymeric LeGratiet
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- Université de Rennes, CNRS, Institut FOTON - UMR 6082, F-22305 Lannion, France
| | - Paolo Bianchini
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Natan T. Shaked
- Tel Aviv University, Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv 6997801, Israel
| | - Bertrand Simon
- LP2N, Institut d’Optique Graduate School, CNRS UMR 5298, Université de Bordeaux, Talence France
| | - Nicolas Verrier
- IRIMAS UR UHA 7499, Université de Haute-Alsace, Mulhouse, France
| | | | - Olivier Haeberlé
- IRIMAS UR UHA 7499, Université de Haute-Alsace, Mulhouse, France
| | - Sheng Wang
- School of Physics and Technology, Wuhan University, China
- Wuhan Institute of Quantum Technology, China
| | - Mengkun Liu
- Department of Physics and Astronomy, Stony Brook University, USA
- National Synchrotron Light Source II, Brookhaven National Laboratory, USA
| | - Yeran Bai
- Boston University Photonics Center, Boston, MA 02215, USA
| | - Ji-Xin Cheng
- Boston University Photonics Center, Boston, MA 02215, USA
| | - Behjat S. Kariman
- Optical Nanoscopy and NIC@IIT, CHT, Istituto Italiano di Tecnologia, Via Enrico Melen 83B, 16152 Genoa, Italy
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Katsumasa Fujita
- Department of Applied Physics and the Advanced Photonics and Biosensing Open Innovation Laboratory (AIST); and the Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Moshe Sinvani
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Zeev Zalevsky
- Faculty of Engineering and the Nano-Technology Center, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Xiangping Li
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Guan-Jie Huang
- Department of Physics and Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Shi-Wei Chu
- Department of Physics and Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Omer Tzang
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Dror Hershkovitz
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Ori Cheshnovsky
- School of Chemistry, The Sackler faculty of Exact Sciences, and the Center for Light matter Interactions, and the Tel Aviv University Center for Nanoscience and Nanotechnology, Tel Aviv 69978, Israel
| | - Mikko J. Huttunen
- Laboratory of Photonics, Physics Unit, Tampere University, FI-33014, Tampere, Finland
| | - Stefan G. Stanciu
- Center for Microscopy – Microanalysis and Information Processing, Politehnica University of Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
| | - Vera N. Smolyaninova
- Department of Physics Astronomy and Geosciences, Towson University, 8000 York Rd., Towson, MD 21252, USA
| | - Igor I. Smolyaninov
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD 20742, USA
| | - Ulf Leonhardt
- Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sahar Sahebdivan
- EMTensor GmbH, TechGate, Donau-City-Strasse 1, 1220 Wien, Austria
| | - Zengbo Wang
- School of Computer Science and Electronic Engineering, Bangor University, Bangor, LL57 1UT, United Kingdom
| | - Boris Luk’yanchuk
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Limin Wu
- Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Alexey V. Maslov
- Department of Radiophysics, University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - Boya Jin
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223-0001, USA
| | - Constantin R. Simovski
- Department of Electronics and Nano-Engineering, Aalto University, FI-00076, Espoo, Finland
- Faculty of Physics and Engineering, ITMO University, 199034, St-Petersburg, Russia
| | - Stephane Perrin
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
| | - Paul Montgomery
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
| | - Sylvain Lecler
- ICube Research Institute, University of Strasbourg - CNRS - INSA de Strasbourg, 300 Bd. Sébastien Brant, 67412 Illkirch, France
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9
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Yuan G, Lv B, Hao C. Application of artificial neural networks in reproductive medicine. HUM FERTIL 2023; 26:1195-1201. [PMID: 36628627 DOI: 10.1080/14647273.2022.2156301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 09/01/2022] [Indexed: 01/12/2023]
Abstract
With the emergence of the age of information, the data on reproductive medicine has improved immensely. Nonetheless, healthcare workers who wish to utilise the relevance and implied value of the various data available to aid clinical decision-making encounter the difficulty of statistically analysing such large data. The application of artificial intelligence becoming widespread in recent years has emerged as a turning point in this regard. Artificial neural networks (ANNs) exhibit beneficial characteristics of comprehensive analysis and autonomous learning, owing to which these are being applied to disease diagnosis, embryo quality assessment, and prediction of pregnancy outcomes. The present report aims to summarise the application of ANNs in the field of reproduction and analyse its further application potential.
