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Xu F, Wu Z, Tan C, Liao Y, Wang Z, Chen K, Pan A. Fourier Ptychographic Microscopy 10 Years on: A Review. Cells 2024; 13:324. [PMID: 38391937 PMCID: PMC10887115 DOI: 10.3390/cells13040324] [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: 12/15/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Fourier ptychographic microscopy (FPM) emerged as a prominent imaging technique in 2013, attracting significant interest due to its remarkable features such as precise phase retrieval, expansive field of view (FOV), and superior resolution. Over the past decade, FPM has become an essential tool in microscopy, with applications in metrology, scientific research, biomedicine, and inspection. This achievement arises from its ability to effectively address the persistent challenge of achieving a trade-off between FOV and resolution in imaging systems. It has a wide range of applications, including label-free imaging, drug screening, and digital pathology. In this comprehensive review, we present a concise overview of the fundamental principles of FPM and compare it with similar imaging techniques. In addition, we present a study on achieving colorization of restored photographs and enhancing the speed of FPM. Subsequently, we showcase several FPM applications utilizing the previously described technologies, with a specific focus on digital pathology, drug screening, and three-dimensional imaging. We thoroughly examine the benefits and challenges associated with integrating deep learning and FPM. To summarize, we express our own viewpoints on the technological progress of FPM and explore prospective avenues for its future developments.
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Affiliation(s)
- Fannuo Xu
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (F.X.); (Z.W.); (C.T.); (Y.L.); (Z.W.); (K.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zipei Wu
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (F.X.); (Z.W.); (C.T.); (Y.L.); (Z.W.); (K.C.)
- School of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Chao Tan
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (F.X.); (Z.W.); (C.T.); (Y.L.); (Z.W.); (K.C.)
- School of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Yizheng Liao
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (F.X.); (Z.W.); (C.T.); (Y.L.); (Z.W.); (K.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiping Wang
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (F.X.); (Z.W.); (C.T.); (Y.L.); (Z.W.); (K.C.)
- School of Physical Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Keru Chen
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (F.X.); (Z.W.); (C.T.); (Y.L.); (Z.W.); (K.C.)
- School of Automation Science and Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - An Pan
- State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (F.X.); (Z.W.); (C.T.); (Y.L.); (Z.W.); (K.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Wu R, Luo Z, Liu M, Zhang H, Zhen J, Yan L, Luo J, Wu Y. Fast Fourier ptychographic quantitative phase microscopy for in vitro label-free imaging. BIOMEDICAL OPTICS EXPRESS 2024; 15:95-113. [PMID: 38223174 PMCID: PMC10783909 DOI: 10.1364/boe.505267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/18/2023] [Accepted: 11/18/2023] [Indexed: 01/16/2024]
Abstract
Quantitative phase microscopy (QPM) is indispensable in biomedical research due to its advantages in unlabeled transparent sample thickness quantification and obtaining refractive index information. Fourier ptychographic microscopy (FPM) is among the most promising QPM methods, incorporating multi-angle illumination and iterative phase recovery for high-resolution quantitative phase imaging (QPI) of large cell populations over a wide field of-view (FOV) in a single pass. However, FPM is limited by data redundancy and sequential acquisition strategies, resulting in low imaging efficiency, which in turn limits its real-time application in in vitro label-free imaging. Here, we report a fast QPM based on Fourier ptychography (FQP-FPM), which uses an optimized annular downsampling and parallel acquisition strategy to minimize the amount of data required in the front end and reduce the iteration time of the back-end algorithm (3.3% and 4.4% of conventional FPM, respectively). Theoretical and data redundancy analyses show that FQP-FPM can realize high-throughput quantitative phase reconstruction at thrice the resolution of the coherent diffraction limit by acquiring only ten raw images, providing a precondition for in vitro label-free real-time imaging. The FQP-FPM application was validated for various in vitro label-free live-cell imaging. Cell morphology and subcellular phenomena in different periods were observed with a synthetic aperture of 0.75 NA at a 10× FOV, demonstrating its advantages and application potential for fast high-throughput QPI.
