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Kim J, Lee SJ. Digital in-line holographic microscopy for label-free identification and tracking of biological cells. Mil Med Res 2024; 11:38. [PMID: 38867274 PMCID: PMC11170804 DOI: 10.1186/s40779-024-00541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Digital in-line holographic microscopy (DIHM) is a non-invasive, real-time, label-free technique that captures three-dimensional (3D) positional, orientational, and morphological information from digital holographic images of living biological cells. Unlike conventional microscopies, the DIHM technique enables precise measurements of dynamic behaviors exhibited by living cells within a 3D volume. This review outlines the fundamental principles and comprehensive digital image processing procedures employed in DIHM-based cell tracking methods. In addition, recent applications of DIHM technique for label-free identification and digital tracking of various motile biological cells, including human blood cells, spermatozoa, diseased cells, and unicellular microorganisms, are thoroughly examined. Leveraging artificial intelligence has significantly enhanced both the speed and accuracy of digital image processing for cell tracking and identification. The quantitative data on cell morphology and dynamics captured by DIHM can effectively elucidate the underlying mechanisms governing various microbial behaviors and contribute to the accumulation of diagnostic databases and the development of clinical treatments.
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Affiliation(s)
- Jihwan Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sang Joon Lee
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea.
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Abbasian V, Darafsheh A. A dataset of digital holograms of normal and thalassemic cells. Sci Data 2024; 11:3. [PMID: 38168104 PMCID: PMC10762191 DOI: 10.1038/s41597-023-02818-4] [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: 08/17/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Digital holographic microscopy (DHM) is an intriguing medical diagnostic tool due to its label-free and quantitative nature, providing high-contrast images of phase samples. By capturing both intensity and phase information, DHM enables the numerical reconstruction of quantitative phase images. However, the lateral resolution is limited by the diffraction limit, which prompted the recent suggestion of microsphere-assisted DHM to enhance the DHM resolution straightforwardly. The use of such a technique as a medical diagnostic tool requires testing and validation of the proposed assays to prove their feasibility and viability. This paper publishes 760 and 609 microsphere-assisted DHM images of normal and thalassemic red blood cells obtained from a normal and thalassemic male individual, respectively.
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Affiliation(s)
- Vahid Abbasian
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Imaging Science Program, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.
| | - Arash Darafsheh
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
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Daigle N, Duan S, Song H, Lima N, Sontz R, Merchant JL, Sawyer TW. Wide field-of-view fluorescence imaging for organ-level lineage tracing of rare intestinal stem cell populations. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:096004. [PMID: 37711357 PMCID: PMC10499363 DOI: 10.1117/1.jbo.28.9.096004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Significance Lineage tracing using fluorescent reporters is a common tool for monitoring the expression of genes and transcription factors in stem cell populations and their progeny. The zinc-binding protein 89 (ZBP-89/Zfp148 mouse gene) is a transcription factor that plays a role in gastrointestinal (GI) stem cell maintenance and cellular differentiation and has been linked to the progression of colon cancer. While lineage tracing is a useful tool, it is commonly performed with high-magnification microscopy on a small field of view within tissue sections, thereby limiting the ability to resolve reporter expression at the organ level. Furthermore, this technique requires extensive tissue processing, which is time consuming and requires euthanizing the animal. Further knowledge could be elucidated by measuring the expression of fluorescent reporters across entire organs with minimal tissue processing. Aim We present the application of wide-field fluorescence imaging for whole-organ lineage tracing of an inducible Zfp148-tdTomato-expressing transgenic mouse line to assess the expression of ZBP-89/Zfp148 in the GI tract. Approach We measured tdTomato fluorescence in ex vivo organs at time points between 24 h and 6 months post-induction. Fluctuations in tdTomato expression were validated by fluorescence microscopy of tissue sections. Results Quantification of the wide field-of-view images showed a statistically significant increase in fluorescent signal across the GI tract between transgenic mice and littermate controls. The results also showed a gradient of decreasing reporter expression from proximal to distal intestine, suggesting a higher abundance of ZBP-89 expressing stem cells, or higher expression of ZBP-89 within the stem cells, in the proximal intestine. Conclusions We demonstrate that wide-field fluorescence imaging is a valuable tool for monitoring whole-organ expression of fluorescent reporters. This technique could potentially be applied in vivo for longitudinal assessment of a single animal, further enhancing our ability to resolve rare stem cell lineages spatially and temporally.
