1
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O'Shaughnessy EC, Lam M, Ryken SE, Wiesner T, Lukasik K, Zuchero JB, Leterrier C, Adalsteinsson D, Gupton SL. pHusion - a robust and versatile toolset for automated detection and analysis of exocytosis. J Cell Sci 2024; 137:jcs261828. [PMID: 38690758 PMCID: PMC11190432 DOI: 10.1242/jcs.261828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
Exocytosis is a fundamental process used by eukaryotes to regulate the composition of the plasma membrane and facilitate cell-cell communication. To investigate exocytosis in neuronal morphogenesis, previously we developed computational tools with a graphical user interface to enable the automatic detection and analysis of exocytic events from fluorescence timelapse images. Although these tools were useful, we found the code was brittle and not easily adapted to different experimental conditions. Here, we developed and validated a robust and versatile toolkit, named pHusion, for the analysis of exocytosis, written in ImageTank, a graphical programming language that combines image visualization and numerical methods. We tested pHusion using a variety of imaging modalities and pH-sensitive fluorophores, diverse cell types and various exocytic markers, to generate a flexible and intuitive package. Using this system, we show that VAMP3-mediated exocytosis occurs 30-times more frequently in melanoma cells compared with primary oligodendrocytes, that VAMP2-mediated fusion events in mature rat hippocampal neurons are longer lasting than those in immature murine cortical neurons, and that exocytic events are clustered in space yet random in time in developing cortical neurons.
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Affiliation(s)
- Ellen C. O'Shaughnessy
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
| | - Mable Lam
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samantha E. Ryken
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
| | - Theresa Wiesner
- NeuroCyto, Aix Marseille Université, CNRS, INP UMR7051, Marseille 13385, France
| | - Kimberly Lukasik
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
| | - J. Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - David Adalsteinsson
- University of North Carolina at Chapel Hill, Department of Mathematics, Chapel Hill, NC 27599, USA
| | - Stephanie L. Gupton
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
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2
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Rehman A, Zhovmer A, Sato R, Mukouyama YS, Chen J, Rissone A, Puertollano R, Liu J, Vishwasrao HD, Shroff H, Combs CA, Xue H. Convolutional neural network transformer (CNNT) for fluorescence microscopy image denoising with improved generalization and fast adaptation. Sci Rep 2024; 14:18184. [PMID: 39107416 PMCID: PMC11303381 DOI: 10.1038/s41598-024-68918-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Deep neural networks can improve the quality of fluorescence microscopy images. Previous methods, based on Convolutional Neural Networks (CNNs), require time-consuming training of individual models for each experiment, impairing their applicability and generalization. In this study, we propose a novel imaging-transformer based model, Convolutional Neural Network Transformer (CNNT), that outperforms CNN based networks for image denoising. We train a general CNNT based backbone model from pairwise high-low Signal-to-Noise Ratio (SNR) image volumes, gathered from a single type of fluorescence microscope, an instant Structured Illumination Microscope. Fast adaptation to new microscopes is achieved by fine-tuning the backbone on only 5-10 image volume pairs per new experiment. Results show that the CNNT backbone and fine-tuning scheme significantly reduces training time and improves image quality, outperforming models trained using only CNNs such as 3D-RCAN and Noise2Fast. We show three examples of efficacy of this approach in wide-field, two-photon, and confocal fluorescence microscopy.
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Affiliation(s)
- Azaan Rehman
- Office of AI Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Alexander Zhovmer
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration (FDA), Silver Spring, MD, 20903, USA
| | - Ryo Sato
- Laboratory of Stem Cell and Neurovascular Research, NHLBI, NIH, Bethesda, MD, 20892, USA
| | - Yoh-Suke Mukouyama
- Laboratory of Stem Cell and Neurovascular Research, NHLBI, NIH, Bethesda, MD, 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIBIB, NIH, Bethesda, MD, 20892, USA
| | - Alberto Rissone
- Laboratory of Protein Trafficking and Organelle Biology, NHLBI, NIH, Bethesda, MD, 20892, USA
| | - Rosa Puertollano
- Laboratory of Protein Trafficking and Organelle Biology, NHLBI, NIH, Bethesda, MD, 20892, USA
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, NIBIB, NIH, Bethesda, MD, 20892, USA
| | | | - Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Christian A Combs
- Light Microscopy Core, National Heart, Lung, and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
| | - Hui Xue
- Office of AI Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
- Health Futures, Microsoft Research, Redmond, Washington, 98052, USA
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3
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Yang Z, Shen X, Jin J, Jiang X, Pan W, Wu C, Yu D, Li P, Feng W, Chen Y. Sonosynthetic Cyanobacteria Oxygenation for Self-Enhanced Tumor-Specific Treatment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400251. [PMID: 38867396 PMCID: PMC11304326 DOI: 10.1002/advs.202400251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/27/2024] [Indexed: 06/14/2024]
Abstract
Photosynthesis, essential for life on earth, sustains diverse processes by providing nutrition in plants and microorganisms. Especially, photosynthesis is increasingly applied in disease treatments, but its efficacy is substantially limited by the well-known low penetration depth of external light. Here, ultrasound-mediated photosynthesis is reported for enhanced sonodynamic tumor therapy using organic sonoafterglow (ultrasound-induced afterglow) nanoparticles combined with cyanobacteria, demonstrating the proof-of-concept sonosynthesis (sonoafterglow-induced photosynthesis) in cancer therapy. Chlorin e6, a typical small-molecule chlorine, is formulated into nanoparticles to stimulate cyanobacteria for sonosynthesis, which serves three roles, i.e., overcoming the tissue-penetration limitations of external light sources, reducing hypoxia, and acting as a sonosensitizer for in vivo tumor suppression. Furthermore, sonosynthetic oxygenation suppresses the expression of hypoxia-inducible factor 1α, leading to reduced stability of downstream SLC7A11 mRNA, which results in glutathione depletion and inactivation of glutathione peroxidase 4, thereby inducing ferroptosis of cancer cells. This study not only broadens the scope of microbial nanomedicine but also offers a distinct direction for sonosynthesis.
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Affiliation(s)
- Zhenyu Yang
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Xiu Shen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Junyi Jin
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Xiaoyan Jiang
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, P. R. China
- School of Medicine, Shanghai University, Shanghai, 200444, P. R. China
| | - Wenqi Pan
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, P. R. China
| | - Chenyao Wu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Dehong Yu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Ping Li
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Wei Feng
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, P. R. China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision, and Brain Health) Wenzhou Institute of Shanghai University, Wenzhou, Zhejiang, 325088, P. R. China
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, P. R. China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision, and Brain Health) Wenzhou Institute of Shanghai University, Wenzhou, Zhejiang, 325088, P. R. China
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Mukherjee S, Klarenbeek J, El Oualid F, van den Broek B, Jalink K. "Radical" differences between two FLIM microscopes affect interpretation of cell signaling dynamics. iScience 2024; 27:110268. [PMID: 39036041 PMCID: PMC11257777 DOI: 10.1016/j.isci.2024.110268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/12/2024] [Accepted: 06/11/2024] [Indexed: 07/23/2024] Open
Abstract
The outcome of cell signaling depends not only on signal strength but also on temporal progression. We use Fluorescence Lifetime Imaging of Resonance Energy Transfer (FLIM/FRET) biosensors to investigate intracellular signaling dynamics. We examined the β1 receptor-Gαs-cAMP signaling axis using both widefield frequency domain FLIM (fdFLIM) and fast confocal time-correlated single photon counting (TCSPC) setups. Unexpectedly, we observed that fdFLIM revealed transient cAMP responses in HeLa and Cos7 cells, contrasting with sustained responses as detected with TCSPC. Investigation revealed no light-induced effects on cAMP generation or breakdown. Rather, folic acid present in the imaging medium appeared to be the culprit, as its excitation with blue light sensitized degradation of β1 agonists. Our findings highlight the impact of subtle phototoxicity on experimental outcomes, advocating confocal TCSPC for reliable analysis of response kinetics and stressing the need for full disclosure of chemical formulations by scientific vendors.
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Affiliation(s)
- Sravasti Mukherjee
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
- Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, the Netherlands
| | - Jeffrey Klarenbeek
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Farid El Oualid
- UbiQ Bio B.V., Science Park 301, Amsterdam 1098 XH, the Netherlands
| | - Bram van den Broek
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
- BioImaging Facility, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
| | - Kees Jalink
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands
- Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, the Netherlands
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5
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Luo X, Lu Z, Jin M, Chen S, Yang J. Efficient high-resolution fluorescence projection imaging over an extended depth of field through optical hardware and deep learning optimizations. BIOMEDICAL OPTICS EXPRESS 2024; 15:3831-3847. [PMID: 38867796 PMCID: PMC11166417 DOI: 10.1364/boe.523312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/27/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
Abstract
Optical microscopy has witnessed notable advancements but has also become more costly and complex. Conventional wide field microscopy (WFM) has low resolution and shallow depth-of-field (DOF), which limits its applications in practical biological experiments. Recently, confocal and light sheet microscopy become major workhorses for biology that incorporate high-precision scanning to perform imaging within an extended DOF but at the sacrifice of expense, complexity, and imaging speed. Here, we propose deep focus microscopy, an efficient framework optimized both in hardware and algorithm to address the tradeoff between resolution and DOF. Our deep focus microscopy achieves large-DOF and high-resolution projection imaging by integrating a deep focus network (DFnet) into light field microscopy (LFM) setups. Based on our constructed dataset, deep focus microscopy features a significantly enhanced spatial resolution of ∼260 nm, an extended DOF of over 30 µm, and broad generalization across diverse sample structures. It also reduces the computational costs by four orders of magnitude compared to conventional LFM technologies. We demonstrate the excellent performance of deep focus microscopy in vivo, including long-term observations of cell division and migrasome formation in zebrafish embryos and mouse livers at high resolution without background contamination.
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Affiliation(s)
- Xin Luo
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Manchang Jin
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Shuai Chen
- Department of Gastroenterology and Hepatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jingyu Yang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
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6
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Shroff H, Testa I, Jug F, Manley S. Live-cell imaging powered by computation. Nat Rev Mol Cell Biol 2024; 25:443-463. [PMID: 38378991 DOI: 10.1038/s41580-024-00702-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Computational methods can help to address this challenge and are now shifting the boundaries of what is possible to capture in living systems. In this Review, we discuss these computational methods focusing on artificial intelligence-based approaches that can be layered on top of commonly used existing microscopies as well as hybrid methods that integrate computation and microscope hardware. We specifically discuss how computational approaches can improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging.