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Affiliation(s)
- Ruofei Wu
- School of Physics and Optoelectronic Engineering, Foshan University, Foshan 528000, China
| | - Zicong Luo
- School of Physics and Optoelectronic Engineering, Foshan University, Foshan 528000, China
| | - Mingdi Liu
- School of Physics and Optoelectronic Engineering, Foshan University, Foshan 528000, China
| | - Haiqi Zhang
- School of Physics and Optoelectronic Engineering, Foshan University, Foshan 528000, China
| | - Junrui Zhen
- School of Physics and Optoelectronic Engineering, Foshan University, Foshan 528000, China
| | - Lisong Yan
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jiaxiong Luo
- School of Physics and Optoelectronic Engineering, Foshan University, Foshan 528000, China
| | - Yanxiong Wu
- School of Physics and Optoelectronic Engineering, Foshan University, Foshan 528000, China
- Ji Hua Laboratory, Foshan, Guangdong 528200, China
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Gao Y, Pan A, Gao H, Wang A, Ma C, Yao B. Design of Fourier ptychographic illuminator for single full-FOV reconstruction. OPTICS EXPRESS 2023; 31:29826-29842. [PMID: 37710774 DOI: 10.1364/oe.500385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
Fourier ptychographic microscopy (FPM) is a spatial-temporal-modulation high-throughput imaging technique via a sequential angle-varied LED illumination. Therefore, the illuminator is one of the key components and the design of this illuminator is significant. However, because of the property of spherical wave, partial coherence, and aperture-induced vignetting, the acquired images must be processed in blocks first, and rely on parallel reconstruction via a graphics processing unit (GPU). The high cost makes it unappealing compared with commercial whole slide imaging system via a low-cost central processing unit (CPU). Especially, the vignetting severely destroys the space-invariant model and induces obvious artifacts in FPM, which is the most difficult problem. The conventional method is to divide the field of view (FOV) into many tiles and omit those imperfect images, which is crude and may discards low frequency information. In this paper, we reevaluated the conditions of vignetting in FPM. Through our analysis, the maximum side length of FOV is 0.759 mm for a single full-FOV reconstruction via a 4×/0.1 NA objective and a 4 mm spacing LED array in theory, while almost 1.0 mm can be achieved in practice due to the tolerance of algorithm. We found that FPM system can treat the vignetting coefficient Vf below 0.1 as brightfield images and Vf lager than 0.9 as darkfield images, respectively. We reported an optimized distribution for designing an illuminator without vignetting effect according to the off-the-shelf commercial products, which can reconstruct full FOV in one time via a CPU. By adjusting the distribution of LED units, the system could retrieve the object with the side length of FOV up to 3.8 mm for a single full-FOV reconstruction, which achieves the largest FOV that a typical 4×/0.1 NA objective with the field number of 22 mm can afford.
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Chen Q, Son J, Jia S. Implementation of miniaturized modular-array fluorescence microscopy for long-term live-cell imaging. APPLIED OPTICS 2023; 62:2456-2461. [PMID: 37132792 DOI: 10.1364/ao.483279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescence microscopy imaging of live cells has provided consistent monitoring of dynamic cellular activities and interactions. However, because current live-cell imaging systems are limited in their adaptability, portable cell imaging systems have been adapted by a variety of strategies, including miniaturized fluorescence microscopy. Here, we provide a protocol for the construction and operational process of miniaturized modular-array fluorescence microscopy (MAM). The MAM system is built in a portable size (15c m×15c m×3c m) and provides in situ cell imaging inside an incubator with a subcellular lateral resolution (∼3µm). We demonstrated the improved stability of the MAM system with fluorescent targets and live HeLa cells, enabling long-term imaging for 12 h without the need for external support or post-processing. We believe the protocol could guide scientists to construct a compact portable fluorescence imaging system and perform time-lapse in situ single-cell imaging and analysis.
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Guo C, Jiang S, Yang L, Song P, Pirhanov A, Wang R, Wang T, Shao X, Wu Q, Cho YK, Zheng G. Depth-multiplexed ptychographic microscopy for high-throughput imaging of stacked bio-specimens on a chip. Biosens Bioelectron 2023; 224:115049. [PMID: 36623342 DOI: 10.1016/j.bios.2022.115049] [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: 08/03/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023]
Abstract
Imaging a large number of bio-specimens at high speed is essential for many biomedical applications. The common strategy is to place specimens at different lateral positions and image them sequentially. Here we report a new on-chip imaging strategy, termed depth-multiplexed ptychographic microscopy (DPM), for parallel imaging and sensing at high speed. Different from the common strategy, DPM stacks multiple specimens in the axial direction and images the entire z-stack all at once. In our prototype platform, we modify a low-cost car mirror for programmable steering of the incident laser beam. A blood-coated image sensor is then placed underneath the stacked sample for acquiring the resulting diffraction patterns. With the captured images, we perform blind recovery of the incident beam angle and model different layers of the stacked sample as different coded surfaces for object reconstruction. For in vitro experiment, we demonstrate time-lapse cell culture monitoring by imaging 3 stacked microfluidic channels on the coded sensor. For high-throughput cytometric analysis, we image 5 stacked brain sections with a 205-mm2 field of view in ∼50 s. Cytometric analysis is also performed to quantify the cellular proliferation biomarkers on the slides. The DPM approach adds a new degree of freedom for data multiplexing in microscopy, enabling parallel imaging of multiple specimens using a single detector. The demonstrated 6-mm depth of field is among the longest ones in microscopy imaging. The novel depth-multiplexed configuration also complements the miniaturization provided by microfluidics devices, offering a solution for on-chip sensing and imaging with efficient sample handling.
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Affiliation(s)
- Chengfei Guo
- Hangzhou Institute of Technology, Xidian University, Hangzhou, 311231, China; Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Shaowei Jiang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Liming Yang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Pengming Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Azady Pirhanov
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Ruihai Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Tianbo Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Xiaopeng Shao
- Hangzhou Institute of Technology, Xidian University, Hangzhou, 311231, China
| | - Qian Wu
- Department of Pathology and Laboratory Medicine, University of Connecticut Health Centre, Farmington, CT, 06030, USA
| | - Yong Ku Cho
- Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
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Wang T, Jiang S, Song P, Wang R, Yang L, Zhang T, Zheng G. Optical ptychography for biomedical imaging: recent progress and future directions [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:489-532. [PMID: 36874495 PMCID: PMC9979669 DOI: 10.1364/boe.480685] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/10/2022] [Accepted: 12/10/2022] [Indexed: 05/25/2023]
Abstract
Ptychography is an enabling microscopy technique for both fundamental and applied sciences. In the past decade, it has become an indispensable imaging tool in most X-ray synchrotrons and national laboratories worldwide. However, ptychography's limited resolution and throughput in the visible light regime have prevented its wide adoption in biomedical research. Recent developments in this technique have resolved these issues and offer turnkey solutions for high-throughput optical imaging with minimum hardware modifications. The demonstrated imaging throughput is now greater than that of a high-end whole slide scanner. In this review, we discuss the basic principle of ptychography and summarize the main milestones of its development. Different ptychographic implementations are categorized into four groups based on their lensless/lens-based configurations and coded-illumination/coded-detection operations. We also highlight the related biomedical applications, including digital pathology, drug screening, urinalysis, blood analysis, cytometric analysis, rare cell screening, cell culture monitoring, cell and tissue imaging in 2D and 3D, polarimetric analysis, among others. Ptychography for high-throughput optical imaging, currently in its early stages, will continue to improve in performance and expand in its applications. We conclude this review article by pointing out several directions for its future development.
