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Luo X, Zhang J, Tan H, Jiang J, Li J, Wen W. Real-Time 3D Tracking of Multi-Particle in the Wide-Field Illumination Based on Deep Learning. Sensors (Basel) 2024; 24:2583. [PMID: 38676200 PMCID: PMC11054292 DOI: 10.3390/s24082583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
In diverse realms of research, such as holographic optical tweezer mechanical measurements, colloidal particle motion state examinations, cell tracking, and drug delivery, the localization and analysis of particle motion command paramount significance. Algorithms ranging from conventional numerical methods to advanced deep-learning networks mark substantial strides in the sphere of particle orientation analysis. However, the need for datasets has hindered the application of deep learning in particle tracking. In this work, we elucidated an efficacious methodology pivoted toward generating synthetic datasets conducive to this domain that resonates with robustness and precision when applied to real-world data of tracking 3D particles. We developed a 3D real-time particle positioning network based on the CenterNet network. After conducting experiments, our network has achieved a horizontal positioning error of 0.0478 μm and a z-axis positioning error of 0.1990 μm. It shows the capability to handle real-time tracking of particles, diverse in dimensions, near the focal plane with high precision. In addition, we have rendered all datasets cultivated during this investigation accessible.
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Affiliation(s)
- Xiao Luo
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong 999077, China;
| | - Jie Zhang
- Advanced Materials Thrust, The Hong Kong University of Science and Technology, Guangzhou 511400, China; (J.Z.); (J.J.); (J.L.)
| | - Handong Tan
- Department of Individualized Interdisciplinary Program (Advanced Materials), The Hong Kong University of Science and Technology, Hong Kong 999077, China;
| | - Jiahao Jiang
- Advanced Materials Thrust, The Hong Kong University of Science and Technology, Guangzhou 511400, China; (J.Z.); (J.J.); (J.L.)
| | - Junda Li
- Advanced Materials Thrust, The Hong Kong University of Science and Technology, Guangzhou 511400, China; (J.Z.); (J.J.); (J.L.)
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong 999077, China;
- Advanced Materials Thrust, The Hong Kong University of Science and Technology, Guangzhou 511400, China; (J.Z.); (J.J.); (J.L.)
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Uribe Castaño L, Mirsanaye K, Kontenis L, Krouglov S, Žurauskas E, Navab R, Yasufuku K, Tsao MS, Akens MK, Wilson BC, Barzda V. Wide-field Stokes polarimetric microscopy for second harmonic generation imaging. J Biophotonics 2023; 16:e202200284. [PMID: 36651498 DOI: 10.1002/jbio.202200284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/09/2022] [Accepted: 01/09/2023] [Indexed: 05/17/2023]
Abstract
We employ wide-field second harmonic generation (SHG) microscopy together with nonlinear Stokes polarimetry for quick ultrastructural investigation of large sample areas (700 μm × 700 μm) in thin histology sections. The Stokes vector components for SHG are obtained from the polarimetric measurements with incident and outgoing linear and circular polarization states. The Stokes components are used to construct the images of polarimetric parameters and deduce the maps of ultrastructural parameters of achiral and chiral nonlinear susceptibility tensor components ratios and cylindrical axis orientation in fibrillar materials. The large area imaging was employed for lung tumor margin investigations. The imaging shows reduced SHG intensity, increased achiral susceptibility ratio values, and preferential orientation of collagen strands along the boarder of tumor margin. The wide-field Stokes polarimetric SHG microscopy opens a possibility of quick large area imaging of ultrastructural parameters of tissue collagen, which can be used for nonlinear histopathology investigations.