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Affiliation(s)
- Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Florian Jug
- Fondazione Human Technopole (HT), Milan, Italy
| | - Suliana Manley
- Institute of Physics, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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7
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Ludvikova L, Simon E, Deygas M, Panier T, Plamont MA, Ollion J, Tebo A, Piel M, Jullien L, Robert L, Le Saux T, Espagne A. Near-infrared co-illumination of fluorescent proteins reduces photobleaching and phototoxicity. Nat Biotechnol 2024; 42:872-876. [PMID: 37537501 PMCID: PMC11180605 DOI: 10.1038/s41587-023-01893-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/30/2023] [Indexed: 08/05/2023]
Abstract
Here we present a method to reduce the photobleaching of fluorescent proteins and the associated phototoxicity. It exploits a photophysical process known as reverse intersystem crossing, which we induce by near-infrared co-illumination during fluorophore excitation. This dual illumination method reduces photobleaching effects 1.5-9.2-fold, can be easily implemented on commercial microscopes and is effective in eukaryotic and prokaryotic cells with a wide range of fluorescent proteins.
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Affiliation(s)
- Lucie Ludvikova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Emma Simon
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Mathieu Deygas
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, Centre National de la Recherche Scientifique (CNRS), Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, Paris, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | | | - Alison Tebo
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Matthieu Piel
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, Centre National de la Recherche Scientifique (CNRS), Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Lydia Robert
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France.
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Thomas Le Saux
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France.
| | - Agathe Espagne
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France.
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8
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Renshaw MJ, Charoy C. Tales from the crick: The art of demo. J Microsc 2024; 294:308-318. [PMID: 38643509 DOI: 10.1111/jmi.13305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/23/2024]
Abstract
Equipment demonstrations (demos) play an important role in the evaluation of new systems. As well as the excitement of exploring emerging technologies, a well-organised demo can help guide procurement decisions and support funding applications. However, it is easy to underestimate the substantial effort required both before and following the demo to maximise its potential impact. Here, we discuss how our approach to demos at the Crick Advanced Light Microscopy Science and Technology Platform (CALM-STP) has evolved over the last few years, emphasising the importance of a documented approach that combines quantitative with qualitative comparisons and engages with your user base in order to build up support for any potential system purchase.
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Affiliation(s)
- Matthew J Renshaw
- Crick Advanced Light Microscopy Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Camille Charoy
- Crick Advanced Light Microscopy Science and Technology Platform, The Francis Crick Institute, London, UK
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9
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Lu Z, Zuo S, Shi M, Fan J, Xie J, Xiao G, Yu L, Wu J, Dai Q. Long-term intravital subcellular imaging with confocal scanning light-field microscopy. Nat Biotechnol 2024:10.1038/s41587-024-02249-5. [PMID: 38802562 DOI: 10.1038/s41587-024-02249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/17/2024] [Indexed: 05/29/2024]
Abstract
Long-term observation of subcellular dynamics in living organisms is limited by background fluorescence originating from tissue scattering or dense labeling. Existing confocal approaches face an inevitable tradeoff among parallelization, resolution and phototoxicity. Here we present confocal scanning light-field microscopy (csLFM), which integrates axially elongated line-confocal illumination with the rolling shutter in scanning light-field microscopy (sLFM). csLFM enables high-fidelity, high-speed, three-dimensional (3D) imaging at near-diffraction-limit resolution with both optical sectioning and low phototoxicity. By simultaneous 3D excitation and detection, the excitation intensity can be reduced below 1 mW mm-2, with 15-fold higher signal-to-background ratio over sLFM. We imaged subcellular dynamics over 25,000 timeframes in optically challenging environments in different species, such as migrasome delivery in mouse spleen, retractosome generation in mouse liver and 3D voltage imaging in Drosophila. Moreover, csLFM facilitates high-fidelity, large-scale neural recording with reduced crosstalk, leading to high orientation selectivity to visual stimuli, similar to two-photon microscopy, which aids understanding of neural coding mechanisms.
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Affiliation(s)
- Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- Zhejiang Hehu Technology, Hangzhou, China
- Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou, China
| | - Siqing Zuo
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Minghui Shi
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Fan
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jingyu Xie
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Guihua Xiao
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Shanghai AI Laboratory, Shanghai, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China.
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10
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Carsten A, Failla AV, Aepfelbacher M. MINFLUX nanoscopy: Visualising biological matter at the nanoscale level. J Microsc 2024. [PMID: 38661499 DOI: 10.1111/jmi.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Since its introduction in 2017, MINFLUX nanoscopy has shown that it can visualise fluorescent molecules with an exceptional localisation precision of a few nanometres. In this overview, we provide a brief insight into technical implementations, fluorescent marker developments and biological studies that have been conducted in connection with MINFLUX imaging and tracking. We also formulate ideas on how MINFLUX nanoscopy and derived technologies could influence bioimaging in the future. This insight is intended as a general starting point for an audience looking for a brief overview of MINFLUX nanoscopy from theory to application.
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Affiliation(s)
- Alexander Carsten
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany
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11
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Ko J, Hyung S, Cheong S, Chung Y, Li Jeon N. Revealing the clinical potential of high-resolution organoids. Adv Drug Deliv Rev 2024; 207:115202. [PMID: 38336091 DOI: 10.1016/j.addr.2024.115202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
The symbiotic interplay of organoid technology and advanced imaging strategies yields innovative breakthroughs in research and clinical applications. Organoids, intricate three-dimensional cell cultures derived from pluripotent or adult stem/progenitor cells, have emerged as potent tools for in vitro modeling, reflecting in vivo organs and advancing our grasp of tissue physiology and disease. Concurrently, advanced imaging technologies such as confocal, light-sheet, and two-photon microscopy ignite fresh explorations, uncovering rich organoid information. Combined with advanced imaging technologies and the power of artificial intelligence, organoids provide new insights that bridge experimental models and real-world clinical scenarios. This review explores exemplary research that embodies this technological synergy and how organoids reshape personalized medicine and therapeutics.
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Affiliation(s)
- Jihoon Ko
- Department of BioNano Technology, Gachon University, Gyeonggi 13120, Republic of Korea
| | - Sujin Hyung
- Precision Medicine Research Institute, Samsung Medical Center, Seoul 08826, Republic of Korea; Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University, Samsung Medical Center, Seoul 08826, Republic of Korea
| | - Sunghun Cheong
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yoojin Chung
- Division of Computer Engineering, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea
| | - Noo Li Jeon
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Qureator, Inc., San Diego, CA, USA.
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12
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Luu P, Fraser SE, Schneider F. More than double the fun with two-photon excitation microscopy. Commun Biol 2024; 7:364. [PMID: 38531976 DOI: 10.1038/s42003-024-06057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.
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Affiliation(s)
- Peter Luu
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Scott E Fraser
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
- Alfred Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Falk Schneider
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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13
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Ren X, Wang C, Wu X, Rong M, Huang R, Liang Q, Shen T, Sun H, Zhang R, Zhang Z, Liu X, Song X, Foley JW. Auxochrome Dimethyl-Dihydroacridine Improves Fluorophores for Prolonged Live-Cell Super-Resolution Imaging. J Am Chem Soc 2024; 146:6566-6579. [PMID: 38422385 DOI: 10.1021/jacs.3c11823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Superior photostability, minimal phototoxicity, red-shifted absorption/emission wavelengths, high brightness, and an enlarged Stokes shift are essential characteristics of top-tier organic fluorophores, particularly for long-lasting super-resolution imaging in live cells (e.g., via stimulated emission depletion (STED) nanoscopy). However, few existing fluorophores possess all of these properties. In this study, we demonstrate a general approach for simultaneously enhancing these parameters through the introduction of 9,9-dimethyl-9,10-dihydroacridine (DMA) as an electron-donating auxochrome. DMA not only induces red shifts in emission wavelengths but also suppresses photooxidative reactions and prevents the formation of triplet states in DMA-based fluorophores, greatly improving photostability and remarkably minimizing phototoxicity. Moreover, the DMA group enhances the fluorophores' brightness and enlarges the Stokes shift. Importantly, the "universal" benefits of attaching the DMA auxochrome have been exemplified in various fluorophores including rhodamines, difluoride-boron complexes, and coumarin derivatives. The resulting fluorophores successfully enabled the STED imaging of organelles and HaloTag-labeled membrane proteins.
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Affiliation(s)
- Xiaojie Ren
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Chao Wang
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Xia Wu
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Mengtao Rong
- School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, Anhui, China
| | - Rong Huang
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Qin Liang
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - Tianruo Shen
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Hongyan Sun
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Ruilong Zhang
- School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, Anhui, China
| | - Zhongping Zhang
- School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601, Anhui, China
| | - Xiaogang Liu
- Singapore University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Xiangzhi Song
- College of Chemistry & Chemical Engineering, Central South University, Changsha 410083, Hunan, China
| | - James W Foley
- Rowland Institute at Harvard, Harvard University, Boston, Massachusetts 02142, United States
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14
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Torres R, Thal LB, McBride JR, Cohen BE, Rosenthal SJ. Quantum Dot Fluorescent Imaging: Using Atomic Structure Correlation Studies to Improve Photophysical Properties. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2024; 128:3632-3640. [PMID: 38476823 PMCID: PMC10926165 DOI: 10.1021/acs.jpcc.3c07367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 03/14/2024]
Abstract
Efforts to study intricate, higher-order cellular functions have called for fluorescence imaging under physiologically relevant conditions such as tissue systems in simulated native buffers. This endeavor has presented novel challenges for fluorescent probes initially designed for use in simple buffers and monolayer cell culture. Among current fluorescent probes, semiconductor nanocrystals, or quantum dots (QDs), offer superior photophysical properties that are the products of their nanoscale architectures and chemical formulations. While their high brightness and photostability are ideal for these biological environments, even state of the art QDs can struggle under certain physiological conditions. A recent method correlating electron microscopy ultrastructure with single-QD fluorescence has begun to highlight subtle structural defects in QDs once believed to have no significant impact on photoluminescence (PL). Specific defects, such as exposed core facets, have been shown to quench QD PL in physiologically accurate conditions. For QD-based imaging in complex cellular systems to be fully realized, mechanistic insight and structural optimization of size and PL should be established. Insight from single QD resolution atomic structure and photophysical correlative studies provides a direct course to synthetically tune QDs to match these challenging environments.