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Affiliation(s)
- Tianbo Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- These authors contributed equally to this work
| | - Shaowei Jiang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- These authors contributed equally to this work
| | - Pengming Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
- These authors contributed equally to this work
| | - Ruihai Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Liming Yang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Terrance Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
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Zhao H, Hui W, Ye Q, Huang K, Shi Q, Tian J, Zhou W. Parallel Fourier ptychographic microscopy reconstruction method based on FPGA. OPTICS EXPRESS 2023; 31:5016-5026. [PMID: 36785454 DOI: 10.1364/oe.478193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Fourier ptychographic microscopy (FPM) can bypass the limitation of spatial bandwidth product to get images with large field-of-view and high resolution. The complicated sequential iterative calculation in the FPM reconstruction process reduces the reconstruction efficiency of the FPM. Therefore, we propose a parallel FPM reconstruction method based on field programmable gate array (FPGA) to accelerate the FPM reconstruction process. Using this method, multiple sub-regions in the Fourier domain can be computed in parallel and we customize a dedicated high-performance computational architecture for this approach. We deploy 4 FPM reconstruct computing architectures with a parallelism of 4 in a FPGA to compute the FPM reconstruction process, achieving the speed nearly 180 times faster than traditional methods. The proposed method provides a new perspective of parallel computing for FPM reconstruction.
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Liang M, Yang C. Implementation of free-space Fourier Ptychography with near maximum system numerical aperture. OPTICS EXPRESS 2022; 30:20321-20332. [PMID: 36224781 PMCID: PMC9363023 DOI: 10.1364/oe.459833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/06/2022] [Accepted: 05/14/2022] [Indexed: 05/25/2023]
Abstract
Over the past decade, the research field of Fourier Ptychographic Microscopy (FPM) has seen numerous innovative developments that significantly expands its utility. Here, we report a high numerical aperture (NA) FPM implementation that incorporates some of these innovations to achieve a synthetic NA of 1.9 - close to the maximum possible synthetic NA of 2 for a free space FPM system. At this high synthetic NA, we experimentally found that it is vital to homogenize the illumination field in order to achieve the best resolution. Our FPM implementation has a full pitch resolution of 266 nm for 465 nm light, and depth of field of 3.6 µm. In comparison, a standard transmission microscope (incoherent) with close to maximum possible NA of 0.95 has a full pitch resolution of 318 nm for 465 nm light, and depth of field of 0.65 µm. While it is generally assumed that a free-space coherent imaging system and a free-space incoherent imaging system operating at their respective maximum NA should give comparable resolution, we experimentally find that an FPM system significantly outperforms its incoherent standard microscopy counterpart in resolution by a factor of 20%. Coupled with FPM's substantially longer effective depth of field (5.5 times longer), our work indicates that, in the near-maximum NA operation regime, the FPM has significant resolution and depth of field advantages over incoherent standard microscopy.
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Wang A, Zhang Z, Wang S, Pan A, Ma C, Yao B. Fourier Ptychographic Microscopy via Alternating Direction Method of Multipliers. Cells 2022; 11:cells11091512. [PMID: 35563818 PMCID: PMC9104836 DOI: 10.3390/cells11091512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
Fourier ptychographic microscopy (FPM) has risen as a promising computational imaging technique that breaks the trade-off between high resolution and large field of view (FOV). Its reconstruction is normally formulated as a blind phase retrieval problem, where both the object and probe have to be recovered from phaseless measured data. However, the stability and reconstruction quality may dramatically deteriorate in the presence of noise interference. Herein, we utilized the concept of alternating direction method of multipliers (ADMM) to solve this problem (termed ADMM-FPM) by breaking it into multiple subproblems, each of which may be easier to deal with. We compared its performance against existing algorithms in both simulated and practical FPM platform. It is found that ADMM-FPM method belongs to a global optimization algorithm with a high degree of parallelism and thus results in a more stable and robust phase recovery under noisy conditions. We anticipate that ADMM will rekindle interest in FPM as more modifications and innovations are implemented in the future.
