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Mangla SK, Kazancoglu Y, Sezer MD, Top N, Sahin I. Optimizing fused deposition modelling parameters based on the design for additive manufacturing to enhance product sustainability. COMPUT IND 2023. [DOI: 10.1016/j.compind.2022.103833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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2
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Machine learning-enabled optimization of extrusion-based 3D printing. Methods 2022; 206:27-40. [PMID: 35963502 DOI: 10.1016/j.ymeth.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 01/02/2023] Open
Abstract
Machine learning (ML) and three-dimensional (3D) printing are among the fastest-growing branches of science. While ML can enable computers to independently learn from available data to make decisions with minimal human intervention, 3D printing has opened up an avenue for modern, multi-material, manufacture of complex 3D structures with a rapid turn-around ability for users with limited manufacturing experience. However, the determination of optimum printing parameters is still a challenge, increasing pre-printing process time and material wastage. Here, we present the first integration of ML and 3D printing through an easy-to-use graphical user interface (GUI) for printing parameter optimization. Unlike the widely held orthogonal design used in most of the 3D printing research, we, for the first time, used nine different computer-aided design (CAD) images and in order to enable ML algorithms to distinguish the difference between designs, we devised a self-designed method to calculate the "complexity index" of CAD designs. In addition, for the first time, the similarity of the print outcomes and CAD images are measured using four different self-designed labeling methods (both manually and automatically) to figure out the best labeling method for ML purposes. Subsequently, we trained eight ML algorithms on 224 datapoints to identify the best ML model for 3D printing applications. The "gradient boosting regression" model yields the best prediction performance with an R-2 score of 0.954. The ML-embedded GUI developed in this study enables users (either skilled or unskilled in 3D printing and/or ML) to simply upload a design (desired to print) to the GUI along with desired printing temperature and pressure to obtain the approximate similarity in the case of actual 3D printing of the uploaded design. This ultimately can prevent error-and-trial steps prior to printing which in return can speed up overall design-to-end-product time with less material waste and more cost-efficiency.
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3
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Rabbi F, Dabbagh SR, Angin P, Yetisen AK, Tasoglu S. Deep Learning-Enabled Technologies for Bioimage Analysis. MICROMACHINES 2022; 13:mi13020260. [PMID: 35208385 PMCID: PMC8880650 DOI: 10.3390/mi13020260] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 02/05/2023]
Abstract
Deep learning (DL) is a subfield of machine learning (ML), which has recently demonstrated its potency to significantly improve the quantification and classification workflows in biomedical and clinical applications. Among the end applications profoundly benefitting from DL, cellular morphology quantification is one of the pioneers. Here, we first briefly explain fundamental concepts in DL and then we review some of the emerging DL-enabled applications in cell morphology quantification in the fields of embryology, point-of-care ovulation testing, as a predictive tool for fetal heart pregnancy, cancer diagnostics via classification of cancer histology images, autosomal polycystic kidney disease, and chronic kidney diseases.
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Affiliation(s)
- Fazle Rabbi
- Department of Mechanical Engineering, Koç University, Sariyer, Istanbul 34450, Turkey; (F.R.); (S.R.D.)
| | - Sajjad Rahmani Dabbagh
- Department of Mechanical Engineering, Koç University, Sariyer, Istanbul 34450, Turkey; (F.R.); (S.R.D.)
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Sariyer, Istanbul 34450, Turkey
- Koc University Is Bank Artificial Intelligence Lab (KUIS AILab), Koç University, Sariyer, Istanbul 34450, Turkey
| | - Pelin Angin
- Department of Computer Engineering, Middle East Technical University, Ankara 06800, Turkey;
| | - Ali Kemal Yetisen
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK;
| | - Savas Tasoglu
- Department of Mechanical Engineering, Koç University, Sariyer, Istanbul 34450, Turkey; (F.R.); (S.R.D.)