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Affiliation(s)
- Ruben Torres
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute for Nanoscale Science and Engineering, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Lucas B. Thal
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute for Nanoscale Science and Engineering, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - James R. McBride
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute for Nanoscale Science and Engineering, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Bruce E. Cohen
- The
Molecular Foundry and Division of Molecular Biophysics & Integrated
Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sandra J. Rosenthal
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute for Nanoscale Science and Engineering, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37240, United States
- Vanderbilt
Interdisciplinary Materials Science Program, Vanderbilt University, Nashville, Tennessee 37240, United States
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15
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Yin J, Liang R, Hou H, Miao Y, Yu L. Light sheet fluorescence microscopy with active optical manipulation. OPTICS LETTERS 2024; 49:1193-1196. [PMID: 38426971 DOI: 10.1364/ol.515280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024]
Abstract
We present a light sheet fluorescence microscopy (LSFM) with active optical manipulation by using linear optical tweezers (LOTs). In this method, two coaxially transmitting laser beams of different wavelengths are shaped using cylindrical lenses to form a linear optical trapping perpendicular to the optical axis and an excitation light sheet (LS) parallel to the optical axis, respectively. Multiple large-sized polystyrene fluorescent microspheres are stably captured by LOTs, and their rotation angles around specific rotation axes are precisely controlled. During a sample rotation, the stationary excitation LS scans the sample to obtain fluorescence sectioning images of the sample at different angles.
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16
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Xu M, Wang H, Tian X, Li B, Wang S, Zhao X, He H. Opsin-Free Activation of Bmp Receptors by a Femtosecond Laser. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308072. [PMID: 38239021 PMCID: PMC10933676 DOI: 10.1002/advs.202308072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/13/2023] [Indexed: 03/14/2024]
Abstract
Bone morphogenetic protein (BMP) signaling plays a vital role in differentiation, organogenesis, and various cell processes. As a member of TGF-β superfamily, the BMP initiation usually accompanies crosstalk with other signaling pathways and simultaneously activates some of them. It is quite challenging to solely initiate an individual pathway. In this study, an opsin-free optical method to specifically activate BMP receptors (BMPR) and subsequent pSmad1/5/8 cascades by a single-time scan of a tightly-focused femtosecond laser in the near infrared range is reported. Via transient two-photon excitation to intrinsic local flavins near the cell membrane, the photoactivation drives conformational changes of preformed BMPR complexes to enable their bonding and phosphorylation of the GS domain in BMPR-I by BMPR-II. The pSmad1/5/8 signaling is initiated by this method, while p38 and pSmad2 are rarely perturbed. Based on a microscopic system, primary adipose-derived stem cells in an area of 420 × 420 µm2 are photoactivated by a single-time laser scanning for 1.5 s and exhibit pSmad1/5/8 upregulation and osteoblastic differentiation after 21 days. Hence, an opsin-free, specific, and noninvasive optical method to initiate BMP signaling, easily accomplished by a two-photon microscope system is reported.
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Affiliation(s)
- Manjun Xu
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Haipeng Wang
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Xiaoying Tian
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Bingyi Li
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Shaoyang Wang
- School of Biomedical EngineeringHainan UniversityHaikou570228China
| | - Xiaohui Zhao
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Hao He
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
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17
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Asmar AJ, Benson ZA, Peskin AP, Chalfoun J, Simon M, Halter M, Plant AL. High-volume, label-free imaging for quantifying single-cell dynamics in induced pluripotent stem cell colonies. PLoS One 2024; 19:e0298446. [PMID: 38377138 PMCID: PMC10878516 DOI: 10.1371/journal.pone.0298446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
To facilitate the characterization of unlabeled induced pluripotent stem cells (iPSCs) during culture and expansion, we developed an AI pipeline for nuclear segmentation and mitosis detection from phase contrast images of individual cells within iPSC colonies. The analysis uses a 2D convolutional neural network (U-Net) plus a 3D U-Net applied on time lapse images to detect and segment nuclei, mitotic events, and daughter nuclei to enable tracking of large numbers of individual cells over long times in culture. The analysis uses fluorescence data to train models for segmenting nuclei in phase contrast images. The use of classical image processing routines to segment fluorescent nuclei precludes the need for manual annotation. We optimize and evaluate the accuracy of automated annotation to assure the reliability of the training. The model is generalizable in that it performs well on different datasets with an average F1 score of 0.94, on cells at different densities, and on cells from different pluripotent cell lines. The method allows us to assess, in a non-invasive manner, rates of mitosis and cell division which serve as indicators of cell state and cell health. We assess these parameters in up to hundreds of thousands of cells in culture for more than 36 hours, at different locations in the colonies, and as a function of excitation light exposure.
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Affiliation(s)
- Anthony J. Asmar
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Zackery A. Benson
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Adele P. Peskin
- Software and Systems Division Information Technology Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Joe Chalfoun
- Software and Systems Division Information Technology Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Mylene Simon
- Software and Systems Division Information Technology Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Michael Halter
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
| | - Anne L. Plant
- Biosystems and Biomaterials Division Material Measurement Lab, NIST Gaithersburg, Gaithersburg, Maryland, United States of America
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18
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Inavalli VVGK, Puente Muñoz V, Draffin JE, Tønnesen J. Fluorescence microscopy shadow imaging for neuroscience. Front Cell Neurosci 2024; 18:1330100. [PMID: 38425431 PMCID: PMC10902105 DOI: 10.3389/fncel.2024.1330100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Fluorescence microscopy remains one of the single most widely applied experimental approaches in neuroscience and beyond and is continuously evolving to make it easier and more versatile. The success of the approach is based on synergistic developments in imaging technologies and fluorophore labeling strategies that have allowed it to greatly diversify and be used across preparations for addressing structure as well as function. Yet, while targeted labeling strategies are a key strength of fluorescence microscopy, they reciprocally impose general limitations on the possible types of experiments and analyses. One recent development that overcomes some of these limitations is fluorescence microscopy shadow imaging, where membrane-bound cellular structures remain unlabeled while the surrounding extracellular space is made to fluoresce to provide a negative contrast shadow image. When based on super-resolution STED microscopy, the technique in effect provides a positive image of the extracellular space geometry and entire neuropil in the field of view. Other noteworthy advantages include the near elimination of the adverse effects of photobleaching and toxicity in live imaging, exhaustive and homogeneous labeling across the preparation, and the ability to apply and adjust the label intensity on the fly. Shadow imaging is gaining popularity and has been applied on its own or combined with conventional positive labeling to visualize cells and synaptic proteins in their parenchymal context. Here, we highlight the inherent limitations of fluorescence microscopy and conventional labeling and contrast these against the pros and cons of recent shadow imaging approaches. Our aim is to describe the brief history and current trajectory of the shadow imaging technique in the neuroscience field, and to draw attention to its ease of application and versatility.
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Affiliation(s)
| | - Virginia Puente Muñoz
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Jonathan E. Draffin
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
| | - Jan Tønnesen
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
- Instituto Biofisika (CSIC/UPV), Leioa, Spain
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19
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Gómez-de-Mariscal E, Del Rosario M, Pylvänäinen JW, Jacquemet G, Henriques R. Harnessing artificial intelligence to reduce phototoxicity in live imaging. J Cell Sci 2024; 137:jcs261545. [PMID: 38324353 PMCID: PMC10912813 DOI: 10.1242/jcs.261545] [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] [Indexed: 02/08/2024] Open
Abstract
Fluorescence microscopy is essential for studying living cells, tissues and organisms. However, the fluorescent light that switches on fluorescent molecules also harms the samples, jeopardizing the validity of results - particularly in techniques such as super-resolution microscopy, which demands extended illumination. Artificial intelligence (AI)-enabled software capable of denoising, image restoration, temporal interpolation or cross-modal style transfer has great potential to rescue live imaging data and limit photodamage. Yet we believe the focus should be on maintaining light-induced damage at levels that preserve natural cell behaviour. In this Opinion piece, we argue that a shift in role for AIs is needed - AI should be used to extract rich insights from gentle imaging rather than recover compromised data from harsh illumination. Although AI can enhance imaging, our ultimate goal should be to uncover biological truths, not just retrieve data. It is essential to prioritize minimizing photodamage over merely pushing technical limits. Our approach is aimed towards gentle acquisition and observation of undisturbed living systems, aligning with the essence of live-cell fluorescence microscopy.
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Affiliation(s)
| | | | - Joanna W. Pylvänäinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku 20100, Finland
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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20
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Pirone D, Bianco V, Miccio L, Memmolo P, Psaltis D, Ferraro P. Beyond fluorescence: advances in computational label-free full specificity in 3D quantitative phase microscopy. Curr Opin Biotechnol 2024; 85:103054. [PMID: 38142647 DOI: 10.1016/j.copbio.2023.103054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/26/2023]
Abstract
Despite remarkable progresses in quantitative phase imaging (QPI) microscopes, their wide acceptance is limited due to the lack of specificity compared with the well-established fluorescence microscopy. In fact, the absence of fluorescent tag prevents to identify subcellular structures in single cells, making challenging the interpretation of label-free 2D and 3D phase-contrast data. Great effort has been made by many groups worldwide to address and overcome such limitation. Different computational methods have been proposed and many more are currently under investigation to achieve label-free microscopic imaging at single-cell level to recognize and quantify different subcellular compartments. This route promises to bridge the gap between QPI and FM for real-world applications.
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Affiliation(s)
- Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Vittorio Bianco
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Lisa Miccio
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Pasquale Memmolo
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Demetri Psaltis
- EPFL, Ecole Polytechnique Fédérale de Lausanne, Optics Laboratory, CH-1015 Lausanne, Switzerland
| | - Pietro Ferraro
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
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21
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Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK. Community-developed checklists for publishing images and image analyses. Nat Methods 2024; 21:170-181. [PMID: 37710020 PMCID: PMC10922596 DOI: 10.1038/s41592-023-01987-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/26/2023] [Indexed: 09/16/2023]
Abstract
Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.