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Affiliation(s)
- Aiye Wang
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (A.W.); (B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Space Precision Measurement Technology, Xi’an 710119, China
| | - Zhuoqun Zhang
- Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 3JD, UK;
| | - Siqi Wang
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, Varennes, QC J3X 1S2, Canada;
| | - An Pan
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (A.W.); (B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (A.P.); (C.M.)
| | - Caiwen Ma
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (A.W.); (B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Space Precision Measurement Technology, Xi’an 710119, China
- Correspondence: (A.P.); (C.M.)
| | - Baoli Yao
- Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, China; (A.W.); (B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Wakefield DL, Graham R, Wong K, Wang S, Hale C, Yu CC. Cellular analysis using label-free parallel array microscopy with Fourier ptychography. BIOMEDICAL OPTICS EXPRESS 2022; 13:1312-1327. [PMID: 35415005 PMCID: PMC8973186 DOI: 10.1364/boe.451128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 06/01/2023]
Abstract
Quantitative phase imaging (QPI) is an ideal method to non-invasively monitor cell populations and provide label-free imaging and analysis. QPI offers enhanced sample characterization and cell counting compared to conventional label-free techniques. We demonstrate this in the current study through a comparison of cell counting data from digital phase contrast (DPC) imaging and from QPI using a system based on Fourier ptychographic microscopy (FPM). Our FPM system offers multi-well, parallel imaging and a QPI-specific cell segmentation method to establish automated and reliable cell counting. Three cell types were studied and FPM showed improvement in the ability to resolve fine details and thin cells, despite limitations of the FPM system incurred by imaging artifacts. Relative to manually counted fluorescence ground-truth, cell counting results after automated segmentation showed improved accuracy with QPI over DPC.
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Affiliation(s)
- Devin L. Wakefield
- Amgen Inc, South San Francisco, CA 94080, USA
- These authors contributed equally to this work
| | - Richard Graham
- Clearbridge Biophotonics FPM Inc, Pasadena, CA 91101, USA (no longer in operation)
- These authors contributed equally to this work
| | - Kevin Wong
- Clearbridge Biophotonics FPM Inc, Pasadena, CA 91101, USA (no longer in operation)
- These authors contributed equally to this work
| | - Songli Wang
- Amgen Inc, South San Francisco, CA 94080, USA
| | | | - Chung-Chieh Yu
- Clearbridge Biophotonics FPM Inc, Pasadena, CA 91101, USA (no longer in operation)
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Zhao H, Hui W, Ye Q, Huang K, Shi Q, Tian J, Zhou W. High-performance heterogeneous FPGA data-flow architecture for Fourier ptychographic microscopy. APPLIED OPTICS 2022; 61:1420-1426. [PMID: 35201025 DOI: 10.1364/ao.448020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Fourier ptychographic microscopy (FPM) is a recently developed computational imaging technique that can achieve both high-resolution and a wide field-of-view via a sequence of low-resolution images. FPM is a complex iterative process, and it is difficult to meet the needs of rapid reconstruction imaging with the conventional FPM deployed on general purpose processors. In this paper, we propose a high-performance heterogeneous field-programmable gate array (FPGA) architecture based on the principle of full pipeline and the data-flow structure for the iterative reconstruction procedure of FPM. By optimizing the architecture network at gate-level logic circuits, the running time of the FPGA-based FPM reconstruction procedure is nearly 20 times faster than conventional methods. Our proposed architecture can be used to develop FPM imaging equipment that meets resource and performance requirements.
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Wang C, Hu M, Takashima Y, Schulz TJ, Brady DJ. Snapshot ptychography on array cameras. OPTICS EXPRESS 2022; 30:2585-2598. [PMID: 35209395 DOI: 10.1364/oe.447499] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
We use convolutional neural networks to recover images optically down-sampled by 6.7 × using coherent aperture synthesis over a 16 camera array. Where conventional ptychography relies on scanning and oversampling, here we apply decompressive neural estimation to recover full resolution image from a single snapshot, although as shown in simulation multiple snapshots can be used to improve signal-to-noise ratio (SNR). In place training on experimental measurements eliminates the need to directly calibrate the measurement system. We also present simulations of diverse array camera sampling strategies to explore how snapshot compressive systems might be optimized.
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Liang M, Bernadt C, Wong SBJ, Choi C, Cote R, Yang C. All-in-focus fine needle aspiration biopsy imaging based on Fourier ptychographic microscopy. J Pathol Inform 2022; 13:100119. [PMID: 36268073 PMCID: PMC9577034 DOI: 10.1016/j.jpi.2022.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Context Cytology is the study of whole cells in diagnostic pathology. Unlike standard histologic thinly sliced specimens, cytologic preparations consist of preparations of whole cells where cells commonly cluster and aggregate. As such, cytology preparations are generally much thicker than histologic slides, resulting in large patches of defocus when examined under the microscope. A diagnostic aggregate of cells often cannot be viewed in focus together, requiring pathologists to continually manipulate the focal plane, complicating the task of accurately assessing the entire cellular aggregate and thus in making a diagnosis. Further, it is extremely difficult to acquire useful uniformly in-focus digital images of cytology preparations for applications such as remote diagnostic evaluations and artificial intelligence models. The predominant current method to address this issue is to acquire digital images at multiple focal planes of the entire slide, which demands long scanning time, complex and expensive scanning systems, and huge storage capacity. Aims Here we report a unique imaging method that can acquire cytologic images efficiently and computationally render all-in-focus digital images that are highly compact. Methods and material This method applies a metric-based digital refocusing to microscopy data collected with a Fourier ptychographic microscope (FPM). The digitally refocused patches of images are then synthesized into an all-in-focus image. Results We report all-in-focus FPM results of thyroid fine needle aspiration (FNA) cytology samples, demonstrating our method’s ability to overcome the height variance of 30 μm caused by cell aggregation, and rendering images at high resolution (corresponds to a standard microscope with objective NA of 0.75) and that are all-in-focus. Conclusions This technology is applicable to standard microscopes, and we believe can have an impact on diagnostic accuracy as well as ease and speed of diagnosing challenging specimens. While we focus on cytology slides here, we anticipate this technology’s advantages will translate well for histology applications. This technique also addresses the issue of remote rapid evaluation of cytology preparations. Finally, we believe that by resolving the focus heterogeneity issues in standard digital images, this technique is a critical advance for applying machine learning to cytology specimens.