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Sariyer, Istanbul 34450, Turkey
- Koc University Is Bank Artificial Intelligence Lab (KUIS AILab), Koç University, Sariyer, Istanbul 34450, Turkey
- Institute of Biomedical Engineering, Boğaziçi University, Çengelköy, Istanbul 34684, Turkey
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany
- Correspondence:
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4
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Dabbagh SR, Alseed MM, Saadat M, Sitti M, Tasoglu S. Biomedical Applications of Magnetic Levitation. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Sajjad Rahmani Dabbagh
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
- Koç University Arçelik Research Center for Creative Industries (KUAR) Koç University Sariyer Istanbul Turkey 34450
| | - M. Munzer Alseed
- Institute of Biomedical Engineering Boğaziçi University Çengelköy Istanbul Turkey 34684
| | - Milad Saadat
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
| | - Metin Sitti
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
- School of Medicine Koç University Istanbul 34450 Turkey
- Physical Intelligence Department Max Planck Institute for Intelligent Systems 70569 Stuttgart Germany
| | - Savas Tasoglu
- Department of Mechanical Engineering Koç University Sariyer Istanbul Turkey 34450
- Koç University Arçelik Research Center for Creative Industries (KUAR) Koç University Sariyer Istanbul Turkey 34450
- Institute of Biomedical Engineering Boğaziçi University Çengelköy Istanbul Turkey 34684
- Physical Intelligence Department Max Planck Institute for Intelligent Systems 70569 Stuttgart Germany
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5
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Delikoyun K, Yaman S, Yilmaz E, Sarigil O, Anil-Inevi M, Telli K, Yalcin-Ozuysal O, Ozcivici E, Tekin HC. HologLev: A Hybrid Magnetic Levitation Platform Integrated with Lensless Holographic Microscopy for Density-Based Cell Analysis. ACS Sens 2021; 6:2191-2201. [PMID: 34124887 DOI: 10.1021/acssensors.0c02587] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In clinical practice, a variety of diagnostic applications require the identification of target cells. Density has been used as a physical marker to distinguish cell populations since metabolic activities could alter the cell densities. Magnetic levitation offers great promise for separating cells at the single cell level within heterogeneous populations with respect to cell densities. Traditional magnetic levitation platforms need bulky and precise optical microscopes to visualize levitated cells. Moreover, the evaluation process of cell densities is cumbersome, which also requires trained personnel for operation. In this work, we introduce a device (HologLev) as a fusion of the magnetic levitation principle and lensless digital inline holographic microscopy (LDIHM). LDIHM provides ease of use by getting rid of bulky and expensive optics. By placing an imaging sensor just beneath the microcapillary channel without any lenses, recorded holograms are processed for determining cell densities through a fully automated digital image processing scheme. The device costs less than $100 and has a compact design that can fit into a pocket. We perform viability tests on the device by levitating three different cell lines (MDA-MB-231, U937, D1 ORL UVA) and comparing them against their dead correspondents. We also tested the differentiation of mouse osteoblastic (7F2) cells by monitoring characteristic variations in their density. Last, the response of MDA-MB-231 cancer cells to a chemotherapy drug was demonstrated in our platform. HologLev provides cost-effective, label-free, fully automated cell analysis in a compact design that could be highly desirable for laboratory and point-of-care testing applications.
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Affiliation(s)
- Kerem Delikoyun
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Sena Yaman
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Esra Yilmaz
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Oyku Sarigil
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Muge Anil-Inevi
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Kubra Telli
- Faculty of Science, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Ozden Yalcin-Ozuysal
- Faculty of Science, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Engin Ozcivici
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - H. Cumhur Tekin
- Faculty of Engineering, Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
- METU MEMS Center, Ankara 06520, Turkey
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6
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Ozdalgic B, Ustun M, Dabbagh SR, Haznedaroglu BZ, Kiraz A, Tasoglu S. Microfluidics for microalgal biotechnology. Biotechnol Bioeng 2021; 118:1545-1563. [PMID: 33410126 DOI: 10.1002/bit.27669] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/01/2021] [Accepted: 01/02/2021] [Indexed: 01/09/2023]
Abstract
Microalgae have expanded their roles as renewable and sustainable feedstocks for biofuel, smart nutrition, biopharmaceutical, cosmeceutical, biosensing, and space technologies. They accumulate valuable biochemical compounds from protein, carbohydrate, and lipid groups, including pigments and carotenoids. Microalgal biomass, which can be adopted for multivalorization under biorefinery settings, allows not only the production of various biofuels but also other value-added biotechnological products. However, state-of-the-art technologies are required to optimize yield, quality, and the economical aspects of both upstream and downstream processes. As such, the need to use microfluidic-based devices for both fundamental research and industrial applications of microalgae, arises due to their microscale sizes and dilute cultures. Microfluidics-based devices are superior to their competitors through their ability to perform multiple functions such as sorting and analyzing small amounts of samples (nanoliter to picoliter) with higher sensitivities. Here, we review emerging applications of microfluidic technologies on microalgal processes in cell sorting, cultivation, harvesting, and applications in biofuels, biosensing, drug delivery, and nutrition.