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Affiliation(s)
- Guanghui Yuan
- Department of Qingdao Medical College, Qingdao University, Qingdao, Shandong, China
| | - Bohan Lv
- Department of Intensive Care Unit, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Cuifang Hao
- Department of Reproductive Medicine, The Affiliated Women and Children's Hospital of Qingdao University, Qingdao, Shandong, China
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10
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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: 2] [Impact Index Per Article: 2.0] [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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11
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Unique Deep Radiomic Signature Shows NMN Treatment Reverses Morphology of Oocytes from Aged Mice. Biomedicines 2022; 10:biomedicines10071544. [PMID: 35884850 PMCID: PMC9313081 DOI: 10.3390/biomedicines10071544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/02/2023] Open
Abstract
The purpose of this study is to develop a deep radiomic signature based on an artificial intelligence (AI) model. This radiomic signature identifies oocyte morphological changes corresponding to reproductive aging in bright field images captured by optical light microscopy. Oocytes were collected from three mice groups: young (4- to 5-week-old) C57BL/6J female mice, aged (12-month-old) mice, and aged mice treated with the NAD+ precursor nicotinamide mononucleotide (NMN), a treatment recently shown to rejuvenate aspects of fertility in aged mice. We applied deep learning, swarm intelligence, and discriminative analysis to images of mouse oocytes taken by bright field microscopy to identify a highly informative deep radiomic signature (DRS) of oocyte morphology. Predictive DRS accuracy was determined by evaluating sensitivity, specificity, and cross-validation, and was visualized using scatter plots of the data associated with three groups: Young, old and Old + NMN. DRS could successfully distinguish morphological changes in oocytes associated with maternal age with 92% accuracy (AUC~1), reflecting this decline in oocyte quality. We then employed the DRS to evaluate the impact of the treatment of reproductively aged mice with NMN. The DRS signature classified 60% of oocytes from NMN-treated aged mice as having a ‘young’ morphology. In conclusion, the DRS signature developed in this study was successfully able to detect aging-related oocyte morphological changes. The significance of our approach is that DRS applied to bright field oocyte images will allow us to distinguish and select oocytes originally affected by reproductive aging and whose quality has been successfully restored by the NMN therapy.
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12
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Live-dead assay on unlabeled cells using phase imaging with computational specificity. Nat Commun 2022; 13:713. [PMID: 35132059 PMCID: PMC8821584 DOI: 10.1038/s41467-022-28214-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Existing approaches to evaluate cell viability involve cell staining with chemical reagents. However, the step of exogenous staining makes these methods undesirable for rapid, nondestructive, and long-term investigation. Here, we present an instantaneous viability assessment of unlabeled cells using phase imaging with computation specificity. This concept utilizes deep learning techniques to compute viability markers associated with the specimen measured by label-free quantitative phase imaging. Demonstrated on different live cell cultures, the proposed method reports approximately 95% accuracy in identifying live and dead cells. The evolution of the cell dry mass and nucleus area for the labeled and unlabeled populations reveal that the chemical reagents decrease viability. The nondestructive approach presented here may find a broad range of applications, from monitoring the production of biopharmaceuticals to assessing the effectiveness of cancer treatments. Common methods for characterising cell viability involve cell staining with chemical reagents. Here the authors report a method for cell viability assessment that does not require labelling; this uses quantitative phase imaging combined with deep learning.
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13
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Chow DJX, Wijesinghe P, Dholakia K, Dunning KR. Does artificial intelligence have a role in the IVF clinic? REPRODUCTION AND FERTILITY 2022; 2:C29-C34. [PMID: 35118395 PMCID: PMC8801019 DOI: 10.1530/raf-21-0043] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022] Open
Abstract
The success of IVF has remained stagnant for a decade. The focus of a great deal of research is to improve on the current ~30% success rate of IVF. Artificial intelligence (AI), or machines that mimic human intelligence, has been gaining traction for its potential to improve outcomes in medicine, such as cancer diagnosis from medical images. In this commentary, we discuss whether AI has the potential to improve fertility outcomes in the IVF clinic. Based on existing research, we examine the potential of adopting AI within multiple facets of an IVF cycle, including egg/sperm and embryo selection, as well as formulation of an IVF treatment regimen. We discuss both the potential benefits and concerns of the patient and clinician in adopting AI in the clinic. We outline hurdles that need to be overcome prior to implementation. We conclude that AI has an important future in improving IVF success.