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14
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Ly VT, Baudin PV, Pansodtee P, Jung EA, Voitiuk K, Rosen YM, Willsey HR, Mantalas GL, Seiler ST, Selberg JA, Cordero SA, Ross JM, Rolandi M, Pollen AA, Nowakowski TJ, Haussler D, Mostajo-Radji MA, Salama SR, Teodorescu M. Picroscope: low-cost system for simultaneous longitudinal biological imaging. Commun Biol 2021; 4:1261. [PMID: 34737378 PMCID: PMC8569150 DOI: 10.1038/s42003-021-02779-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/05/2021] [Indexed: 01/02/2023] Open
Abstract
Simultaneous longitudinal imaging across multiple conditions and replicates has been crucial for scientific studies aiming to understand biological processes and disease. Yet, imaging systems capable of accomplishing these tasks are economically unattainable for most academic and teaching laboratories around the world. Here, we propose the Picroscope, which is the first low-cost system for simultaneous longitudinal biological imaging made primarily using off-the-shelf and 3D-printed materials. The Picroscope is compatible with standard 24-well cell culture plates and captures 3D z-stack image data. The Picroscope can be controlled remotely, allowing for automatic imaging with minimal intervention from the investigator. Here, we use this system in a range of applications. We gathered longitudinal whole organism image data for frogs, zebrafish, and planaria worms. We also gathered image data inside an incubator to observe 2D monolayers and 3D mammalian tissue culture models. Using this tool, we can measure the behavior of entire organisms or individual cells over long-time periods.
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Affiliation(s)
- Victoria T Ly
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
| | - Pierre V Baudin
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Pattawong Pansodtee
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Erik A Jung
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Kateryna Voitiuk
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Yohei M Rosen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Gary L Mantalas
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Spencer T Seiler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - John A Selberg
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sergio A Cordero
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Jayden M Ross
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Alex A Pollen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Tomasz J Nowakowski
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mohammed A Mostajo-Radji
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94143, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
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15
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Chen C, Lu YN, Huang H, Yan K, Jiang Z, He X, Kong Y, Liu C, Liu F, Xue L, Wang S. PhaseRMiC: phase real-time microscope camera for live cell imaging. BIOMEDICAL OPTICS EXPRESS 2021; 12:5261-5271. [PMID: 34513255 PMCID: PMC8407842 DOI: 10.1364/boe.430115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 05/20/2023]
Abstract
We design a novel phase real-time microscope camera (PhaseRMiC) for live cell phase imaging. PhaseRMiC has a simple and cost-effective configuration only consisting of a beam splitter and a board-level camera with two CMOS imaging chips. Moreover, integrated with 3-D printed structures, PhaseRMiC has a compact size of 136×91×60 mm3, comparable to many commercial microscope cameras, and can be directly connected to the microscope side port. Additionally, PhaseRMiC can be well adopted in real-time phase imaging proved with satisfied accuracy, good stability and large field of view. Considering its compact and cost-effective device design as well as real-time phase imaging capability, PhaseRMiC is a preferred solution for live cell imaging.
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Affiliation(s)
- Chao Chen
- Computational Optics Laboratory, School of Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yu-Nan Lu
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing 210095, China
| | - Huachuan Huang
- School of Manufacture Science and Engineering, Key Laboratory of Testing Technology for Manufacturing Process, Ministry of Education, Southwest University of Science and Technology, Mianyang 621010, China
| | - Keding Yan
- Advanced Institute of Micro-Nano Intelligent Sensing (AIMNIS), School of Electronic Information Engineering, Xi'an Technological University, Xi'an, Shaanxi 710032, China
| | - Zhilong Jiang
- Computational Optics Laboratory, School of Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaoliang He
- Computational Optics Laboratory, School of Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Kong
- Computational Optics Laboratory, School of Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Cheng Liu
- Computational Optics Laboratory, School of Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
- Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Fei Liu
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Xue
- College of Electronics and Information Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Shouyu Wang
- Computational Optics Laboratory, School of Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing 210095, China
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16
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Son J, Mandracchia B, Jia S. Miniaturized modular-array fluorescence microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:7221-7235. [PMID: 33408992 PMCID: PMC7747904 DOI: 10.1364/boe.410605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 05/20/2023]
Abstract
Fluorescence live-cell imaging allows for continuous interrogation of cellular behaviors, and the recent development of portable live-cell imaging platforms has rapidly transformed conventional schemes with high adaptability, cost-effective functionalities and easy accessibility to cell-based assays. However, broader applications remain restrictive due to compatibility with conventional cell culture workflow and biochemical sensors, accessibility to up-right physiological imaging, or parallelization of data acquisition. Here, we introduce miniaturized modular-array fluorescence microscopy (MAM) for compact live-cell imaging in flexible formats. We advance the current miniscopy technology to devise an up-right modular architecture, each combining a gradient-index (GRIN) objective and individually-addressed illumination and acquisition components. Parallelization of an array of such modular devices allows for multi-site data acquisition in situ using conventional off-the-shelf cell chambers. Compared with existing methods, the device offers a high fluorescence sensitivity and efficiency, exquisite spatiotemporal resolution (∼3 µm and up to 60 Hz), a configuration compatible with conventional cell culture assays and physiological imaging, and an effective parallelization of data acquisition. The system has been demonstrated using various calibration and biological samples and experimental conditions, representing a promising solution to time-lapse in situ single-cell imaging and analysis.