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Affiliation(s)
- Berin Ozdalgic
- Graduate School of Sciences and Engineering, Koc University, Sariyer, Istanbul, Turkey.,Department of Medical Services and Techniques, Advanced Vocational School, Dogus University, Istanbul, Turkey
| | - Merve Ustun
- Graduate School of Sciences and Engineering, Koc University, Sariyer, Istanbul, Turkey
| | - Sajjad Rahmani Dabbagh
- Department of Mechanical Engineering, Engineering Faculty, Koc University, Sariyer, Istanbul, Turkey.,Koc University Arcelik Research Center for Creative Industries (KUAR), Koc University, Sariyer, Istanbul, Turkey
| | - Berat Z Haznedaroglu
- Center for Life Sciences and Technologies, Bogazici University, Bebek, Istanbul, Turkey.,Institute of Environmental Sciences, Bogazici University, Bebek, Istanbul, Turkey
| | - Alper Kiraz
- Department of Physics, Koc University, Sariyer, Istanbul, Turkey.,Department of Electrical Engineering, Koc University, Sariyer, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, Koc University, Sariyer, Istanbul, Turkey
| | - Savas Tasoglu
- Department of Mechanical Engineering, Engineering Faculty, Koc University, Sariyer, Istanbul, Turkey.,Koc University Arcelik Research Center for Creative Industries (KUAR), Koc University, Sariyer, Istanbul, Turkey.,Center for Life Sciences and Technologies, Bogazici University, Bebek, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, Koc University, Sariyer, Istanbul, Turkey.,Institute of Biomedical Engineering, Bogazici University, Cengelkoy, Istanbul, Turkey
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7
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Dabbagh SR, Becher E, Ghaderinezhad F, Havlucu H, Ozcan O, Ozkan M, Yetisen AK, Tasoglu S. Increasing the packing density of assays in paper-based microfluidic devices. BIOMICROFLUIDICS 2021; 15:011502. [PMID: 33569089 PMCID: PMC7864678 DOI: 10.1063/5.0042816] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 05/04/2023]
Abstract
Paper-based devices have a wide range of applications in point-of-care diagnostics, environmental analysis, and food monitoring. Paper-based devices can be deployed to resource-limited countries and remote settings in developed countries. Paper-based point-of-care devices can provide access to diagnostic assays without significant user training to perform the tests accurately and timely. The market penetration of paper-based assays requires decreased device fabrication costs, including larger packing density of assays (i.e., closely packed features) and minimization of assay reagents. In this review, we discuss fabrication methods that allow for increasing packing density and generating closely packed features in paper-based devices. To ensure that the paper-based device is low-cost, advanced fabrication methods have been developed for the mass production of closely packed assays. These emerging methods will enable minimizing the volume of required samples (e.g., liquid biopsies) and reagents in paper-based microfluidic devices.
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Affiliation(s)
| | - Elaina Becher
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Fariba Ghaderinezhad
- Department of Mechanical Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Hayati Havlucu
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Sariyer, Istanbul 34450, Turkey
| | - Oguzhan Ozcan
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Sariyer, Istanbul 34450, Turkey
| | - Mehmed Ozkan
- Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Çengelköy, Istanbul 34684, Turkey
| | - Ali Kemal Yetisen
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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8
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Dabbagh SR, Rabbi F, Doğan Z, Yetisen AK, Tasoglu S. Machine learning-enabled multiplexed microfluidic sensors. BIOMICROFLUIDICS 2020; 14:061506. [PMID: 33343782 PMCID: PMC7733540 DOI: 10.1063/5.0025462] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
High-throughput, cost-effective, and portable devices can enhance the performance of point-of-care tests. Such devices are able to acquire images from samples at a high rate in combination with microfluidic chips in point-of-care applications. However, interpreting and analyzing the large amount of acquired data is not only a labor-intensive and time-consuming process, but also prone to the bias of the user and low accuracy. Integrating machine learning (ML) with the image acquisition capability of smartphones as well as increasing computing power could address the need for high-throughput, accurate, and automatized detection, data processing, and quantification of results. Here, ML-supported diagnostic technologies are presented. These technologies include quantification of colorimetric tests, classification of biological samples (cells and sperms), soft sensors, assay type detection, and recognition of the fluid properties. Challenges regarding the implementation of ML methods, including the required number of data points, image acquisition prerequisites, and execution of data-limited experiments are also discussed.