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Affiliation(s)
- Christopher Schmied
- Fondazione Human Technopole, Milano, Italy.
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Michael S Nelson
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Sergiy Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gert-Jan Bakker
- Medical BioSciences Department, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Cristina Bertocchi
- Laboratory for Molecular Mechanics of Cell Adhesions, Pontificia Universidad Católica de Chile Santiago, Santiago de Chile, Chile
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | | | | | - Jan Brocher
- Scientific Image Processing and Analysis, BioVoxxel, Ludwigshafen, Germany
| | - Mariana T Carvalho
- Nanophotonics and BioImaging Facility at INL, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | | | - Jana Christopher
- Biochemistry Center Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Beth A Cimini
- Imaging Platform, Broad Institute, Cambridge, MA, USA
| | - Eduardo Conde-Sousa
- i3S, Instituto de Investigação e Inovação Em Saúde and INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Michael Ebner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Rupert Ecker
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- TissueGnostics GmbH, Vienna, Austria
| | - Kevin Eliceiri
- Department of Medical Physics and Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Julia Fernandez-Rodriguez
- Centre for Cellular Imaging Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Nadia Halidi
- Advanced Light Microscopy Unit, Centre for Genomic Regulation, Barcelona, Spain
| | - Mathias Hammer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Matthew Hartley
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Hinxton, UK
| | - Marie Held
- Centre for Cell Imaging, the University of Liverpool, Liverpool, UK
| | | | - Varun Kapoor
- Department of AI Research, Kapoor Labs, Paris, France
| | | | | | - Sylvia Le Dévédec
- Division of Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | | | - Penghuan Liu
- Key Laboratory for Modern Measurement Technology and Instruments of Zhejiang Province, College of Optical and Electronic Technology, China Jiliang University, Hangzhou, China
| | - Gabriel G Martins
- Advanced Imaging Facility, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Kota Miura
- Bioimage Analysis and Research, Heidelberg, Germany
| | | | - Roland Nitschke
- Life Imaging Center, Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany
| | - Alison North
- Bio-Imaging Resource Center, the Rockefeller University, New York, NY, USA
| | - Adam C Parslow
- Baker Institute Microscopy Platform, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Alex Payne-Dwyer
- School of Physics, Engineering and Technology, University of York, Heslington, UK
| | - Laure Plantard
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Rizwan Ali
- King Abdullah International Medical Research Center (KAIMRC), Medical Research Core Facility and Platforms (MRCFP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Britta Schroth-Diez
- Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Dresden, Germany
| | | | - Ryan T Scott
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Arne Seitz
- BioImaging and Optics Platform, Faculty of Life Sciences (SV), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Olaf Selchow
- Microscopy and BioImaging Consulting, Image Processing and Large Data Handling, Gera, Germany
| | - Ved P Sharma
- Bio-Imaging Resource Center, the Rockefeller University, New York, NY, USA
| | | | - Sathya Srinivasan
- Imaging and Morphology Support Core, Oregon National Primate Research Center, OHSU West Campus, Beaverton, OR, USA
| | | | - Douglas Taatjes
- Department of Pathology and Laboratory Medicine, Microscopy Imaging Center, Center for Biomedical Shared Resources, University of Vermont, Burlington, VT, USA
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22
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Shi Y, Tabet JS, Milkie DE, Daugird TA, Yang CQ, Ritter AT, Giovannucci A, Legant WR. Smart lattice light-sheet microscopy for imaging rare and complex cellular events. Nat Methods 2024; 21:301-310. [PMID: 38167656 PMCID: PMC11216155 DOI: 10.1038/s41592-023-02126-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
Light-sheet microscopes enable rapid high-resolution imaging of biological specimens; however, biological processes span spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality. Here, to overcome this limitation, we present smartLLSM, a microscope that incorporates artificial intelligence-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light-sheet microscopy (LLSM). We apply this approach to two unique processes: cell division and immune synapse formation. In each context, smartLLSM provides population-level statistics across thousands of cells and autonomously captures multicolor three-dimensional datasets or four-dimensional time-lapse movies of rare events at rates that dramatically exceed human capabilities. From this, we quantify the effects of Taxol dose on spindle structure and kinetochore dynamics in dividing cells and of antigen strength on cytotoxic T lymphocyte engagement and lytic granule polarization at the immune synapse. Overall, smartLLSM efficiently detects rare events within heterogeneous cell populations and records these processes with high spatiotemporal four-dimensional imaging over statistically significant replicates.
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Affiliation(s)
- Yu Shi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimmy S Tabet
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Q Yang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Andrea Giovannucci
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Wesley R Legant
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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23
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Gritti N, Power RM, Graves A, Huisken J. Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging. Nat Methods 2024; 21:311-321. [PMID: 38177507 PMCID: PMC10864180 DOI: 10.1038/s41592-023-02127-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
Time-lapse fluorescence microscopy is key to unraveling biological development and function; however, living systems, by their nature, permit only limited interrogation and contain untapped information that can only be captured by more invasive methods. Deep-tissue live imaging presents a particular challenge owing to the spectral range of live-cell imaging probes/fluorescent proteins, which offer only modest optical penetration into scattering tissues. Herein, we employ convolutional neural networks to augment live-imaging data with deep-tissue images taken on fixed samples. We demonstrate that convolutional neural networks may be used to restore deep-tissue contrast in GFP-based time-lapse imaging using paired final-state datasets acquired using near-infrared dyes, an approach termed InfraRed-mediated Image Restoration (IR2). Notably, the networks are remarkably robust over a wide range of developmental times. We employ IR2 to enhance the information content of green fluorescent protein time-lapse images of zebrafish and Drosophila embryo/larval development and demonstrate its quantitative potential in increasing the fidelity of cell tracking/lineaging in developing pescoids. Thus, IR2 is poised to extend live imaging to depths otherwise inaccessible.
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Affiliation(s)
- Nicola Gritti
- Morgridge Institute for Research, Madison, WI, USA
- Mesoscopic Imaging Facility, European Molecular Biology Laboratory Barcelona, Barcelona, Spain
| | - Rory M Power
- Morgridge Institute for Research, Madison, WI, USA
- EMBL Imaging Center, European Molecular Biology Laboratory Heidelberg, Heidelberg, Germany
| | | | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin Madison, Madison, WI, USA.
- Department of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
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24
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Mahapatra S, Ma S, Dong B, Zhang C. Quantification of cellular phototoxicity of organelle stains by the dynamics of microtubule polymerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576021. [PMID: 38293099 PMCID: PMC10827188 DOI: 10.1101/2024.01.17.576021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Being able to quantify the phototoxicity of dyes and drugs in live cells allows biologists to better understand cell responses to exogenous stimuli during imaging. This capability further helps to design fluorescent labels with lower phototoxicity and drugs with better efficacy. Conventional ways to evaluate cellular phototoxicity rely on late-stage measurements of individual or different populations of cells. Here, we developed a quantitative method using intracellular microtubule polymerization as a rapid and sensitive marker to quantify early-stage phototoxicity. Implementing this method, we assessed the photosensitization induced by organelle dyes illuminated with different excitation wavelengths. Notably, fluorescent markers targeting mitochondria, nuclei, and endoplasmic reticulum exhibited diverse levels of phototoxicity. Furthermore, leveraging a real-time precision opto-control technology allowed us to evaluate the synergistic effect of light and dyes on specific organelles. Studies in hypoxia revealed enhanced phototoxicity of Mito-Tracker Red CMXRos that is not correlated with the generation of reactive oxygen species but a different deleterious pathway in low oxygen conditions. Teaser Microtubule dynamics in live cells allow quantification of cellular phototoxicity of fluorescent dyes in various conditions.
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25
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Chen C, Smith ZJ, Fang J, Chu K. Organelle-specific phase contrast microscopy (OS-PCM) enables facile correlation study of organelles and proteins. BIOMEDICAL OPTICS EXPRESS 2024; 15:199-211. [PMID: 38223195 PMCID: PMC10783919 DOI: 10.1364/boe.510243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/29/2023] [Accepted: 12/03/2023] [Indexed: 01/16/2024]
Abstract
Current methods for studying organelle and protein interactions and correlations depend on multiplex fluorescent labeling, which is experimentally complex and harmful to cells. Here we propose to solve this challenge via OS-PCM, where organelles are imaged and segmented without labels, and combined with standard fluorescence microscopy of protein distributions. In this work, we develop new neural networks to obtain unlabeled organelle, nucleus and membrane predictions from a single 2D image. Automated analysis is also implemented to obtain quantitative information regarding the spatial distribution and co-localization of both protein and organelle, as well as their relationship to the landmark structures of nucleus and membrane. Using mitochondria and DRP1 protein as a proof-of-concept, we conducted a correlation study where only DRP1 is labeled, with results consistent with prior reports utilizing multiplex labeling. Thus our work demonstrates that OS-PCM simplifies the correlation study of organelles and proteins.
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Affiliation(s)
- Chen Chen
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Zachary J Smith
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui 230027, China
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jingde Fang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Kaiqin Chu
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230027, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
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26
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Pain C, Kriechbaumer V, Candeo A. Observing ER Dynamics over Long Timescales Using Light Sheet Fluorescence Microscopy. Methods Mol Biol 2024; 2772:323-335. [PMID: 38411826 DOI: 10.1007/978-1-0716-3710-4_25] [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] [Indexed: 02/28/2024]
Abstract
The recent significant progress in developmental bio-imaging of live multicellular organisms has been greatly facilitated by the development of light sheet fluorescence microscopy (LSFM). Both commercial and custom LSFM systems offer the best means for long-term rapid data collection over a wide field of view at single-cell resolution. This is thanks to the low light exposure required for imaging and consequent limited photodamage to the biological sample, and the development of custom holders and mounting techniques that allow for specimens to be imaged in near-normal physiological conditions. This method has been successfully applied to plant cell biology and is currently seen as one of the most efficient techniques for 3D time-lapse imaging for quantitative studies. LSFM allows one to capture and quantify dynamic processes across various levels, from plant subcellular compartments to whole cells, tissues, and entire plant organs. Here we present a method to carry out LSFM on Arabidopsis leaves expressing fluorescent markers targeted to the ER. We will focus on a protocol to mount the sample, test the phototoxicity of the LSFM system, set up a LSFM experiment, and monitor the dynamics of the ER during heat shock.