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17
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Diederich B, Lachmann R, Carlstedt S, Marsikova B, Wang H, Uwurukundo X, Mosig AS, Heintzmann R. A versatile and customizable low-cost 3D-printed open standard for microscopic imaging. Nat Commun 2020; 11:5979. [PMID: 33239615 PMCID: PMC7688980 DOI: 10.1038/s41467-020-19447-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
Modern microscopes used for biological imaging often present themselves as black boxes whose precise operating principle remains unknown, and whose optical resolution and price seem to be in inverse proportion to each other. With UC2 (You. See. Too.) we present a low-cost, 3D-printed, open-source, modular microscopy toolbox and demonstrate its versatility by realizing a complete microscope development cycle from concept to experimental phase. The self-contained incubator-enclosed brightfield microscope monitors monocyte to macrophage cell differentiation for seven days at cellular resolution level (e.g. 2 μm). Furthermore, by including very few additional components, the geometry is transferred into a 400 Euro light sheet fluorescence microscope for volumetric observations of a transgenic Zebrafish expressing green fluorescent protein (GFP). With this, we aim to establish an open standard in optics to facilitate interfacing with various complementary platforms. By making the content and comprehensive documentation publicly available, the systems presented here lend themselves to easy and straightforward replications, modifications, and extensions. Open standard microscopy is urgently needed to give low-cost solutions to researchers and to overcome the reproducibility crisis in science. Here the authors present a 3D-printed, open-source modular microscopy toolbox UC2 (You. See. Too.) for a few hundred Euros.
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Affiliation(s)
- Benedict Diederich
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straβe 9, 07745, Jena, Germany. .,Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, Friedrich-Schiller-University, Jena, Germany.
| | - René Lachmann
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straβe 9, 07745, Jena, Germany.,Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Swen Carlstedt
- Jena University Hospital, Institute of Biochemistry II, Am Klinikum 1, Jena, Germany
| | - Barbora Marsikova
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straβe 9, 07745, Jena, Germany.,Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Haoran Wang
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straβe 9, 07745, Jena, Germany
| | - Xavier Uwurukundo
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straβe 9, 07745, Jena, Germany
| | - Alexander S Mosig
- Jena University Hospital, Institute of Biochemistry II, Am Klinikum 1, Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straβe 9, 07745, Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Helmholtzweg 4, Friedrich-Schiller-University, Jena, Germany.,Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
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18
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Pan A, Zuo C, Yao B. High-resolution and large field-of-view Fourier ptychographic microscopy and its applications in biomedicine. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2020; 83:096101. [PMID: 32679569 DOI: 10.1088/1361-6633/aba6f0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Fourier ptychographic microscopy (FPM) is a promising and fast-growing computational imaging technique with high resolution, wide field-of-view (FOV) and quantitative phase recovery, which effectively tackles the problems of phase loss, aberration-introduced artifacts, narrow depth-of-field and the trade-off between resolution and FOV in conventional microscopy simultaneously. In this review, we provide a comprehensive roadmap of microscopy, the fundamental principles, advantages, and drawbacks of existing imaging techniques, and the significant roles that FPM plays in the development of science. Since FPM is an optimization problem in nature, we discuss the framework and related work. We also reveal the connection of Euler's formula between FPM and structured illumination microscopy. We review recent advances in FPM, including the implementation of high-precision quantitative phase imaging, high-throughput imaging, high-speed imaging, three-dimensional imaging, mixed-state decoupling, and introduce the prosperous biomedical applications. We conclude by discussing the challenging problems and future applications. FPM can be extended to a kind of framework to tackle the phase loss and system limits in the imaging system. This insight can be used easily in speckle imaging, incoherent imaging for retina imaging, large-FOV fluorescence imaging, etc.
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Affiliation(s)
- An Pan
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an 710119, People's Republic of China. University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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19
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Rodríguez-Pena A, Uranga-Solchaga J, Ortiz-de-Solórzano C, Cortés-Domínguez I. Spheroscope: A custom-made miniaturized microscope for tracking tumour spheroids in microfluidic devices. Sci Rep 2020; 10:2779. [PMID: 32066786 PMCID: PMC7026415 DOI: 10.1038/s41598-020-59673-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/03/2020] [Indexed: 01/08/2023] Open
Abstract
3D cell culture models consisting of self-assembled tumour cells in suspension, commonly known as tumour spheroids, are becoming mainstream for high-throughput anticancer drug screening. A usual measurable outcome of screening studies is the growth rate of the spheroids in response to treatment. This is commonly quantified on images obtained using complex, expensive, optical microscopy systems, equipped with high-quality optics and customized electronics. Here we present a novel, portable, miniaturized microscope made of low-cost, mass-producible parts, which produces both fluorescence and phase-gradient contrast images. Since phase-gradient contrast imaging is based on oblique illumination, epi-illumination is used for both modalities, thus simplifying the design of the system. We describe the system, characterize its performance on synthetic samples and show proof-of-principle applications of the system consisting in imaging and monitoring the formation and growth of lung and pancreas cancer tumour spheroids within custom made microfluidic devices.