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Affiliation(s)
| | - Fazle Rabbi
- Department of Mechanical Engineering, Koç University, Sariyer, Istanbul 34450, Turkey
| | | | - Ali Kemal Yetisen
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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9
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Yaman S, Tekin HC. Magnetic Susceptibility-Based Protein Detection Using Magnetic Levitation. Anal Chem 2020; 92:12556-12563. [DOI: 10.1021/acs.analchem.0c02479] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sena Yaman
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
- METU MEMS Center, Ankara 06520, Turkey
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10
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Ghaderinezhad F, Ceylan Koydemir H, Tseng D, Karinca D, Liang K, Ozcan A, Tasoglu S. Sensing of electrolytes in urine using a miniaturized paper-based device. Sci Rep 2020; 10:13620. [PMID: 32788641 PMCID: PMC7423618 DOI: 10.1038/s41598-020-70456-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
Analyzing electrolytes in urine, such as sodium, potassium, calcium, chloride, and nitrite, has significant diagnostic value in detecting various conditions, such as kidney disorder, urinary stone disease, urinary tract infection, and cystic fibrosis. Ideally, by regularly monitoring these ions with the convenience of dipsticks and portable tools, such as cellphones, informed decision making is possible to control the consumption of these ions. Here, we report a paper-based sensor for measuring the concentration of sodium, potassium, calcium, chloride, and nitrite in urine, accurately quantified using a smartphone-enabled platform. By testing the device with both Tris buffer and artificial urine containing a wide range of electrolyte concentrations, we demonstrate that the proposed device can be used for detecting potassium, calcium, chloride, and nitrite within the whole physiological range of concentrations, and for binary quantification of sodium concentration.
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Affiliation(s)
- Fariba Ghaderinezhad
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Hatice Ceylan Koydemir
- Electrical and Computer Engineering, University of California, Los Angeles, CA, 90095, USA.,Bioengineering, University of California, Los Angeles, CA, 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Derek Tseng
- Electrical and Computer Engineering, University of California, Los Angeles, CA, 90095, USA.,Bioengineering, University of California, Los Angeles, CA, 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Doruk Karinca
- Computer Science, University of California, Los Angeles, CA, 90095, USA
| | - Kyle Liang
- Computer Science, University of California, Los Angeles, CA, 90095, USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering, University of California, Los Angeles, CA, 90095, USA. .,Bioengineering, University of California, Los Angeles, CA, 90095, USA. .,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
| | - Savas Tasoglu
- Department of Mechanical Engineering, Koc University, Sariyer, Istanbul, 34450, Turkey. .,Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Sariyer, Istanbul, 34450, Turkey. .,Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Çengelköy, Istanbul, 34684, Turkey. .,Koc University Research Center for Translational Medicine, Koç University, Sariyer, Istanbul, 34450, Turkey.
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Yang K, Wu J, Santos S, Liu Y, Zhu L, Lin F. Recent development of portable imaging platforms for cell-based assays. Biosens Bioelectron 2019; 124-125:150-160. [DOI: 10.1016/j.bios.2018.10.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/22/2022]
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12
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Yaman S, Anil-Inevi M, Ozcivici E, Tekin HC. Magnetic Force-Based Microfluidic Techniques for Cellular and Tissue Bioengineering. Front Bioeng Biotechnol 2018; 6:192. [PMID: 30619842 PMCID: PMC6305723 DOI: 10.3389/fbioe.2018.00192] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/23/2018] [Indexed: 01/21/2023] Open
Abstract
Live cell manipulation is an important biotechnological tool for cellular and tissue level bioengineering applications due to its capacity for guiding cells for separation, isolation, concentration, and patterning. Magnetic force-based cell manipulation methods offer several advantages, such as low adverse effects on cell viability and low interference with the cellular environment. Furthermore, magnetic-based operations can be readily combined with microfluidic principles by precisely allowing control over the spatiotemporal distribution of physical and chemical factors for cell manipulation. In this review, we present recent applications of magnetic force-based cell manipulation in cellular and tissue bioengineering with an emphasis on applications with microfluidic components. Following an introduction of the theoretical background of magnetic manipulation, components of magnetic force-based cell manipulation systems are described. Thereafter, different applications, including separation of certain cell fractions, enrichment of rare cells, and guidance of cells into specific macro- or micro-arrangements to mimic natural cell organization and function, are explained. Finally, we discuss the current challenges and limitations of magnetic cell manipulation technologies in microfluidic devices with an outlook on future developments in the field.
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