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Affiliation(s)
- Darren J X Chow
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia.,Australian Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide, Australia.,Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
| | - Philip Wijesinghe
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Kishan Dholakia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia.,SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom.,School of Biological Sciences, The University of Adelaide, Adelaide, Australia.,Department of Physics, College of Science, Yonsei University, Seoul, South Korea
| | - Kylie R Dunning
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, Australia.,Australian Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide, Australia.,Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, Australia
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14
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Jo Y, Cho H, Park WS, Kim G, Ryu D, Kim YS, Lee M, Park S, Lee MJ, Joo H, Jo H, Lee S, Lee S, Min HS, Heo WD, Park Y. Label-free multiplexed microtomography of endogenous subcellular dynamics using generalizable deep learning. Nat Cell Biol 2021; 23:1329-1337. [PMID: 34876684 DOI: 10.1038/s41556-021-00802-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023]
Abstract
Simultaneous imaging of various facets of intact biological systems across multiple spatiotemporal scales is a long-standing goal in biology and medicine, for which progress is hindered by limits of conventional imaging modalities. Here we propose using the refractive index (RI), an intrinsic quantity governing light-matter interaction, as a means for such measurement. We show that major endogenous subcellular structures, which are conventionally accessed via exogenous fluorescence labelling, are encoded in three-dimensional (3D) RI tomograms. We decode this information in a data-driven manner, with a deep learning-based model that infers multiple 3D fluorescence tomograms from RI measurements of the corresponding subcellular targets, thereby achieving multiplexed microtomography. This approach, called RI2FL for refractive index to fluorescence, inherits the advantages of both high-specificity fluorescence imaging and label-free RI imaging. Importantly, full 3D modelling of absolute and unbiased RI improves generalization, such that the approach is applicable to a broad range of new samples without retraining to facilitate immediate applicability. The performance, reliability and scalability of this technology are extensively characterized, and its various applications within single-cell profiling at unprecedented scales (which can generate new experimentally testable hypotheses) are demonstrated.
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Affiliation(s)
- YoungJu Jo
- 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.,Departments of Applied Physics and of Biology, Stanford University, Stanford, CA, USA
| | | | - Wei Sun 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
| | - 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
| | - 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
| | - Young Seo 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.,Graduate School of Medial Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Moosung 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
| | - Sangwoo Park
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju, Republic of Korea
| | - Mahn Jae Lee
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea.,Graduate School of Medial Science and Engineering, KAIST, Daejeon, Republic of Korea
| | | | | | - Seongsoo Lee
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju, Republic of Korea
| | - Sumin Lee
- Tomocube, Daejeon, Republic of Korea
| | | | - Won Do Heo
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea. .,KAIST Institute for the BioCentury, KAIST, Daejeon, Republic of Korea.
| | - 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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15
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Atzitz Y, Dudaie M, Barnea I, Shaked NT. Sperm Inspection for In Vitro Fertilization via Self-Assembled Microdroplet Formation and Quantitative Phase Microscopy. Cells 2021; 10:3317. [PMID: 34943823 PMCID: PMC8699486 DOI: 10.3390/cells10123317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
We present a new method for the selection of individual sperm cells using a microfluidic device that automatically traps each cell in a separate microdroplet that then individually self-assembles with other microdroplets, permitting the controlled measurement of the cells using quantitative phase microscopy. Following cell trapping and droplet formation, we utilize quantitative phase microscopy integrated with bright-field imaging for individual sperm morphology and motility inspection. We then perform individual sperm selection using a single-cell micromanipulator, which is enhanced by the microdroplet-trapping procedure described above. This method can improve sperm selection for intracytoplasmic sperm injection, a common type of in vitro fertilization procedure.
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Affiliation(s)
| | | | | | - Natan T. Shaked
- Department of Biomedical, Engineering Tel Aviv University, Tel Aviv 6997801, Israel; (Y.A.); (M.D.); (I.B.)