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Affiliation(s)
- Noelle Daigle
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Suzann Duan
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Heyu Song
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Natzem Lima
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
| | - Ricky Sontz
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | | | - Travis W. Sawyer
- University of Arizona, Wyant College of Optical Sciences, Tucson, Arizona, United States
- University of Arizona, College of Medicine, Tucson, Arizona, United States
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Khan T, John B, Niemann R, Paarmann A, Wolf M, Thämer M. Compact oblique-incidence nonlinear widefield microscopy with paired-pixel balanced imaging. OPTICS EXPRESS 2023; 31:28792-28804. [PMID: 37710691 DOI: 10.1364/oe.495903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/10/2023] [Indexed: 09/16/2023]
Abstract
Nonlinear (vibrational) microscopy has emerged as a successful tool for the investigation of molecular systems as it combines label-free chemical characterization with spatial resolution on the sub-micron scale. In addition to the molecular recognition, the physics of the nonlinear interactions allows in principle to obtain structural information on the molecular level such as molecular orientations. Due to technical limitations such as the relatively complex imaging geometry with the required oblique sample irradiation and insufficient sensitivity of the instrument this detailed molecular information is typically not accessible using widefield imaging. Here, we present, what we believe to be, a new microscope design that addresses both challenges. We introduce a simplified imaging geometry that enables the measurement of distortion-free widefield images with free space oblique sample irradiation achieving high spatial resolution (∼1 µm). Furthermore, we present a method based on a paired-pixel balanced detection system for sensitivity improvement. With this technique, we demonstrate a substantial enhancement of the signal-to-noise ratio of up to a factor of 10. While both experimental concepts presented in this work are very general and can, in principle, be applied to various microscopy techniques, we demonstrate their performance for the specific case of heterodyned, sum frequency generation (SFG) microscopy.
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Rosemary essential oil and its components 1,8-cineole and α-pinene induce ROS-dependent lethality and ROS-independent virulence inhibition in Candida albicans. PLoS One 2022; 17:e0277097. [DOI: 10.1371/journal.pone.0277097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
The essential oil from Rosmarinus officinalis L., a composite mixture of plant-derived secondary metabolites, exhibits antifungal activity against virulent candidal species. Here we report the impact of rosemary oil and two of its components, the monoterpene α-pinene and the monoterpenoid 1,8-cineole, against Candida albicans, which induce ROS-dependent cell death at high concentrations and inhibit hyphal morphogenesis and biofilm formation at lower concentrations. The minimum inhibitory concentrations (100% inhibition) for both rosemary oil and 1,8-cineole were 4500 μg/ml and 3125 μg/ml for α-pinene, with the two components exhibiting partial synergy (FICI = 0.55 ± 0.07). At MIC and 1/2 MIC, rosemary oil and its components induced a generalized cell wall stress response, causing damage to cellular and organelle membranes, along with elevated chitin production and increased cell surface adhesion and elasticity, leading to complete vacuolar segregation, mitochondrial depolarization, elevated reactive oxygen species, microtubule dysfunction, and cell cycle arrest mainly at the G1/S phase, consequently triggering cell death. Interestingly, the same oils at lower fractional MIC (1/8-1/4) inhibited virulence traits, including reduction of mycelium (up to 2-fold) and biofilm (up to 4-fold) formation, through a ROS-independent mechanism.
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Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A. The BioImage Archive - Building a Home for Life-Sciences Microscopy Data. J Mol Biol 2022; 434:167505. [PMID: 35189131 DOI: 10.1016/j.jmb.2022.167505] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 01/15/2023]
Abstract
Despite the huge impact of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. In its initial development BioImage Archive accepts bioimaging data associated with publications, in any format, from any imaging modality from the molecular to the organism scale, excluding medical imaging. The BioImage Archive will ensure reproducibility of published studies that derive results from image data and reduce duplication of effort. Most importantly, the BioImage Archive will help scientists to generate new insights through reuse of existing data to answer new biological questions, and provision of training, testing and benchmarking data for development of tools for image analysis. The archive is available at https://www.ebi.ac.uk/bioimage-archive/.
