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Ma P, Chen Y. Beyond conventional wisdom: unveiling quantitative insights in fluorescence lifetime imaging via realistic simulation of biological systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572686. [PMID: 38187652 PMCID: PMC10769356 DOI: 10.1101/2023.12.20.572686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) and photometry (FLiP) are illuminating the dynamics of biological signals. Because fluorescence lifetime is an intensive property of a fluorophore that is insensitive to sensor expression levels, it excels over fluorescence intensity measurements by allowing comparison across animals, over chronic time periods, and quantitation of the absolute levels of biological signals. However, the insensitivity of lifetime to sensor expression level does not always hold true in biological experiments where autofluorescence, ambient light, dark currents and afterpulses of the detectors are present. To quantitatively evaluate the potential and limitations of fluorescence lifetime measurements, we introduce FLiSimBA, a flexible platform enabling realistic F luorescence Li fetime Sim ulation for B iological A pplications. FLiSimBA accurately recapitulates experimental data and provides quantitative analyses. Using FLiSimBA, we determine the photons required for minimum detectable differences in lifetime and quantify the impact of hardware innovation. Furthermore, we challenge the conventional view that fluorescence lifetime is insensitive to sensor expression levels and define the conditions in which sensor express levels do not result in statistically significant difference in biological experiments. Thus, we introduce an adaptable simulation tool that allows systematic exploration of parameters to define experimental advantages and limitations in biological applications. Moreover, we provide a statistical framework and quantitative insights into the impact of key experimental parameters on signal-to-noise ratio and fluorescence lifetime responses. Our tool and results will enable the growing community of FLIM users and developers to optimize FLIM experiments, expose limitations, and identify opportunities for future innovation of fluorescence lifetime technologies.
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Baronnier J, Mahler B, Dujardin C, Houel J. Low-Temperature Emission Dynamics of Methylammonium Lead Bromide Hybrid Perovskite Thin Films at the Sub-Micrometer Scale. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2376. [PMID: 37630961 PMCID: PMC10458237 DOI: 10.3390/nano13162376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
We study the low-temperature (T = 4.7 K) emission dynamics of a thin film of methylammonium lead bromide (MAPbBr3), prepared via the anti-solvent method. Using intensity-dependent (over 5 decades) hyperspectral microscopy under quasi-resonant (532 nm) continuous wave excitation, we revealed spatial inhomogeneities in the thin film emission. This was drastically different at the band-edge (∼550 nm, sharp peaks) than in the emission tail (∼568 nm, continuum of emission). We are able to observe regions of the film at the micrometer scale where emission is dominated by excitons, in between regions of trap emission. Varying the density of absorbed photons by the MAPbBr3 thin films, two-color fluorescence lifetime imaging microscopy unraveled the emission dynamics: a fast, resolution-limited (∼200 ps) monoexponential tangled with a stretched exponential decay. We associate the first to the relaxation of excitons and the latter to trap emission dynamics. The obtained stretching exponents can be interpreted as the result of a two-dimensional electron diffusion process: Förster resonant transfer mechanism. Furthermore, the non-vanishing fast monoexponential component even in the tail of the MAPbBr3 emission indicates the subsistence of localized excitons. Finally, we estimate the density of traps in MAPbBr3 thin films prepared using the anti-solvent method at n∼1017 cm-3.