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Affiliation(s)
- Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alessia Candeo
- Dipartimento di Fisica, Politecnico di Milano, Milan, Italy.
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, UK.
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27
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Shen YJ, Liao EY, Tai TM, Liao YH, Sun CK, Lee CK, See S, Chen HW. Deep learning-based photodamage reduction on harmonic generation microscope at low-level optical power. JOURNAL OF BIOPHOTONICS 2024; 17:e202300285. [PMID: 37738103 DOI: 10.1002/jbio.202300285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The trade-off between high-quality images and cellular health in optical bioimaging is a crucial problem. We demonstrated a deep-learning-based power-enhancement (PE) model in a harmonic generation microscope (HGM), including second harmonic generation (SHG) and third harmonic generation (THG). Our model can predict high-power HGM images from low-power images, greatly reducing the risk of phototoxicity and photodamage. Furthermore, the PE model trained only on normal skin data can also be used to predict abnormal skin data, enabling the dermatopathologist to successfully identify and label cancer cells. The PE model shows potential for in-vivo and ex-vivo HGM imaging.
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Affiliation(s)
- Yi-Jiun Shen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
| | - En-Yu Liao
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Yi-Hua Liao
- Department of Dermatology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Kuang Sun
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei, Taiwan
| | | | - Simon See
- NVIDIA AI Technology Center, NVIDIA, Taipei, Taiwan
| | - Hung-Wen Chen
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Photonics Technologies, National Tsing Hua University, Hsinchu, Taiwan
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28
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Mellor NG, Chung SA, Graham ES, Day BW, Unsworth CP. Eliciting calcium transients with UV nanosecond laser stimulation in adult patient-derived glioblastoma brain cancer cells in vitro. J Neural Eng 2023; 20:066026. [PMID: 37988746 DOI: 10.1088/1741-2552/ad0e7d] [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: 10/03/2022] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
Objective.Glioblastoma (GBM) is the most common and lethal type of high-grade adult brain cancer. The World Health Organization have classed GBM as an incurable disease because standard treatments have yielded little improvement with life-expectancy being 6-15 months after diagnosis. Different approaches are now crucial to discover new knowledge about GBM communication/function in order to establish alternative therapies for such an aggressive adult brain cancer. Calcium (Ca2+) is a fundamental cell molecular messenger employed in GBM being involved in a wide dynamic range of cellular processes. Understanding how the movement of Ca2+behaves and modulates activity in GBM at the single-cell level is relatively unexplored but holds the potential to yield opportunities for new therapeutic strategies and approaches for cancer treatment.Approach.In this article we establish a spatially and temporally precise method for stimulating Ca2+transients in three patient-derived GBM cell-lines (FPW1, RN1, and RKI1) such that Ca2+communication can be studied from single-cell to larger network scales. We demonstrate that this is possible by administering a single optimized ultra-violet (UV) nanosecond laser pulse to trigger GBM Ca2+transients.Main results.We determine that 1.58µJµm-2is the optimal UV nanosecond laser pulse energy density necessary to elicit a single Ca2+transient in the GBM cell-lines whilst maintaining viability, functionality, the ability to be stimulated many times in an experiment, and to trigger further Ca2+communication in a larger network of GBM cells.Significance.Using adult patient-derived mesenchymal GBM brain cancer cell-lines, the most aggressive form of GBM cancer, this work is the first of its kind as it provides a new effective modality of which to stimulate GBM cells at the single-cell level in an accurate, repeatable, and reliable manner; and is a first step toward Ca2+communication in GBM brain cancer cells and their networks being more effectively studied.
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Affiliation(s)
- Nicholas G Mellor
- Department of Engineering Science, The University of Auckland, Auckland, New Zealand
| | - Sylvia A Chung
- Adult Cancer Program, Lowy Cancer Research Centre, The University of New South Wales, Sydney, Australia
| | - E Scott Graham
- Department of Molecular Medicine and Pathology & The Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Bryan W Day
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Charles P Unsworth
- Department of Engineering Science, The University of Auckland, Auckland, New Zealand
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29
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Zhang G, Li X, Zhang Y, Han X, Li X, Yu J, Liu B, Wu J, Yu L, Dai Q. Bio-friendly long-term subcellular dynamic recording by self-supervised image enhancement microscopy. Nat Methods 2023; 20:1957-1970. [PMID: 37957429 PMCID: PMC10703694 DOI: 10.1038/s41592-023-02058-9] [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: 10/21/2022] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Fluorescence microscopy has become an indispensable tool for revealing the dynamic regulation of cells and organelles. However, stochastic noise inherently restricts optical interrogation quality and exacerbates observation fidelity when balancing the joint demands of high frame rate, long-term recording and low phototoxicity. Here we propose DeepSeMi, a self-supervised-learning-based denoising framework capable of increasing signal-to-noise ratio by over 12 dB across various conditions. With the introduction of newly designed eccentric blind-spot convolution filters, DeepSeMi effectively denoises images with no loss of spatiotemporal resolution. In combination with confocal microscopy, DeepSeMi allows for recording organelle interactions in four colors at high frame rates across tens of thousands of frames, monitoring migrasomes and retractosomes over a half day, and imaging ultra-phototoxicity-sensitive Dictyostelium cells over thousands of frames. Through comprehensive validations across various samples and instruments, we prove DeepSeMi to be a versatile and biocompatible tool for breaking the shot-noise limit.
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Affiliation(s)
- Guoxun Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xiaopeng Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanlong Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xiaofei Han
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Xinyang Li
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jinqiang Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Boqi Liu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Shanghai AI Laboratory, Shanghai, China.
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
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30
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Liu G, Zheng H, Zhou R, Li H, Dai J, Wei J, Li D, Meng X, Wang C, Lu G. Ultrabright organic fluorescent probe for quantifying the dynamics of cytosolic/nuclear lipid droplets. Biosens Bioelectron 2023; 241:115707. [PMID: 37783066 DOI: 10.1016/j.bios.2023.115707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Lipid droplets (LDs) are extremely active organelles that play a crucial role in energy metabolism, membrane formation, and the production of lipid-derived signaling molecules by regulating lipid storage and release. Nevertheless, directly limited by the lack of superior fluorescent probes, studies of LDs dynamic motion velocity have been rarely reported, especially for nuclear LDs. Herein, a novel organic fluorescent probe Lipi-Bright has been rationally developed based on bridged cyclization of distyrylbenzene. The fully ring-fused molecule structure endows the probe with high photostability. Moreover, this new fluorescent probe displays the features of excellent LDs staining specificity as well as ultrahigh fluorescence brightness. Lipi-Bright labeled LDs was dozens of times brighter than representative probes BODIPY 493/503 or Nile Red. Consequently, by in-situ time-lapse fluorescence imaging, the dynamics of LDs have been quantitatively studied. For instance, the velocities of cytosolic LDs (37 ± 15 nm/s) are found to be obviously faster than those of nuclear LDs (24 ± 4 nm/s), and both the cytosolic LDs and the nuclear LDs would be moved faster or slower depend on the various stimulations. Overall, this work providing plentiful information on LDs dynamics will greatly facilitate the in-depth investigation of lipid metabolism.
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Affiliation(s)
- Guannan Liu
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Huanlong Zheng
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Ri Zhou
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China.
| | - Huaiyu Li
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Jianan Dai
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Jinbei Wei
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Di Li
- College of Materials Science and Engineering, Jilin University, Changchun, 130012, China
| | - Xing Meng
- School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830017, China
| | - Chenguang Wang
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China.
| | - Geyu Lu
- State Key Laboratory of Integrated Optoelectronics, Key Laboratory of Advanced Gas Sensors of Jilin Province, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
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31
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Kim M, Chen C, Yaari Z, Frederiksen R, Randall E, Wollowitz J, Cupo C, Wu X, Shah J, Worroll D, Lagenbacher RE, Goerzen D, Li YM, An H, Wang Y, Heller DA. Nanosensor-based monitoring of autophagy-associated lysosomal acidification in vivo. Nat Chem Biol 2023; 19:1448-1457. [PMID: 37322156 PMCID: PMC10721723 DOI: 10.1038/s41589-023-01364-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Autophagy is a cellular process with important functions that drive neurodegenerative diseases and cancers. Lysosomal hyperacidification is a hallmark of autophagy. Lysosomal pH is currently measured by fluorescent probes in cell culture, but existing methods do not allow for quantitative, transient or in vivo measurements. In the present study, we developed near-infrared optical nanosensors using organic color centers (covalent sp3 defects on carbon nanotubes) to measure autophagy-mediated endolysosomal hyperacidification in live cells and in vivo. The nanosensors localize to the lysosomes, where the emission band shifts in response to local pH, enabling spatial, dynamic and quantitative mapping of subtle changes in lysosomal pH. Using the sensor, we observed cellular and intratumoral hyperacidification on administration of mTORC1 and V-ATPase modulators, revealing that lysosomal acidification mirrors the dynamics of S6K dephosphorylation and LC3B lipidation while diverging from p62 degradation. This sensor enables the transient and in vivo monitoring of the autophagy-lysosomal pathway.
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Affiliation(s)
- Mijin Kim
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chen Chen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zvi Yaari
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Jaina Wollowitz
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christian Cupo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaojian Wu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Janki Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Worroll
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rachel E Lagenbacher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dana Goerzen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Yue-Ming Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Heeseon An
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Maryland NanoCenter, University of Maryland, College Park, MD, USA
| | - Daniel A Heller
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine, Cornell University, New York, NY, USA.