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16
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Popescu G. Large-scale phase retrieval. LIGHT, SCIENCE & APPLICATIONS 2021; 10:175. [PMID: 34475382 PMCID: PMC8413447 DOI: 10.1038/s41377-021-00616-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Gabriel Popescu
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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17
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Tian L, Hunt B, Bell MAL, Yi J, Smith JT, Ochoa M, Intes X, Durr NJ. Deep Learning in Biomedical Optics. Lasers Surg Med 2021; 53:748-775. [PMID: 34015146 PMCID: PMC8273152 DOI: 10.1002/lsm.23414] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 01/02/2023]
Abstract
This article reviews deep learning applications in biomedical optics with a particular emphasis on image formation. The review is organized by imaging domains within biomedical optics and includes microscopy, fluorescence lifetime imaging, in vivo microscopy, widefield endoscopy, optical coherence tomography, photoacoustic imaging, diffuse tomography, and functional optical brain imaging. For each of these domains, we summarize how deep learning has been applied and highlight methods by which deep learning can enable new capabilities for optics in medicine. Challenges and opportunities to improve translation and adoption of deep learning in biomedical optics are also summarized. Lasers Surg. Med. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- L. Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - B. Hunt
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - M. A. L. Bell
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - J. Yi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
| | - J. T. Smith
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, New York NY 12180
| | - M. Ochoa
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, New York NY 12180
| | - X. Intes
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, New York NY 12180
| | - N. J. Durr
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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18
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Chen X, Kandel ME, Popescu G. Spatial light interference microscopy: principle and applications to biomedicine. ADVANCES IN OPTICS AND PHOTONICS 2021; 13:353-425. [PMID: 35494404 PMCID: PMC9048520 DOI: 10.1364/aop.417837] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this paper, we review spatial light interference microscopy (SLIM), a common-path, phase-shifting interferometer, built onto a phase-contrast microscope, with white-light illumination. As one of the most sensitive quantitative phase imaging (QPI) methods, SLIM allows for speckle-free phase reconstruction with sub-nanometer path-length stability. We first review image formation in QPI, scattering, and full-field methods. Then, we outline SLIM imaging from theory and instrumentation to diffraction tomography. Zernike's phase-contrast microscopy, phase retrieval in SLIM, and halo removal algorithms are discussed. Next, we discuss the requirements for operation, with a focus on software developed in-house for SLIM that enables high-throughput acquisition, whole slide scanning, mosaic tile registration, and imaging with a color camera. We introduce two methods for solving the inverse problem using SLIM, white-light tomography, and Wolf phase tomography. Lastly, we review the applications of SLIM in basic science and clinical studies. SLIM can study cell dynamics, cell growth and proliferation, cell migration, mass transport, etc. In clinical settings, SLIM can assist with cancer studies, reproductive technology, blood testing, etc. Finally, we review an emerging trend, where SLIM imaging in conjunction with artificial intelligence brings computational specificity and, in turn, offers new solutions to outstanding challenges in cell biology and pathology.
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19
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Kandel ME, Kim E, Lee YJ, Tracy G, Chung HJ, Popescu G. Multiscale Assay of Unlabeled Neurite Dynamics Using Phase Imaging with Computational Specificity. ACS Sens 2021; 6:1864-1874. [PMID: 33882232 PMCID: PMC8815662 DOI: 10.1021/acssensors.1c00100] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Primary neuronal cultures have been widely used to study neuronal morphology, neurophysiology, neurodegenerative processes, and molecular mechanism of synaptic plasticity underlying learning and memory. However, the unique behavioral properties of neurons make them challenging to study, with phenotypic differences expressed as subtle changes in neuronal arborization rather than easy-to-assay features such as cell count. The need to analyze morphology, growth, and intracellular transport has motivated the development of increasingly sophisticated microscopes and image analysis techniques. Due to its high-contrast, high-specificity output, many assays rely on confocal fluorescence microscopy, genetic methods, or antibody staining techniques. These approaches often limit the ability to measure quantitatively dynamic activity such as intracellular transport and growth. In this work, we describe a method for label-free live-cell cell imaging with antibody staining specificity by estimating the associated fluorescence signals via quantitative phase imaging and deep convolutional neural networks. This computationally inferred fluorescence image is then used to generate a semantic segmentation map, annotating subcellular compartments of live unlabeled neural cultures. These synthetic fluorescence maps were further applied to study the time-lapse development of hippocampal neurons, highlighting the relationships between the cellular dry mass production and the dynamic transport activity within the nucleus and neurites. Our implementation provides a high-throughput strategy to analyze neural network arborization dynamically, with high specificity and without the typical phototoxicity and photobleaching limitations associated with fluorescent markers.