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Affiliation(s)
- Justine Baronnier
- Université Claude Bernard Lyon 1, Institut Lumière-Matière UMR5306 CNRS, F-69622 Villeurbanne, France
| | - Benoit Mahler
- Université Claude Bernard Lyon 1, Institut Lumière-Matière UMR5306 CNRS, F-69622 Villeurbanne, France
| | - Christophe Dujardin
- Université Claude Bernard Lyon 1, Institut Lumière-Matière UMR5306 CNRS, F-69622 Villeurbanne, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Julien Houel
- Université Claude Bernard Lyon 1, Institut Lumière-Matière UMR5306 CNRS, F-69622 Villeurbanne, France
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Zang Z, Xiao D, Wang Q, Jiao Z, Chen Y, Li DDU. Compact and robust deep learning architecture for fluorescence lifetime imaging and FPGA implementation. Methods Appl Fluoresc 2023; 11. [PMID: 36863024 DOI: 10.1088/2050-6120/acc0d9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/01/2023] [Indexed: 03/04/2023]
Abstract
This paper reports a bespoke adder-based deep learning network for time-domain fluorescence lifetime imaging (FLIM). By leveraging thel1-norm extraction method, we propose a 1D Fluorescence Lifetime AdderNet (FLAN) without multiplication-based convolutions to reduce the computational complexity. Further, we compressed fluorescence decays in temporal dimension using a log-scale merging technique to discard redundant temporal information derived as log-scaling FLAN (FLAN+LS). FLAN+LS achieves 0.11 and 0.23 compression ratios compared with FLAN and a conventional 1D convolutional neural network (1D CNN) while maintaining high accuracy in retrieving lifetimes. We extensively evaluated FLAN and FLAN+LS using synthetic and real data. A traditional fitting method and other non-fitting, high-accuracy algorithms were compared with our networks for synthetic data. Our networks attained a minor reconstruction error in different photon-count scenarios. For real data, we used fluorescent beads' data acquired by a confocal microscope to validate the effectiveness of real fluorophores, and our networks can differentiate beads with different lifetimes. Additionally, we implemented the network architecture on a field-programmable gate array (FPGA) with a post-quantization technique to shorten the bit-width, thereby improving computing efficiency. FLAN+LS on hardware achieves the highest computing efficiency compared to 1D CNN and FLAN. We also discussed the applicability of our network and hardware architecture for other time-resolved biomedical applications using photon-efficient, time-resolved sensors.
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Affiliation(s)
- Zhenya Zang
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Dong Xiao
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Quan Wang
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Ziao Jiao
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
| | - Yu Chen
- Department of Physics, University of Strathclyde, Glasgow G4 0NG, United Kingdom
| | - David Day Uei Li
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1XQ, United Kingdom
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Gao S, Li M, Smith JT, Intes X. Design and characterization of a time-domain optical tomography platform for mesoscopic lifetime imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:4637-4651. [PMID: 36187247 PMCID: PMC9484415 DOI: 10.1364/boe.460216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/17/2022] [Accepted: 07/12/2022] [Indexed: 06/16/2023]
Abstract
We report on the system design and instrumental characteristics of a novel time-domain mesoscopic fluorescence molecular tomography (TD-MFMT) system for multiplexed molecular imaging in turbid media. The system is equipped with a supercontinuum pulsed laser for broad spectral excitation, based on a high-density descanned raster scanning intensity-based acquisition for 2D and 3D imaging and augmented with a high-dynamical range linear time-resolved single-photon avalanche diode (SPAD) array for lifetime quantification. We report on the system's spatio-temporal and spectral characteristics and its sensitivity and specificity in controlled experimental settings. Also, a phantom study is undertaken to test the performance of the system to image deeply-seated fluorescence inclusions in tissue-like media. In addition, ex vivo tumor xenograft imaging is performed to validate the system's applicability to the biological sample. The characterization results manifest the capability to sense small fluorescence concentrations (on the order of nanomolar) while quantifying fluorescence lifetimes and lifetime-based parameters at high resolution. The phantom results demonstrate the system's potential to perform 3D multiplexed imaging thanks to spectral and lifetime contrast in the mesoscopic range (at millimeters depth). The ex vivo imaging exhibits the prospect of TD-MFMT to resolve intra-tumoral heterogeneity in a depth-dependent manner.
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Affiliation(s)
- Shan Gao
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Mengzhou Li
- Biomedical Engineering Department, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jason T. Smith
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xavier Intes
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Controlled Synthesis of Luminescent Xanthene Dyes and Use of Ionic Liquid in Thermochromic Reaction. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103092. [PMID: 35630571 PMCID: PMC9143205 DOI: 10.3390/molecules27103092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/12/2023]
Abstract
In this study, we demonstrate six novel xanthene derivatives and their spectroscopic and chemical properties. The presented synthesis examination allowed us to obtain two different compounds during one step, with open and closed lactone rings substituted with different length alkyl chains. Increasing the reaction efficiency to 77% was obtained using the microwave-assisted method. Moreover, the modification of O-alkylation synthesis in an ecofriendly way using a ball mill led to achieving exclusively one opened ring product. All of the synthesized compounds showed different spectroscopic behaviors in comparison with the different organic dyes; the typical concentration quenching of luminescence was not observed. The relationship between the length of the alkyl chain and the time of luminescence decay is presented. Synthetized closed forms of dyes turned out to be promising leuco dyes. For the first time, an ionic liquid was used as a developer of synthesized xanthene derivatives (as leuco dyes), which led to obtaining an irreversible thermochromic marker.