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Affiliation(s)
- Leonardo Uribe Castaño
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Kamdin Mirsanaye
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Lukas Kontenis
- Laser Research Centre, Faculty of Physics, Vilnius University, Vilnius, Lithuania
- Light Conversion, Vilnius, Lithuania
| | - Serguei Krouglov
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Edvardas Žurauskas
- Department of Pathology, Forensic Medicine and Pharmacology, Vilnius University, Vilnius, Lithuania
| | - Roya Navab
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kazuhiro Yasufuku
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Margarete K Akens
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Techna Institute, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Brian C Wilson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Virginijus Barzda
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Laser Research Centre, Faculty of Physics, Vilnius University, Vilnius, Lithuania
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Wang T, Chen Y, Wang B, Wu M. Recent progress of second near-infrared (NIR-II) fluorescence microscopy in bioimaging. Front Physiol 2023; 14:1126805. [PMID: 36895633 PMCID: PMC9990761 DOI: 10.3389/fphys.2023.1126805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Visualizing biological tissues in vivo at a cellular or subcellular resolution to explore molecular signaling and cell behaviors is a crucial direction for research into biological processes. In vivo imaging can provide quantitative and dynamic visualization/mapping in biology and immunology. New microscopy techniques combined with near-infrared region fluorophores provide additional avenues for further progress in vivo bioimaging. Based on the development of chemical materials and physical optoelectronics, new NIR-II microscopy techniques are emerging, such as confocal and multiphoton microscopy, light-sheet fluorescence microscopy (LSFM), and wide-field microscopy. In this review, we introduce the characteristics of in vivo imaging using NIR-II fluorescence microscopy. We also cover the recent advances in NIR-II fluorescence microscopy techniques in bioimaging and the potential for overcoming current challenges.
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Affiliation(s)
- Tian Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingying Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingfu Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Becerril-Castro IB, Calderon I, Ockova J, Liebel M, van Hulst NF, Giannini V, Alvarez-Puebla RA. Direct Modular Printing of Plasmonic Chemosensors. ACS Appl Mater Interfaces 2022; 14:57165-57170. [PMID: 36516398 PMCID: PMC9801379 DOI: 10.1021/acsami.2c17202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Here, we present and implement a new approach for producing modular inkjet-printable surface-enhanced Raman scattering (SERS) chemosensors. These sensors, combined with a rapid large field-of-view imaging system allow for fast imaging of the chemical characteristics of a sample. The performance of these materials is illustrated by printing a pH sensor on paper and interrogating aqueous solutions at different pH values. Results show single-shot images exceeding 9 mm2 which are readily read out via SERS imaging.
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Affiliation(s)
- I. Brian Becerril-Castro
- Department
of Inorganic and Physical Chemistry, Universitat
Rovira i Virgili, Marcel·lí Domingo SN (Edificio N5), 43007 Tarragona, Spain
| | - Irene Calderon
- Department
of Inorganic and Physical Chemistry, Universitat
Rovira i Virgili, Marcel·lí Domingo SN (Edificio N5), 43007 Tarragona, Spain
| | - Jana Ockova
- ICFO, Av. Carl Friedrich Gauss 3, 08860 Barcelona, Spain
| | - Matz Liebel
- ICFO, Av. Carl Friedrich Gauss 3, 08860 Barcelona, Spain
| | - Niek F. van Hulst
- ICFO, Av. Carl Friedrich Gauss 3, 08860 Barcelona, Spain
- ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Vincenzo Giannini
- Instituto
de Estructura de la Materia (IEM), Consejo
Superior de Investigaciones Científicas (CSIC), Serrano 121, 28006 Madrid, Spain
- Technology
Innovation Institute, Masdar City 50819, Abu Dhabi, United Arab Emirates
- Centre of
Excellence ENSEMBLE3 sp. z o.o., Wolczynska 133, 01-919 Warsaw, Poland
| | - Ramon A. Alvarez-Puebla
- Department
of Inorganic and Physical Chemistry, Universitat
Rovira i Virgili, Marcel·lí Domingo SN (Edificio N5), 43007 Tarragona, Spain
- ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain
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Kubalová I, Němečková A, Weisshart K, Hřibová E, Schubert V. Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes. Int J Mol Sci 2021; 22:ijms22041903. [PMID: 33672992 PMCID: PMC7917581 DOI: 10.3390/ijms22041903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
| | - Alžběta Němečková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | | | - Eva Hřibová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic; (A.N.); (E.H.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466 Seeland, Germany;
- Correspondence: ; Tel.: +49-394-825-212
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Celotto M, De Luca C, Muratore P, Resta F, Allegra Mascaro AL, Pavone FS, De Bonis G, Paolucci PS. Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques. Methods Protoc 2020; 3:E14. [PMID: 32023996 PMCID: PMC7189682 DOI: 10.3390/mps3010014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 12/25/2022] Open
Abstract
Slow waves (SWs) are spatio-temporal patterns of cortical activity that occur both during natural sleep and anesthesia and are preserved across species. Even though electrophysiological recordings have been largely used to characterize brain states, they are limited in the spatial resolution and cannot target specific neuronal population. Recently, large-scale optical imaging techniques coupled with functional indicators overcame these restrictions, and new pipelines of analysis and novel approaches of SWs modelling are needed to extract relevant features of the spatio-temporal dynamics of SWs from these highly spatially resolved data-sets. Here we combined wide-field fluorescence microscopy and a transgenic mouse model expressing a calcium indicator (GCaMP6f) in excitatory neurons to study SW propagation over the meso-scale under ketamine anesthesia. We developed a versatile analysis pipeline to identify and quantify the spatio-temporal propagation of the SWs. Moreover, we designed a computational simulator based on a simple theoretical model, which takes into account the statistics of neuronal activity, the response of fluorescence proteins and the slow waves dynamics. The simulator was capable of synthesizing artificial signals that could reliably reproduce several features of the SWs observed in vivo, thus enabling a calibration tool for the analysis pipeline. Comparison of experimental and simulated data shows the robustness of the analysis tools and its potential to uncover mechanistic insights of the Slow Wave Activity (SWA).