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32
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Belay B, Figueiras E, Hyttinen J, Ahola A. Multifocal optical projection microscopy enables label-free 3D measurement of cardiomyocyte cluster contractility. Sci Rep 2023; 13:19788. [PMID: 37957157 PMCID: PMC10643565 DOI: 10.1038/s41598-023-46510-4] [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: 04/25/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived cardiomyocyte (CM) models have become an attractive tool for in vitro cardiac disease modeling and drug studies. These models are moving towards more complex three-dimensional microphysiological organ-on-chip systems. Label-free imaging-based techniques capable of quantifying contractility in 3D are needed, as traditional two-dimensional methods are ill-suited for 3D applications. Here, we developed multifocal (MF) optical projection microscopy (OPM) by integrating an electrically tunable lens to our in-house built optical projection tomography setup for extended depth of field brightfield imaging in CM clusters. We quantified cluster biomechanics by implementing our previously developed optical flow-based CM video analysis for MF-OPM. To demonstrate, we acquired and analyzed multiangle and multifocal projection videos of beating hiPSC-CM clusters in 3D hydrogel. We further quantified cluster contractility response to temperature and adrenaline and observed changes to beating rate and relaxation. Challenges emerge from light penetration and overlaying textures in larger clusters. However, our findings indicate that MF-OPM is suitable for contractility studies of 3D clusters. Thus, for the first time, MF-OPM is used in CM studies and hiPSC-CM 3D cluster contraction is quantified in multiple orientations and imaging planes.
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Affiliation(s)
- Birhanu Belay
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland.
| | - Edite Figueiras
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Jari Hyttinen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
| | - Antti Ahola
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland.
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33
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Wang H, Han G, Tang H, Zhang R, Liu Z, Sun Y, Liu B, Geng J, Zhang Z. Synchronous Photoactivation-Imaging Fluorophores Break Limitations of Photobleaching and Phototoxicity in Live-cell Microscopy. Anal Chem 2023; 95:16243-16250. [PMID: 37890170 DOI: 10.1021/acs.analchem.3c03064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Fluorescence microscopy is one of the most important tools in the studies of cell biology and many other fields, but two fundamental issues, photobleaching and phototoxicity, associated with the fluorophores have still limited its use for long-term and strong-illumination imaging of live cells. Here, we report a new concept of fluorophore engineering chemistry, synchronous photoactivation-imaging (SPI) fluorophores, activating and exciting fluorophores by a single light source to thus avoid the repeated switches between activation and excitation lights. The chemically reconstructed, nonemissive fluorophores can be photolyzed to allow continuous replenishing of "bright-state" probes detectable by standard fluorescent microscopes in the imaging process so as to bypass the photobleaching barrier to greatly extend the imaging period. Equally importantly, SPI fluorophores substantially reduce photocytotoxicity due to the scavenging of reactive oxygen species (ROS) by a photoactivable group and the slow release of "bright-state" probes to minimize ROS generation. Using SPI fluorophores, the time-lapsed confocal (>16 h) and super-resolution (>3 h) imaging of subcellular organelles under intensive illumination (50 MW/cm2) were achieved in live cells.
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Affiliation(s)
- Hong Wang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Guangmei Han
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Hesen Tang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Ruilong Zhang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Zhengjie Liu
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Yingqiang Sun
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Bianhua Liu
- Institute of Solid-State Physics, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Junlong Geng
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
| | - Zhongping Zhang
- Institute of Physical Science and Information Technology, School of Chemistry and Chemical Engineering, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Anhui University, Hefei 230601, Anhui, China
- Institute of Solid-State Physics, Chinese Academy of Sciences, Hefei 230031, Anhui, China
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Harada T, Hata S, Takagi R, Komori T, Fukuyama M, Chinen T, Kitagawa D. An antioxidant screen identifies ascorbic acid for prevention of light-induced mitotic prolongation in live cell imaging. Commun Biol 2023; 6:1107. [PMID: 37914777 PMCID: PMC10620154 DOI: 10.1038/s42003-023-05479-6] [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: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/03/2023] Open
Abstract
Phototoxicity is an important issue in fluorescence live imaging of light-sensitive cellular processes such as mitosis. Among several approaches to reduce phototoxicity, the addition of antioxidants to the media has been used as a simple method. Here, we analyzed the impact of phototoxicity on the mitotic progression in fluorescence live imaging of human cells and performed a screen to identify the most efficient antioxidative agents that reduce it. Quantitative analysis shows that high amounts of light illumination cause various mitotic defects such as prolonged mitosis and delays of chromosome alignment and centrosome separation. Among several antioxidants, our screen reveals that ascorbic acid significantly alleviates these phototoxic effects in mitosis. Furthermore, we demonstrate that adding ascorbic acid to the media enables fluorescence imaging of mitotic events at very high temporal resolution without obvious photodamage. Thus, this study provides an optimal method to effectively reduce the phototoxic effects in fluorescence live cell imaging.
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Affiliation(s)
- Tomoki Harada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shoji Hata
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Honcho Kawaguchi, Saitama, Japan.
| | - Rioka Takagi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takuma Komori
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
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Wang G, Li L, Sorrells JE, Chen J, Tu H. Gentle label-free nonlinear optical imaging relaxes linear-absorption-mediated triplet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561579. [PMID: 37873348 PMCID: PMC10592717 DOI: 10.1101/2023.10.09.561579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sample health is critical for live-cell fluorescence microscopy and has promoted light-sheet microscopy that restricts its ultraviolet-visible excitation to one plane inside a three-dimensional sample. It is thus intriguing that laser-scanning nonlinear optical microscopy, which similarly restricts its near-infrared excitation, has not broadly enabled gentle label-free molecular imaging. We hypothesize that intense near-infrared excitation induces phototoxicity via linear absorption of intrinsic biomolecules with subsequent triplet buildup, rather than the commonly assumed mechanism of nonlinear absorption. Using a reproducible phototoxicity assay based on the time-lapse elevation of auto-fluorescence (hyper-fluorescence) from a homogeneous tissue model (chicken breast), we provide strong evidence supporting this hypothesis. Our study justifies a simple imaging technique, e.g., rapidly scanned sub-80-fs excitation with full triplet-relaxation, to mitigate this ubiquitous linear-absorption-mediated phototoxicity independent of sample types. The corresponding label-free imaging can track freely moving C. elegans in real-time at an irradiance up to one-half of water optical breakdown.
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Khatib TO, Amanso AM, Knippler CM, Pedro B, Summerbell ER, Zohbi NM, Konen JM, Mouw JK, Marcus AI. A live-cell platform to isolate phenotypically defined subpopulations for spatial multi-omic profiling. PLoS One 2023; 18:e0292554. [PMID: 37819930 PMCID: PMC10566726 DOI: 10.1371/journal.pone.0292554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/22/2023] [Indexed: 10/13/2023] Open
Abstract
Numerous techniques have been employed to deconstruct the heterogeneity observed in normal and diseased cellular populations, including single cell RNA sequencing, in situ hybridization, and flow cytometry. While these approaches have revolutionized our understanding of heterogeneity, in isolation they cannot correlate phenotypic information within a physiologically relevant live-cell state with molecular profiles. This inability to integrate a live-cell phenotype-such as invasiveness, cell:cell interactions, and changes in spatial positioning-with multi-omic data creates a gap in understanding cellular heterogeneity. We sought to address this gap by employing lab technologies to design a detailed protocol, termed Spatiotemporal Genomic and Cellular Analysis (SaGA), for the precise imaging-based selection, isolation, and expansion of phenotypically distinct live cells. This protocol requires cells expressing a photoconvertible fluorescent protein and employs live cell confocal microscopy to photoconvert a user-defined single cell or set of cells displaying a phenotype of interest. The total population is then extracted from its microenvironment, and the optically highlighted cells are isolated using fluorescence activated cell sorting. SaGA-isolated cells can then be subjected to multi-omics analysis or cellular propagation for in vitro or in vivo studies. This protocol can be applied to a variety of conditions, creating protocol flexibility for user-specific research interests. The SaGA technique can be accomplished in one workday by non-specialists and results in a phenotypically defined cellular subpopulations for integration with multi-omics techniques. We envision this approach providing multi-dimensional datasets exploring the relationship between live cell phenotypes and multi-omic heterogeneity within normal and diseased cellular populations.
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Affiliation(s)
- Tala O. Khatib
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia, United States of America
| | - Angelica M. Amanso
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Christina M. Knippler
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Brian Pedro
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Emily R. Summerbell
- Office of Intramural Training and Education, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Najdat M. Zohbi
- Graduate Medical Education, Piedmont Macon Medical, Macon, Georgia, United States of America
| | - Jessica M. Konen
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Janna K. Mouw
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Adam I. Marcus
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia, United States of America
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Araújo-Gomes N, Zambito G, Johnbosco C, Calejo I, Leijten J, Löwik C, Karperien M, Mezzanotte L, Teixeira LM. Bioluminescence imaging on-chip platforms for non-invasive high-content bioimaging. Biosens Bioelectron 2023; 237:115510. [PMID: 37442028 DOI: 10.1016/j.bios.2023.115510] [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: 03/10/2023] [Revised: 06/09/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023]
Abstract
Incorporating non-invasive biosensing features in organ-on-chip models is of paramount importance for a wider implementation of these advanced in vitro microfluidic platforms. Optical biosensors, based on Bioluminescence Imaging (BLI), enable continuous, non-invasive, and in-situ imaging of cells, tissues or miniaturized organs without the drawbacks of conventional fluorescence imaging. Here, we report the first-of-its-kind integration and optimization of BLI in microfluidic chips, for non-invasive imaging of multiple biological readouts. The cell line HEK293T-GFP was engineered to express NanoLuc® luciferase under the control of a constitutive promoter and were cultured on-chip in 3D, in standard ECM-like hydrogels, to assess optimal cell detection conditions. Using real-time in-vitro dual-color microscopy, Bioluminescence (BL) and fluorescence (FL) were detectable using distinct imaging setups. Detection of the bioluminescent signals were observed at single cell resolution on-chip 20 min post-addition of Furimazine substrate and under perfusion. All hydrogels enabled BLI with higher signal-to-noise ratios as compared to fluorescence. For instance, agarose gels showed a ∼5-fold greater BL signal over background after injection of the substrate as compared to the FL signal. The use of BLI with microfluidic chip technologies opens up the potential for simultaneous in situ detection with continuous monitoring of multicolor cell reporters. Moreover, this can be achieved in a non-invasive manner. BL has great promise as a highly desirable biosensor for studying organ-on-chip platforms.
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Affiliation(s)
- Nuno Araújo-Gomes
- Department of Developmental Bioengineering, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Giorgia Zambito
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Castro Johnbosco
- Department of Developmental Bioengineering, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Isabel Calejo
- Department of Developmental Bioengineering, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Jeroen Leijten
- Department of Developmental Bioengineering, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Clemens Löwik
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marcel Karperien
- Department of Developmental Bioengineering, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Laura Mezzanotte
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Liliana Moreira Teixeira
- Department of Advanced Organ Bioengineering and Therapeutics, University of Twente, Enschede, the Netherlands.