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Affiliation(s)
- Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jason R Swedlow
- Division of Computational Biology, Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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Si L, Li N, Huang T, Du S, Dong Y, Yao Y, Ma H. Computational image translation from Mueller matrix polarimetry to bright-field microscopy. JOURNAL OF BIOPHOTONICS 2022; 15:e202100242. [PMID: 34775685 DOI: 10.1002/jbio.202100242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/18/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Mueller matrix (MM) polarimetry can provide comprehensive information about the polarization properties that are closely related to the microstructural features and has demonstrated its potential in biomedical studies and clinical practices, and bright-field microscopy is widely used in pathological diagnosis as the golden standard. In this work, we improve the throughput of MM microscopy by learning a statistical transformation between these two imaging systems based on deep learning. Using this approach, the MM microscope can generate an image that is equivalent to a bright-field microscope image of the matching field of view. We add new transformative capability to the existing MM imaging system without requiring extra hardware. The translation model is based on conditional generative adversarial network with customized loss functions. We demonstrated the effectiveness of our approach on liver and breast tissues and evaluated the performance by four quantitative similarity assessment methods in pixel, image and distribution levels, respectively.
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Affiliation(s)
- Lu Si
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Naiqi Li
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Tongyu Huang
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Department of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Shan Du
- Department of Pathology, University of Chinese Academy of Sciences Shenzhen Hospital, Shenzhen, China
| | - Yang Dong
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Yue Yao
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Hui Ma
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Department of Biomedical Engineering, Tsinghua University, Beijing, China
- Department of Physics, Tsinghua University, Beijing, China
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Efstathiou C, Draviam VM. Electrically tunable lenses - eliminating mechanical axial movements during high-speed 3D live imaging. J Cell Sci 2021; 134:271866. [PMID: 34409445 DOI: 10.1242/jcs.258650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The successful investigation of photosensitive and dynamic biological events, such as those in a proliferating tissue or a dividing cell, requires non-intervening high-speed imaging techniques. Electrically tunable lenses (ETLs) are liquid lenses possessing shape-changing capabilities that enable rapid axial shifts of the focal plane, in turn achieving acquisition speeds within the millisecond regime. These human-eye-inspired liquid lenses can enable fast focusing and have been applied in a variety of cell biology studies. Here, we review the history, opportunities and challenges underpinning the use of cost-effective high-speed ETLs. Although other, more expensive solutions for three-dimensional imaging in the millisecond regime are available, ETLs continue to be a powerful, yet inexpensive, contender for live-cell microscopy.
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Affiliation(s)
- Christoforos Efstathiou
- School of Biological and Chemical Sciences , Queen Mary University of London, London, E1 4NS, UK
| | - Viji M Draviam
- School of Biological and Chemical Sciences , Queen Mary University of London, London, E1 4NS, UK
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Reigoto AM, Andrade SA, Seixas MCRR, Costa ML, Mermelstein C. A comparative study on the use of microscopy in pharmacology and cell biology research. PLoS One 2021; 16:e0245795. [PMID: 33481885 PMCID: PMC7822289 DOI: 10.1371/journal.pone.0245795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/07/2021] [Indexed: 12/26/2022] Open
Abstract
Microscopy is the main technique to visualize and study the structure and function of cells. The impact of optical and electron microscopy techniques is enormous in all fields of biomedical research. It is possible that different research areas rely on microscopy in diverse ways. Here, we analyzed comparatively the use of microscopy in pharmacology and cell biology, among other biomedical sciences fields. We collected data from articles published in several major journals in these fields. We analyzed the frequency of use of different optical and electron microscopy techniques: bright field, phase contrast, differential interference contrast, polarization, conventional fluorescence, confocal, live cell imaging, super resolution, transmission and scanning electron microscopy, and cryoelectron microscopy. Our analysis showed that the use of microscopy has a distinctive pattern in each research area, and that nearly half of the articles from pharmacology journals did not use any microscopy method, compared to the use of microscopy in almost all the articles from cell biology journals. The most frequent microscopy methods in all the journals in all areas were bright field and fluorescence (conventional and confocal). Again, the pattern of use was different: while the most used microscopy methods in pharmacology were bright field and conventional fluorescence, in cell biology the most used methods were conventional and confocal fluorescence, and live cell imaging. We observed that the combination of different microscopy techniques was more frequent in cell biology, with up to 6 methods in the same article. To correlate the use of microscopy with the research theme of each article, we analyzed the proportion of microscopy figures with the use of cell culture. We analyzed comparatively the vocabulary of each biomedical sciences field, by the identification of the most frequent words in the articles. The collection of data described here shows a vast difference in the use of microscopy among different fields of biomedical sciences. The data presented here could be valuable in other scientific and educational contexts.
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Affiliation(s)
- Agatha M. Reigoto
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sarah A. Andrade
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marianna C. R. R. Seixas
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manoel L. Costa
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudia Mermelstein
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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