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Affiliation(s)
- Mikhail E Kandel
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Eunjae Kim
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Young Jae Lee
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Gregory Tracy
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, United States
| | - Hee Jung Chung
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, United States
| | - Gabriel Popescu
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Jiao Y, He YR, Kandel ME, Liu X, Lu W, Popescu G. Computational interference microscopy enabled by deep learning. APL PHOTONICS 2021; 6:046103. [PMID: 35308602 PMCID: PMC8931864 DOI: 10.1063/5.0041901] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Quantitative phase imaging (QPI) has been widely applied in characterizing cells and tissues. Spatial light interference microscopy (SLIM) is a highly sensitive QPI method due to its partially coherent illumination and common path interferometry geometry. However, SLIM's acquisition rate is limited because of the four-frame phase-shifting scheme. On the other hand, off-axis methods such as diffraction phase microscopy (DPM) allow for single-shot QPI. However, the laser-based DPM system is plagued by spatial noise due to speckles and multiple reflections. In a parallel development, deep learning was proven valuable in the field of bioimaging, especially due to its ability to translate one form of contrast into another. Here, we propose using deep learning to produce synthetic, SLIM-quality, and high-sensitivity phase maps from DPM using single-shot images as the input. We used an inverted microscope with its two ports connected to the DPM and SLIM modules such that we have access to the two types of images on the same field of view. We constructed a deep learning model based on U-net and trained on over 1000 pairs of DPM and SLIM images. The model learned to remove the speckles in laser DPM and overcame the background phase noise in both the test set and new data. The average peak signal-to-noise ratio, Pearson correlation coefficient, and structural similarity index measure were 29.97, 0.79, and 0.82 for the test dataset. Furthermore, we implemented the neural network inference into the live acquisition software, which now allows a DPM user to observe in real-time an extremely low-noise phase image. We demonstrated this principle of computational interference microscopy imaging using blood smears, as they contain both erythrocytes and leukocytes, under static and dynamic conditions.
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Affiliation(s)
- Yuheng Jiao
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuchen R. He
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mikhail E. Kandel
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Xiaojun Liu
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wenlong Lu
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Gabriel Popescu
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Author to whom correspondence should be addressed:
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21
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Valiuškaitė V, Raudonis V, Maskeliūnas R, Damaševičius R, Krilavičius T. Deep Learning Based Evaluation of Spermatozoid Motility for Artificial Insemination. SENSORS (BASEL, SWITZERLAND) 2020; 21:E72. [PMID: 33374461 PMCID: PMC7795243 DOI: 10.3390/s21010072] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022]
Abstract
We propose a deep learning method based on the Region Based Convolutional Neural Networks (R-CNN) architecture for the evaluation of sperm head motility in human semen videos. The neural network performs the segmentation of sperm heads, while the proposed central coordinate tracking algorithm allows us to calculate the movement speed of sperm heads. We have achieved 91.77% (95% CI, 91.11-92.43%) accuracy of sperm head detection on the VISEM (A Multimodal Video Dataset of Human Spermatozoa) sperm sample video dataset. The mean absolute error (MAE) of sperm head vitality prediction was 2.92 (95% CI, 2.46-3.37), while the Pearson correlation between actual and predicted sperm head vitality was 0.969. The results of the experiments presented below will show the applicability of the proposed method to be used in automated artificial insemination workflow.
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Affiliation(s)
- Viktorija Valiuškaitė
- Department of Control Systems, Kaunas University of Technology, 51423 Kaunas, Lithuania; (V.V.); (V.R.)
| | - Vidas Raudonis
- Department of Control Systems, Kaunas University of Technology, 51423 Kaunas, Lithuania; (V.V.); (V.R.)
| | - Rytis Maskeliūnas
- Department of Multimedia Engineering, Kaunas University of Technology, 51423 Kaunas, Lithuania;
| | - Robertas Damaševičius
- Department of Applied Informatics, Vytautas Magnus University, 44404 Kaunas, Lithuania;
- Faculty of Applied Mathematics, Silesian University of Technology, 444-100 Gliwice, Poland
| | - Tomas Krilavičius
- Department of Applied Informatics, Vytautas Magnus University, 44404 Kaunas, Lithuania;
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