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38
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Zhao J, Liu L, Wang T, Zhang J, Wang X, Du X, Hao R, Liu J, Liu Y, Liu Y. Quantitative phase imaging of living red blood cells combining digital holographic microscopy and deep learning. JOURNAL OF BIOPHOTONICS 2023; 16:e202300090. [PMID: 37321984 DOI: 10.1002/jbio.202300090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/17/2023]
Abstract
Digital holographic microscopy as a non-contacting, non-invasive, and highly accurate measurement technology, is becoming a valuable method for quantitatively investigating cells and tissues. Reconstruction of phases from a digital hologram is a key step in quantitative phase imaging for biological and biomedical research. This study proposes a two-stage deep convolutional neural network named VY-Net, to realize the effective and robust phase reconstruction of living red blood cells. The VY-Net can obtain the phase information of an object directly from a single-shot off-axis digital hologram. We also propose two new indices to evaluate the reconstructed phases. In experiments, the mean of the structural similarity index of reconstructed phases can reach 0.9309, and the mean of the accuracy of reconstructions of reconstructed phases is as high as 91.54%. An unseen phase map of a living human white blood cell is successfully reconstructed by the trained VY-Net, demonstrating its strong generality.
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Affiliation(s)
- Jiaxi Zhao
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Liu
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Tianhe Wang
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Jing Zhang
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiangzhou Wang
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaohui Du
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruqian Hao
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Juanxiu Liu
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Yi Liu
- School of Physics, University of Electronic Science and Technology of China, Chengdu, China
| | - Yong Liu
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
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39
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Monfort T, Azzollini S, Brogard J, Clémençon M, Slembrouck-Brec A, Forster V, Picaud S, Goureau O, Reichman S, Thouvenin O, Grieve K. Dynamic full-field optical coherence tomography module adapted to commercial microscopes allows longitudinal in vitro cell culture study. Commun Biol 2023; 6:992. [PMID: 37770552 PMCID: PMC10539404 DOI: 10.1038/s42003-023-05378-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Dynamic full-field optical coherence tomography (D-FFOCT) has recently emerged as a label-free imaging tool, capable of resolving cell types and organelles within 3D live samples, whilst monitoring their activity at tens of milliseconds resolution. Here, a D-FFOCT module design is presented which can be coupled to a commercial microscope with a stage top incubator, allowing non-invasive label-free longitudinal imaging over periods of minutes to weeks on the same sample. Long term volumetric imaging on human induced pluripotent stem cell-derived retinal organoids is demonstrated, highlighting tissue and cell organization processes such as rosette formation and mitosis as well as cell shape and motility. Imaging on retinal explants highlights single 3D cone and rod structures. An optimal workflow for data acquisition, postprocessing and saving is demonstrated, resulting in a time gain factor of 10 compared to prior state of the art. Finally, a method to increase D-FFOCT signal-to-noise ratio is demonstrated, allowing rapid organoid screening.
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Affiliation(s)
- Tual Monfort
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
- CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, 28 rue de Charenton, F-75012, Paris, France
- Paris Eye Imaging Group, Quinze-Vingts National Eye Hospital, INSERM-DGOS, CIC 1423, 28 rue de Charenton, Paris, 75012, France
| | - Salvatore Azzollini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Jérémy Brogard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Marilou Clémençon
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Amélie Slembrouck-Brec
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Valerie Forster
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Serge Picaud
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Olivier Goureau
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Sacha Reichman
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Olivier Thouvenin
- Institut Langevin, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France
| | - Kate Grieve
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France.
- CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, 28 rue de Charenton, F-75012, Paris, France.
- Paris Eye Imaging Group, Quinze-Vingts National Eye Hospital, INSERM-DGOS, CIC 1423, 28 rue de Charenton, Paris, 75012, France.
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40
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Xu (徐伟青) LW, Jazani S, Kilic Z, Pressé S. Single-Molecule Reaction-Diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556378. [PMID: 37732202 PMCID: PMC10508780 DOI: 10.1101/2023.09.05.556378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
We propose to capture reaction-diffusion on a molecule-by-molecule basis from the fastest acquirable timescale, namely individual photon arrivals. We illustrate our method on intrinsically disordered human proteins, the linker histone H1.0 as well as its chaperone prothymosin α , as these diffuse through an illuminated confocal spot and interact forming larger ternary complexes on millisecond timescales. Most importantly, single-molecule reaction-diffusion, smRD, reveals single molecule properties without trapping or otherwise confining molecules to surfaces. We achieve smRD within a Bayesian paradigm and term our method Bayes-smRD. Bayes-smRD is further free of the average, bulk, results inherent to the analysis of long photon arrival traces by fluorescence correlation spectroscopy. In learning from thousands of photon arrivals continuous spatial positions and discrete conformational and photophysical state changes, Bayes-smRD estimates kinetic parameters on a molecule-by-molecule basis with two to three orders of magnitude less data than tools such as fluorescence correlation spectroscopy thereby also dramatically reducing sample photodamage.
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Affiliation(s)
- Lance W.Q. Xu (徐伟青)
- Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins Medicine, Baltimore, MD 21205, USA
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Science, Arizona State University, Tempe, AZ 85287, USA
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41
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Li X, Wu Y, Su Y, Rey-Suarez I, Matthaeus C, Updegrove TB, Wei Z, Zhang L, Sasaki H, Li Y, Guo M, Giannini JP, Vishwasrao HD, Chen J, Lee SJJ, Shao L, Liu H, Ramamurthi KS, Taraska JW, Upadhyaya A, La Riviere P, Shroff H. Three-dimensional structured illumination microscopy with enhanced axial resolution. Nat Biotechnol 2023; 41:1307-1319. [PMID: 36702897 PMCID: PMC10497409 DOI: 10.1038/s41587-022-01651-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/16/2022] [Indexed: 01/27/2023]
Abstract
The axial resolution of three-dimensional structured illumination microscopy (3D SIM) is limited to ∼300 nm. Here we present two distinct, complementary methods to improve axial resolution in 3D SIM with minimal or no modification to the optical system. We show that placing a mirror directly opposite the sample enables four-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with ∼120-nm lateral and 160-nm axial resolution. We also developed a deep learning method achieving ∼120-nm isotropic resolution. This method can be combined with denoising to facilitate volumetric imaging spanning dozens of timepoints. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers and visualizing cytoskeletal dynamics within T cells in the early stages of immune synapse formation.
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Affiliation(s)
- Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA.
| | - Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA.
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Leica Microsystems, Inc., Deerfield, IL, USA
- SVision, LLC, Bellevue, WA, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Ivan Rey-Suarez
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Claudia Matthaeus
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhuang Wei
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Hideki Sasaki
- Leica Microsystems, Inc., Deerfield, IL, USA
- SVision, LLC, Bellevue, WA, USA
| | - Yue Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Min Guo
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - John P Giannini
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Shih-Jong J Lee
- Leica Microsystems, Inc., Deerfield, IL, USA
- SVision, LLC, Bellevue, WA, USA
| | - Lin Shao
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Huafeng Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- MBL Fellows, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- MBL Fellows, Marine Biological Laboratory, Woods Hole, MA, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
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Mandracchia B, Liu W, Hua X, Forghani P, Lee S, Hou J, Nie S, Xu C, Jia S. Optimal sparsity allows reliable system-aware restoration of fluorescence microscopy images. SCIENCE ADVANCES 2023; 9:eadg9245. [PMID: 37647399 PMCID: PMC10468132 DOI: 10.1126/sciadv.adg9245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence microscopy is one of the most indispensable and informative driving forces for biological research, but the extent of observable biological phenomena is essentially determined by the content and quality of the acquired images. To address the different noise sources that can degrade these images, we introduce an algorithm for multiscale image restoration through optimally sparse representation (MIRO). MIRO is a deterministic framework that models the acquisition process and uses pixelwise noise correction to improve image quality. Our study demonstrates that this approach yields a remarkable restoration of the fluorescence signal for a wide range of microscopy systems, regardless of the detector used (e.g., electron-multiplying charge-coupled device, scientific complementary metal-oxide semiconductor, or photomultiplier tube). MIRO improves current imaging capabilities, enabling fast, low-light optical microscopy, accurate image analysis, and robust machine intelligence when integrated with deep neural networks. This expands the range of biological knowledge that can be obtained from fluorescence microscopy.
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Affiliation(s)
- Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Soojung Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jessica Hou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuyi Nie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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43
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Fuchs H, Jahn K, Hu X, Meister R, Binter M, Framme C. Breaking a Dogma: High-Throughput Live-Cell Imaging in Real-Time with Hoechst 33342. Adv Healthc Mater 2023; 12:e2300230. [PMID: 36934382 DOI: 10.1002/adhm.202300230] [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: 01/21/2023] [Revised: 03/14/2023] [Indexed: 03/20/2023]
Abstract
Automated high-throughput live cell imaging (LCI) enables investigation of substance effects on cells in vitro. Usually, cell number is analyzed by phase-contrast imaging, which is reliable only for a few cell types. Therefore, an accurate cell counting method, such as staining the nuclei with Hoechst 33342 before LCI, will be desirable. However, since the mid-1980s, the dogma exists that Hoechst can only be used for endpoint analyses because of its cytotoxic properties and the potentially phototoxic effects of the excitation light. Since microscopic camera sensitivity has significantly improved, this study investigates whether this dogma is still justified. Therefore, exposure parameters are optimized using a 4× objective, and the minimum required Hoechst concentration is evaluated, allowing LCI at 30-min intervals over 5 days. Remarkably, a Hoechst concentration of only 57 × 10-9 m significantly inhibits proliferation and thus impairs cell viability. However, Hoechst concentrations between 7 × 10-9 and 28 × 10-9 m can be determined, which are neither cytotoxic nor impacting cell viability, proliferation, or signaling pathways. The method can be adapted to regular inverted fluorescence microscopes and allows, for example, to determine the cytotoxicity of a substance or the transduction efficiency, with the advantage that the analysis can be repeated at any desired time point.