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Affiliation(s)
- Marco Celotto
- Department of Physics, “Sapienza” University of Rome, 00185 Rome, Italy; (M.C.); (C.D.L.); (P.M.)
- IIT—Neural Computation Lab, CNCS@UniTn, 38068 Rovereto, Italy
| | - Chiara De Luca
- Department of Physics, “Sapienza” University of Rome, 00185 Rome, Italy; (M.C.); (C.D.L.); (P.M.)
- INFN, 00185 Rome, Italy;
- PhD Program in Behavioural Neuroscience,“Sapienza” University of Rome, 00185 Rome, Italy
| | - Paolo Muratore
- Department of Physics, “Sapienza” University of Rome, 00185 Rome, Italy; (M.C.); (C.D.L.); (P.M.)
- PhD Program in Cognitive Neuroscience, SISSA, 34136 Trieste, Italy
| | - Francesco Resta
- LENS, University of Florence, 50019 Florence, Italy; (F.R.); (A.L.A.M.); (F.S.P.)
| | - Anna Letizia Allegra Mascaro
- LENS, University of Florence, 50019 Florence, Italy; (F.R.); (A.L.A.M.); (F.S.P.)
- Istituto di Neuroscienze, CNR, 56124 Pisa, Italy
| | - Francesco Saverio Pavone
- LENS, University of Florence, 50019 Florence, Italy; (F.R.); (A.L.A.M.); (F.S.P.)
- Department of Physics, University of Florence, 50019 Florence, Italy
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Conti E, Allegra Mascaro AL, Pavone FS. Large Scale Double-Path Illumination System with Split Field of View for the All-Optical Study of Inter-and Intra-Hemispheric Functional Connectivity on Mice. Methods Protoc 2019; 2:E11. [PMID: 31164593 DOI: 10.3390/mps2010011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 12/26/2022] Open
Abstract
Recent improvements in optical tools that can perturb brain activity and simultaneously reveal the elicited alterations in the associated regions offer an exceptional means to understand and map the connectivity of the brain. In this work, we exploit a combination of recently developed optical tools to monitor neural population at the meso-scale level and to mould the cortical patterns of targeted neuronal population. Our goal was to investigate the propagation of neuronal activity over the mouse cortex that is triggered by optogenetic stimulation in the contralateral hemisphere. Towards this aim, we developed a wide-field fluorescence microscope that is characterized by a double illumination path allowing for the optogenetic stimulation of the transfected area in the left hemisphere and the simultaneous recording of cortical activity in the right hemisphere. The microscope was further implemented with a custom shutter in order to split the LED illumination path, resulting in a half-obscured field of view. By avoiding the spectral crosstalk between GCaMP6f and channelrhodopsin 2 (ChR2), this system offered the possibility of simultaneous “pumping and probing” of inter-hemispheric functional connectivity on Thy1-GCaMP6f mice.