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Affiliation(s)
- A Rodríguez-Pena
- IDISNA, Ciberonc and Solid Tumours and Biomarkers Program, Center for Applied Medical Research, University of Navarra, 31008, Pamplona, Spain
| | - J Uranga-Solchaga
- USCAL, S.L. Ingeniería Mecatrónica + Dirección, Pol. Industrial Arazuri-Orcoyen, Calle C - No1, 31160, Orcoyen, Spain
| | - C Ortiz-de-Solórzano
- IDISNA, Ciberonc and Solid Tumours and Biomarkers Program, Center for Applied Medical Research, University of Navarra, 31008, Pamplona, Spain
| | - I Cortés-Domínguez
- IDISNA, Ciberonc and Solid Tumours and Biomarkers Program, Center for Applied Medical Research, University of Navarra, 31008, Pamplona, Spain.
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20
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Chan ACS, Kim J, Pan A, Xu H, Nojima D, Hale C, Wang S, Yang C. Parallel Fourier ptychographic microscopy for high-throughput screening with 96 cameras (96 Eyes). Sci Rep 2019; 9:11114. [PMID: 31366957 PMCID: PMC6668459 DOI: 10.1038/s41598-019-47146-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/11/2019] [Indexed: 11/23/2022] Open
Abstract
We report the implementation of a parallel microscopy system (96 Eyes) that is capable of simultaneous imaging of all wells on a 96-well plate. The optical system consists of 96 microscopy units, where each unit is made out of a four element objective, made through a molded injection process, and a low cost CMOS camera chip. By illuminating the sample with angle varying light and applying Fourier Ptychography, we can improve the effective brightfield imaging numerical aperture of the objectives from 0.23 to 0.3, and extend the depth of field from ±5 μm to ±15 μm. The use of Fourier Ptychography additionally allows us to computationally correct the objectives’ aberrations out of the rendered images, and provides us with the ability to render phase images. The 96 Eyes acquires raw data at a rate of 0.7 frame per second (all wells) and the data are processed with 4 cores of graphical processing units (GPUs; GK210, Nvidia Tesla K80, USA). The system is also capable of fluorescence imaging (excitation = 465 nm, emission = 510 nm) at the native resolution of the objectives. We demonstrate the capability of this system by imaging S1P1-eGFP-Human bone osteosarcoma epithelial (U2OS) cells.
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Affiliation(s)
- Antony C S Chan
- Division of Engineering & Applied Science, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Jinho Kim
- Division of Engineering & Applied Science, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA.,Samsung Engineering, 26 Sangil-ro 6-gil, Gangdong-gu, Seoul, Korea
| | - An Pan
- Division of Engineering & Applied Science, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA.,State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Han Xu
- Amgen South San Francisco, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA.,A2 Biotherapeutics, 2260 Townsgate Rd, Westlask Village, CA, 91361, USA
| | - Dana Nojima
- Amgen South San Francisco, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA.,Merck, 630 Gateway Blvd, South San Francisco, CA, 94080, USA
| | - Christopher Hale
- Amgen South San Francisco, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Songli Wang
- Amgen South San Francisco, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Changhuei Yang
- Division of Engineering & Applied Science, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA.
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21
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Scholz G, Mariana S, Dharmawan AB, Syamsu I, Hörmann P, Reuse C, Hartmann J, Hiller K, Prades JD, Wasisto HS, Waag A. Continuous Live-Cell Culture Imaging and Single-Cell Tracking by Computational Lensfree LED Microscopy. SENSORS 2019; 19:s19051234. [PMID: 30862101 PMCID: PMC6427468 DOI: 10.3390/s19051234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 11/29/2022]
Abstract
Continuous cell culture monitoring as a way of investigating growth, proliferation, and kinetics of biological experiments is in high demand. However, commercially available solutions are typically expensive and large in size. Digital inline-holographic microscopes (DIHM) can provide a cost-effective alternative to conventional microscopes, bridging the gap towards live-cell culture imaging. In this work, a DIHM is built from inexpensive components and applied to different cell cultures. The images are reconstructed by computational methods and the data are analyzed with particle detection and tracking methods. Counting of cells as well as movement tracking of living cells is demonstrated, showing the feasibility of using a field-portable DIHM for basic cell culture investigation and bringing about the potential to deeply understand cell motility.
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Affiliation(s)
- Gregor Scholz
- Institute of Semiconductor Technology (IHT), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | - Shinta Mariana
- Institute of Semiconductor Technology (IHT), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | - Agus Budi Dharmawan
- Institute of Semiconductor Technology (IHT), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Faculty of Information Technology, Universitas Tarumanagara, Jakarta 11440, Indonesia.
| | - Iqbal Syamsu
- Institute of Semiconductor Technology (IHT), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Research Center for Electronics and Telecommunication, Indonesian Institute of Sciences (LIPI), Bandung 40135, Indonesia.
| | - Philipp Hörmann
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | - Carsten Reuse
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | - Jana Hartmann
- Institute of Semiconductor Technology (IHT), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | - Karsten Hiller
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | - Joan Daniel Prades
- MIND-IN²UB, Department of Electronic and Biomedical Engineering, University of Barcelona, 08028 Barcelona, Spain.
| | - Hutomo Suryo Wasisto
- Institute of Semiconductor Technology (IHT), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
| | - Andreas Waag
- Institute of Semiconductor Technology (IHT), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
- Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany.