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Affiliation(s)
- Heiko Fuchs
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Kirsten Jahn
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Xiaonan Hu
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Roland Meister
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Maximilian Binter
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Carsten Framme
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
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44
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Ling Z, Han K, Liu W, Hua X, Jia S. Volumetric live-cell autofluorescence imaging using Fourier light-field microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:4237-4245. [PMID: 37799690 PMCID: PMC10549745 DOI: 10.1364/boe.495506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/07/2023]
Abstract
This study introduces a rapid, volumetric live-cell imaging technique for visualizing autofluorescent sub-cellular structures and their dynamics by employing high-resolution Fourier light-field microscopy. We demonstrated this method by capturing lysosomal autofluorescence in fibroblasts and HeLa cells. Additionally, we conducted multicolor imaging to simultaneously observe lysosomal autofluorescence and fluorescently-labeled organelles such as lysosomes and mitochondria. We further analyzed the data to quantify the interactions between lysosomes and mitochondria. This research lays the foundation for future exploration of native cellular states and functions in three-dimensional environments, effectively reducing photodamage and eliminating the necessity for exogenous labels.
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Affiliation(s)
- Zhi Ling
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Keyi Han
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Wenhao Liu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Xuanwen Hua
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Shu Jia
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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45
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Dunn KJ, Berger AJ. Three-dimensional angular scattering simulations inform analysis of scattering from single cells. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:086501. [PMID: 37564163 PMCID: PMC10411915 DOI: 10.1117/1.jbo.28.8.086501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/16/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Significance Organelle sizes, which are indicative of cellular status, have implications for drug development and immunology research. At the single cell level, such information could be used to study the heterogeneity of cell response to drugs or pathogens. Aim Angularly resolved elastic light scattering is known to be sensitive to changes in organelle size distribution. We developed a Mie theory-based simulation of angular scattering from single cells to quantify the effects of noise on scattering and size estimates. Approach We simulated randomly sampled organelle sizes (drawn from a log normal distribution), interference between different organelles' scattering, and detector noise. We quantified each noise source's effect upon the estimated mean and standard deviation of organelle size distributions. Results The results demonstrate that signal-to-noise ratio in the angular scattering increased with the number of scatterers, cell area, and exposure time and decreased with the size distribution width. The error in estimating the mean of the size distributions remained below 5% for nearly all experimental parameters tested, but the widest size distribution tested (standard deviation of 600 nm) reached 20%. Conclusions The simulator revealed that sparse sampling of a broad size distribution can dominate the mismatch between actual and predicted size parameters. Alternative estimation strategies could reduce the discrepancy.
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Affiliation(s)
- Kaitlin J. Dunn
- University of Rochester, Institute of Optics, Rochester, New York, United States
| | - Andrew J. Berger
- University of Rochester, Institute of Optics, Rochester, New York, United States
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46
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Bouchard C, Wiesner T, Deschênes A, Bilodeau A, Turcotte B, Gagné C, Lavoie-Cardinal F. Resolution enhancement with a task-assisted GAN to guide optical nanoscopy image analysis and acquisition. NAT MACH INTELL 2023; 5:830-844. [PMID: 37615032 PMCID: PMC10442226 DOI: 10.1038/s42256-023-00689-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/12/2023] [Indexed: 08/25/2023]
Abstract
Super-resolution fluorescence microscopy methods enable the characterization of nanostructures in living and fixed biological tissues. However, they require the adjustment of multiple imaging parameters while attempting to satisfy conflicting objectives, such as maximizing spatial and temporal resolution while minimizing light exposure. To overcome the limitations imposed by these trade-offs, post-acquisition algorithmic approaches have been proposed for resolution enhancement and image-quality improvement. Here we introduce the task-assisted generative adversarial network (TA-GAN), which incorporates an auxiliary task (for example, segmentation, localization) closely related to the observed biological nanostructure characterization. We evaluate how the TA-GAN improves generative accuracy over unassisted methods, using images acquired with different modalities such as confocal, bright-field, stimulated emission depletion and structured illumination microscopy. The TA-GAN is incorporated directly into the acquisition pipeline of the microscope to predict the nanometric content of the field of view without requiring the acquisition of a super-resolved image. This information is used to automatically select the imaging modality and regions of interest, optimizing the acquisition sequence by reducing light exposure. Data-driven microscopy methods like the TA-GAN will enable the observation of dynamic molecular processes with spatial and temporal resolutions that surpass the limits currently imposed by the trade-offs constraining super-resolution microscopy.
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Affiliation(s)
- Catherine Bouchard
- Institute Intelligence and Data (IID), Université Laval, Quebec City, Quebec Canada
- CERVO Brain Research Center, Quebec City, Quebec Canada
| | - Theresa Wiesner
- Institute Intelligence and Data (IID), Université Laval, Quebec City, Quebec Canada
- CERVO Brain Research Center, Quebec City, Quebec Canada
| | | | - Anthony Bilodeau
- Institute Intelligence and Data (IID), Université Laval, Quebec City, Quebec Canada
- CERVO Brain Research Center, Quebec City, Quebec Canada
| | - Benoît Turcotte
- Institute Intelligence and Data (IID), Université Laval, Quebec City, Quebec Canada
- CERVO Brain Research Center, Quebec City, Quebec Canada
| | - Christian Gagné
- Institute Intelligence and Data (IID), Université Laval, Quebec City, Quebec Canada
- Département de génie électrique et de génie informatique, Université Laval, Quebec City, Quebec Canada
| | - Flavie Lavoie-Cardinal
- Institute Intelligence and Data (IID), Université Laval, Quebec City, Quebec Canada
- CERVO Brain Research Center, Quebec City, Quebec Canada
- Département de psychiatrie et de neurosciences, Université Laval, Quebec City, Quebec Canada
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47
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Sanders S, Jensen Y, Reimer R, Bosse JB. From the beginnings to multidimensional light and electron microscopy of virus morphogenesis. Adv Virus Res 2023; 116:45-88. [PMID: 37524482 DOI: 10.1016/bs.aivir.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Individual functional viral morphogenesis events are often dynamic, short, and infrequent and might be obscured by other pathways and dead-end products. Volumetric live cell imaging has become an essential tool for studying viral morphogenesis events. It allows following entire dynamic processes while providing functional evidence that the imaged process is involved in viral production. Moreover, it allows to capture many individual events and allows quantitative analysis. Finally, the correlation of volumetric live-cell data with volumetric electron microscopy (EM) can provide crucial insights into the ultrastructure and mechanisms of viral morphogenesis events. Here, we provide an overview and discussion of suitable imaging methods for volumetric correlative imaging of viral morphogenesis and frame them in a historical summary of their development.
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Affiliation(s)
- Saskia Sanders
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Yannick Jensen
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Jens B Bosse
- Department of Virology, Hannover Medical School, Hannover, Germany; Leibniz Institute of Virology (LIV), Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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48
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Xie E, Ahmad S, Smyth RP, Sieben C. Advanced fluorescence microscopy in respiratory virus cell biology. Adv Virus Res 2023; 116:123-172. [PMID: 37524480 DOI: 10.1016/bs.aivir.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.
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Affiliation(s)
- Enyu Xie
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany; Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Christian Sieben
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany.
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49
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Wang R, Butt D, Cross S, Verkade P, Achim A. Bright-field to fluorescence microscopy image translation for cell nuclei health quantification. BIOLOGICAL IMAGING 2023; 3:e12. [PMID: 38510164 PMCID: PMC10951917 DOI: 10.1017/s2633903x23000120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/05/2023] [Accepted: 05/29/2023] [Indexed: 03/22/2024]
Abstract
Microscopy is a widely used method in biological research to observe the morphology and structure of cells. Amongst the plethora of microscopy techniques, fluorescent labeling with dyes or antibodies is the most popular method for revealing specific cellular organelles. However, fluorescent labeling also introduces new challenges to cellular observation, as it increases the workload, and the process may result in nonspecific labeling. Recent advances in deep visual learning have shown that there are systematic relationships between fluorescent and bright-field images, thus facilitating image translation between the two. In this article, we propose the cross-attention conditional generative adversarial network (XAcGAN) model. It employs state-of-the-art GANs (GANs) to solve the image translation task. The model uses supervised learning and combines attention-based networks to explore spatial information during translation. In addition, we demonstrate the successful application of XAcGAN to infer the health state of translated nuclei from bright-field microscopy images. The results show that our approach achieves excellent performance both in terms of image translation and nuclei state inference.
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Affiliation(s)
- Ruixiong Wang
- Visual Information Laboratory, University of Bristol, Bristol, United Kingdom
| | - Daniel Butt
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Stephen Cross
- Wolfson Bioimaging Facility, University of Bristol, Bristol, United Kingdom
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Alin Achim
- Visual Information Laboratory, University of Bristol, Bristol, United Kingdom
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50
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Chen YI, Chang YJ, Sun Y, Liao SC, Santacruz SR, Yeh HC. Spatial resolution enhancement in photon-starved STED imaging using deep learning-based fluorescence lifetime analysis. NANOSCALE 2023; 15:9449-9456. [PMID: 37159237 PMCID: PMC10460507 DOI: 10.1039/d3nr00305a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
As a super-resolution imaging method, stimulated emission depletion (STED) microscopy has unraveled fine intracellular structures and provided insights into nanoscale organizations in cells. Although image resolution can be further enhanced by continuously increasing the STED-beam power, the resulting photodamage and phototoxicity are major issues for real-world applications of STED microscopy. Here we demonstrate that, with 50% less STED-beam power, the STED image resolution can be improved up to 1.45-fold using the separation of photons by a lifetime tuning (SPLIT) scheme combined with a deep learning-based phasor analysis algorithm termed flimGANE (fluorescence lifetime imaging based on a generative adversarial network). This work offers a new approach for STED imaging in situations where only a limited photon budget is available.
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Affiliation(s)
- Yuan-I Chen
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
| | - Yin-Jui Chang
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
| | - Yuansheng Sun
- ISS, Inc., 1602 Newton Drive, Champaign, IL, 61822, USA
| | - Shih-Chu Liao
- ISS, Inc., 1602 Newton Drive, Champaign, IL, 61822, USA
| | - Samantha R Santacruz
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
- Electrical & Computer Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Hsin-Chih Yeh
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
- Texas Materials Institute, University of Texas at Austin, Austin, TX, USA
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