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Yan Z, Zhang H, Wang X, Gaňová M, Lednický T, Zhu H, Liu X, Korabečná M, Chang H, Neužil P. An image-to-answer algorithm for fully automated digital PCR image processing. LAB ON A CHIP 2022; 22:1333-1343. [PMID: 35258048 DOI: 10.1039/d1lc01175h] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The digital polymerase chain reaction (dPCR) is an irreplaceable variant of PCR techniques due to its capacity for absolute quantification and detection of rare deoxyribonucleic acid (DNA) sequences in clinical samples. Image processing methods, including micro-chamber positioning and fluorescence analysis, determine the reliability of the dPCR results. However, typical methods demand high requirements for the chip structure, chip filling, and light intensity uniformity. This research developed an image-to-answer algorithm with single fluorescence image capture and known image-related error removal. We applied the Hough transform to identify partitions in the images of dPCR chips, the 2D Fourier transform to rotate the image, and the 3D projection transformation to locate and correct the positions of all partitions. We then calculated each partition's average fluorescence amplitudes and generated a 3D fluorescence intensity distribution map of the image. We subsequently corrected the fluorescence non-uniformity between partitions based on the map and achieved statistical results of partition fluorescence intensities. We validated the proposed algorithms using different contents of the target DNA. The proposed algorithm is independent of the dPCR chip structure damage and light intensity non-uniformity. It also provides a reliable alternative to analyze the results of chip-based dPCR systems.
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Affiliation(s)
- Zhiqiang Yan
- School of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R. China.
| | - Haoqing Zhang
- School of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R. China.
| | - Xinlu Wang
- School of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R. China.
| | - Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00, Brno, Czech Republic
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00, Brno, Czech Republic
| | - Hanliang Zhu
- School of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R. China.
| | - Xiaocheng Liu
- School of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R. China.
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Honglong Chang
- School of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R. China.
| | - Pavel Neužil
- School of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R. China.
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Zhang Y, Qiao L, Ren Y, Wang X, Gao M, Tang Y, Jeff Xi J, Fu TM, Jiang X. Two dimensional barcode-inspired automatic analysis for arrayed microfluidic immunoassays. BIOMICROFLUIDICS 2013; 7:34110. [PMID: 24404030 PMCID: PMC3695989 DOI: 10.1063/1.4811278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/03/2013] [Indexed: 05/09/2023]
Abstract
The usability of many high-throughput lab-on-a-chip devices in point-of-care applications is currently limited by the manual data acquisition and analysis process, which are labor intensive and time consuming. Based on our original design in the biochemical reactions, we proposed here a universal approach to perform automatic, fast, and robust analysis for high-throughput array-based microfluidic immunoassays. Inspired by two-dimensional (2D) barcodes, we incorporated asymmetric function patterns into a microfluidic array. These function patterns provide quantitative information on the characteristic dimensions of the microfluidic array, as well as mark its orientation and origin of coordinates. We used a computer program to perform automatic analysis for a high-throughput antigen/antibody interaction experiment in 10 s, which was more than 500 times faster than conventional manual processing. Our method is broadly applicable to many other microchannel-based immunoassays.
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Affiliation(s)
- Yi Zhang
- College of Engineering and School of Physics, Peking University, Beijing 100871, China ; National Center for Nanoscience and Technology, Beijing 100190, China
| | - Lingbo Qiao
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China ; Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, China
| | - Yunke Ren
- College of Engineering and School of Physics, Peking University, Beijing 100871, China
| | - Xuwei Wang
- State Key Laboratory for Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080, China
| | - Ming Gao
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - Yunfang Tang
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jianzhong Jeff Xi
- College of Engineering and School of Physics, Peking University, Beijing 100871, China
| | - Tzung-May Fu
- College of Engineering and School of Physics, Peking University, Beijing 100871, China
| | - Xingyu Jiang
- National Center for Nanoscience and Technology, Beijing 100190, China
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