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Smith JT, Rudkouskaya A, Gao S, Gupta JM, Ulku A, Bruschini C, Charbon E, Weiss S, Barroso M, Intes X, Michalet X. In vitro and in vivo NIR fluorescence lifetime imaging with a time-gated SPAD camera. OPTICA 2022; 9:532-544. [PMID: 35968259 PMCID: PMC9368735 DOI: 10.1364/optica.454790] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/27/2022] [Indexed: 05/20/2023]
Abstract
Near-infrared (NIR) fluorescence lifetime imaging (FLI) provides a unique contrast mechanism to monitor biological parameters and molecular events in vivo. Single-photon avalanche diode (SPAD) cameras have been recently demonstrated in FLI microscopy (FLIM) applications, but their suitability for in vivo macroscopic FLI (MFLI) in deep tissues remains to be demonstrated. Herein, we report in vivo NIR MFLI measurement with SwissSPAD2, a large time-gated SPAD camera. We first benchmark its performance in well-controlled in vitro experiments, ranging from monitoring environmental effects on fluorescence lifetime, to quantifying Förster resonant energy transfer (FRET) between dyes. Next, we use it for in vivo studies of target-drug engagement in live and intact tumor xenografts using FRET. Information obtained with SwissSPAD2 was successfully compared to that obtained with a gated intensified charge-coupled device (ICCD) camera, using two different approaches. Our results demonstrate that SPAD cameras offer a powerful technology for in vivo preclinical applications in the NIR window.
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Affiliation(s)
- Jason T. Smith
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York 12208, USA
| | - Shan Gao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Juhi M. Gupta
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Arin Ulku
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Claudio Bruschini
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Edoardo Charbon
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York 12208, USA
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
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Thiele JC, Nevskyi O, Helmerich DA, Sauer M, Enderlein J. Advanced Data Analysis for Fluorescence-Lifetime Single-Molecule Localization Microscopy. FRONTIERS IN BIOINFORMATICS 2021; 1:740281. [PMID: 36303750 PMCID: PMC9581058 DOI: 10.3389/fbinf.2021.740281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence-lifetime single molecule localization microscopy (FL-SMLM) adds the lifetime dimension to the spatial super-resolution provided by SMLM. Independent of intensity and spectrum, this lifetime information can be used, for example, to quantify the energy transfer efficiency in Förster Resonance Energy Transfer (FRET) imaging, to probe the local environment with dyes that change their lifetime in an environment-sensitive manner, or to achieve image multiplexing by using dyes with different lifetimes. We present a thorough theoretical analysis of fluorescence-lifetime determination in the context of FL-SMLM and compare different lifetime-fitting approaches. In particular, we investigate the impact of background and noise, and give clear guidelines for procedures that are optimized for FL-SMLM. We do also present and discuss our public-domain software package “Fluorescence-Lifetime TrackNTrace,” which converts recorded fluorescence microscopy movies into super-resolved FL-SMLM images.
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Affiliation(s)
- Jan Christoph Thiele
- Third Institute of Physics—Biophysics, Georg August University, Göttingen, Germany
- *Correspondence: Jan Christoph Thiele, ; Jörg Enderlein,
| | - Oleksii Nevskyi
- Third Institute of Physics—Biophysics, Georg August University, Göttingen, Germany
| | - Dominic A. Helmerich
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Jörg Enderlein
- Third Institute of Physics—Biophysics, Georg August University, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Georg August University, Göttingen, Germany
- *Correspondence: Jan Christoph Thiele, ; Jörg Enderlein,
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