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Boorboor S, Jadhav, Ananth M, Talmage D, Role, Kaufman A. Visualization of Neuronal Structures in Wide-Field Microscopy Brain Images. IEEE Trans Vis Comput Graph 2018; 25:10.1109/TVCG.2018.2864852. [PMID: 30136950 PMCID: PMC6382602 DOI: 10.1109/tvcg.2018.2864852] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wide-field microscopes are commonly used in neurobiology for experimental studies of brain samples. Available visualization tools are limited to electron, two-photon, and confocal microscopy datasets, and current volume rendering techniques do not yield effective results when used with wide-field data. We present a workflow for the visualization of neuronal structures in wide-field microscopy images of brain samples. We introduce a novel gradient-based distance transform that overcomes the out-of-focus blur caused by the inherent design of wide-field microscopes. This is followed by the extraction of the 3D structure of neurites using a multi-scale curvilinear filter and cell-bodies using a Hessian-based enhancement filter. The response from these filters is then applied as an opacity map to the raw data. Based on the visualization challenges faced by domain experts, our workflow provides multiple rendering modes to enable qualitative analysis of neuronal structures, which includes separation of cell-bodies from neurites and an intensity-based classification of the structures. Additionally, we evaluate our visualization results against both a standard image processing deconvolution technique and a confocal microscopy image of the same specimen. We show that our method is significantly faster and requires less computational resources, while producing high quality visualizations. We deploy our workflow in an immersive gigapixel facility as a paradigm for the processing and visualization of large, high-resolution, wide-field microscopy brain datasets.
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Abstract
One of the major limitations of flow cytometry (FCM) is the absence of an intracellular view. Automated microscopy and image analysis, together with technological developments, led to new approaches in cytometry that bypass the above limitation, introducing high resolution, high content, and large statistical sampling. However, few attempts have been made, until now, to translate the wide repertoire of FCM assays into high-content image screening. This unit describes the implementation of an acquisition and analysis protocol for evaluation of the cell cycle by automated microscopy. The approach grants the possibility to perform simultaneous analysis of a high number of different parameters. A large part of this unit is devoted to the description of hardware features that can optimize the recorded information together with the acquisition and analysis procedures employed to produce good-quality data.
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Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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Abstract
Nanostructured optical components, such as nanolenses, direct light at subwavelength scales to enable, among others, high-resolution lithography, miniaturization of photonic circuits, and nanoscopic imaging of biostructures. A major challenge in fabricating nanolenses is the appropriate positioning of the lens with respect to the sample while simultaneously ensuring it adopts the optimal size and shape for the intended use. One application of particular interest is the enhancement of contrast and signal-to-noise ratio in the imaging of nanoscale objects, especially over wide fields-of-view (FOVs), which typically come with limited resolution and sensitivity for imaging nano-objects. Here we present a self-assembly method for fabricating time- and temperature-tunable nanolenses based on the condensation of a polymeric liquid around a nanoparticle, which we apply to the high-throughput on-chip detection of spheroids smaller than 40 nm, rod-shaped particles with diameter smaller than 20 nm, and biofunctionalized nanoparticles, all across an ultralarge FOV of >20 mm(2). Previous nanoparticle imaging efforts across similar FOVs have detected spheroids no smaller than 100 nm, and therefore our results demonstrate the detection of particles >15-fold smaller in volume, which in free space have >240 times weaker Rayleigh scattering compared to the particle sizes detected in earlier wide-field imaging work. This entire platform, with its tunable nanolens condensation and wide-field imaging functions, is also miniaturized into a cost-effective and portable device, which might be especially important for field use, mobile sensing, and diagnostics applications, including, for example, the measurement of viral load in bodily fluids.
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Affiliation(s)
- Euan McLeod
- Electrical Engineering Department, University of California, Los Angeles, California 90095, United States
- Bioengineering Department, University of California, Los Angeles, California 90095, United States
| | - Chau Nguyen
- Chemistry & Biochemistry Department, University of California, Los Angeles, California 90095, United States
| | - Patrick Huang
- Bioengineering Department, University of California, Los Angeles, California 90095, United States
| | - Wei Luo
- Electrical Engineering Department, University of California, Los Angeles, California 90095, United States
- Bioengineering Department, University of California, Los Angeles, California 90095, United States
| | - Muhammed Veli
- Electrical Engineering Department, University of California, Los Angeles, California 90095, United States
| | - Aydogan Ozcan
- Electrical Engineering Department, University of California, Los Angeles, California 90095, United States
- Bioengineering Department, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, California 90095, United States
- Address correspondence to ; http://innovate.ee.ucla.edu/
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