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22
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Sasagawa K, Kimura A, Haruta M, Noda T, Tokuda T, Ohta J. Highly sensitive lens-free fluorescence imaging device enabled by a complementary combination of interference and absorption filters. BIOMEDICAL OPTICS EXPRESS 2018; 9:4329-4344. [PMID: 30615707 PMCID: PMC6157770 DOI: 10.1364/boe.9.004329] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 05/28/2023]
Abstract
We report a lens-free fluorescence imaging device using a composite filter composed of an interference filter and an absorption filter, each applied to one side of a fiber optic plate (FOP). The transmission of angled excitation light through the interference filter is absorbed by the absorption filter. The auto-fluorescence of the absorption filter is reduced by the reflection from the interference filter of normally incident excitation light. As a result, high-performance rejection of excitation light is achieved in a lens-free device. The FOP provides a flat, hard imaging device surface that does not degrade the spatial resolution. We demonstrate excitation rejection of approximately 108:1 at a wavelength of 450 nm in a fabricated lens-free device. The resolution of fluorescence imaging is approximately 12 µm. Time-lapse imaging of cells containing green fluorescent protein was performed in a 5-µm thin-film chamber. The small dimensions of the device allow observation of cell culturing in a CO2 incubator. We also demonstrate that the proposed lens-free filter is compatible with super-resolution bright-field imaging techniques. These features open a way to develop a high-performance, dual-mode, lens-free imaging device that is expected to be a powerful tool for many applications, such as imaging of labeled cells and point-of-care assay.
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Affiliation(s)
- Kiyotaka Sasagawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara,
Japan
| | - Ayaka Kimura
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara,
Japan
| | - Makito Haruta
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara,
Japan
| | - Toshihiko Noda
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara,
Japan
| | - Takashi Tokuda
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara,
Japan
| | - Jun Ohta
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara,
Japan
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23
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Kamal T, Yang L, Lee WM. In situ retrieval and correction of aberrations in moldless lenses using Fourier ptychography. OPTICS EXPRESS 2018; 26:2708-2719. [PMID: 29401807 DOI: 10.1364/oe.26.002708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 06/07/2023]
Abstract
Liquid droplets cured at low temperatures or using ultraviolet light are primary approaches for fabricating refractive lenses without molds. Until now the performance of moldless lens fabrication process relied heavily on this step to precisely control the shape of each liquid droplet. Hence, a major hurdle in lenses fabricated from liquid droplets is the large variability of droplet shapes because they are sensitive to small amounts of interfacial forces. The shape of the final droplet critically affects the imaging performance of the lenses and cannot be reversed easily. Here, we aim to overcome this hurdle by performing in situ aberration correction using Fourier ptychography techniques. We demonstrate, for the first time, that computational optics can reverse high amounts of optical aberrations in moldless lenses and achieve high resolution imaging. In terms of imaging resolution, we successfully increased the resolving power of low powered moldless elastomer lenses by almost three-fold, from a numerical aperture of 0.035 to 0.099. The computational approach directly elucidates the spatially varying wavefront aberrations from each lens using the same imaging system. This provides direct feedback of droplet lens fabrication techniques without the need for advanced wavefront correction methods. The application of computational imaging onto moldless lenses, using consumer digital imaging systems, lends itself to the global efforts in decentralising high resolution image intensive scientific tools to the wider community.
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24
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Henley BM, Cohen BN, Kim CH, Gold HD, Srinivasan R, McKinney S, Deshpande P, Lester HA. Reliable Identification of Living Dopaminergic Neurons in Midbrain Cultures Using RNA Sequencing and TH-promoter-driven eGFP Expression. J Vis Exp 2017. [PMID: 28287593 DOI: 10.3791/54981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In Parkinson's Disease (PD) there is widespread neuronal loss throughout the brain with pronounced degeneration of dopaminergic neurons in the SNc, leading to bradykinesia, rigidity, and tremor. The identification of living dopaminergic neurons in primary Ventral Mesencephalic (VM) cultures using a fluorescent marker provides an alternative way to study the selective vulnerability of these neurons without relying on the immunostaining of fixed cells. Here, we isolate, dissociate, and culture mouse VM neurons for 3 weeks. We then identify dopaminergic neurons in the cultures using eGFP fluorescence (driven by a Tyrosine Hydroxylase (TH) promoter). Individual neurons are harvested into microcentrifuge tubes using glass micropipettes. Next, we lyse the harvested cells, and conduct cDNA synthesis and transposon-mediated "tagmentation" to produce single cell RNA-Seq libraries1,2,3,4,5. After passing a quality-control check, single-cell libraries are sequenced and subsequent analysis is carried out to measure gene expression. We report transcriptome results for individual dopaminergic and GABAergic neurons isolated from midbrain cultures. We report that 100% of the live TH-eGFP cells that were harvested and sequenced were dopaminergic neurons. These techniques will have widespread applications in neuroscience and molecular biology.
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Affiliation(s)
- Beverley M Henley
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech);
| | - Bruce N Cohen
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech)
| | - Charlene H Kim
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech)
| | - Heather D Gold
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech)
| | - Rahul Srinivasan
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech)
| | - Sheri McKinney
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech)
| | - Purnima Deshpande
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech)
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology (Caltech)
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