Relevant bibliographies by topics / Multiplexed fluorescence imaging

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Multiplexed fluorescence imaging'

Author: Grafiati
Published: 29 April 2023

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Journal articles on the topic "Multiplexed fluorescence imaging"

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Cappella, Paolo, and Fabio Gasparri. "Highly Multiplexed Phenotypic Imaging for Cell Proliferation Studies." Journal of Biomolecular Screening 19, no. 1 (July 29, 2013): 145–57. http://dx.doi.org/10.1177/1087057113495712.

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The application of multiplexed imaging technologies in phenotypic drug discovery (PDD) enables profiling of complex cellular perturbations in response to drug treatment. High-content analysis (HCA) is among the most pursued approaches in PDD, with a proven capability to identify compounds with a given cellular mechanism of action (MOA), as well as to unveil unexpected drug cellular activities. The ability of fluorescent image-based cytometric techniques to dissect the phenotypic heterogeneity of cell populations depends on the degree of multiplexing achievable. At present, most high-content assays employ up to four cellular markers separately detected in distinct fluorescence channels. We explored the possibility to increase HCA multiplexing through analysis of multiple proliferation markers in the same fluorescence channel by taking advantage of the different timing of antigen appearance during the cell cycle, or differential intracellular localization. Simultaneous analysis of DAPI staining and five immunofluorescence markers (BrdU incorporation, active caspase-3, phospho-histone H3, phospho-S6, and Ki-67) resulted in the first six-marker high-content assay readily applicable to compound MOA studies. This approach allows detection of rare cell subpopulations, unveiling a high degree of phenotypic heterogeneity in exponentially growing cell cultures and variability in the individual cell response to antiproliferative drugs.
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Liu, Hsiou-Yuan, Jingshan Zhong, and Laura Waller. "Multiplexed phase-space imaging for 3D fluorescence microscopy." Optics Express 25, no. 13 (June 21, 2017): 14986. http://dx.doi.org/10.1364/oe.25.014986.

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Luo, Teng, Ting Zhou, Yihua Zhao, Liwei Liu, and Junle Qu. "Multiplexed fluorescence lifetime imaging by concentration-dependent quenching." Journal of Materials Chemistry B 6, no. 13 (2018): 1912–19. http://dx.doi.org/10.1039/c8tb00095f.

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Ko, Jina, Juhyun Oh, Maaz S. Ahmed, Jonathan C. T. Carlson, and Ralph Weissleder. "Ultra‐fast Cycling for Multiplexed Cellular Fluorescence Imaging." Angewandte Chemie 132, no. 17 (April 20, 2020): 6906–13. http://dx.doi.org/10.1002/ange.201915153.

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Ko, Jina, Juhyun Oh, Maaz S. Ahmed, Jonathan C. T. Carlson, and Ralph Weissleder. "Ultra‐fast Cycling for Multiplexed Cellular Fluorescence Imaging." Angewandte Chemie International Edition 59, no. 17 (March 6, 2020): 6839–46. http://dx.doi.org/10.1002/anie.201915153.

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Gamber, Kevin, Arne Christians, Spencer Schwarz, Adam Northcutt, Jason Forys, Thomas Campbell, and Crystal Winkeler. "Quantitative Immune Profiling of Human Tumor Tissues with Multiplexed ChipCytometry." Journal of Immunology 206, no. 1_Supplement (May 1, 2021): 68.05. http://dx.doi.org/10.4049/jimmunol.206.supp.68.05.

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Abstract Cancer therapies that rely on manipulating or engineering immune cells have shown much promise in recent years for effectively combating a broad array of cancer types. In order to determine the effectiveness of such therapies, it is necessary to accurately profile the complement of immune cell types present in the tumor microenvironment. Methods to reliably obtain immune cell signatures require the combination of powerful resolution to discriminate cell boundaries, broad dynamic range to capture markers of varying expression levels, and accurate cell segmentation across a wide range of cell sizes and morphologies. Many methods for quantitative immune cell profiling have demonstrated shortcomings when it comes to the aforementioned attributes. To remedy these shortcomings, we present here ChipCytometry, an imaging technology for immune profiling of cells and sectioned tissues. ChipCytometry is a fluorescence-based imaging system that utilizes multiplexed immuno-fluorescence staining in combination with high-dynamic-range (HDR) imaging to facilitate quantitative phenotyping of individual cells within tissue samples. Employing this technology to profile metastatic and primary tumors, multiple biomarkers were stained in iterative multiplex assays to profile single cells with an AI-powered cell segmentation algorithm. The HDR imaging allows for both strong and weak fluorescent signals to be simultaneously obtained without loss of sensitivity. This immune profiling was completed on 6 different cryosectioned human tumor tissues (head & neck, liver, lung, breast, colon, and pancreas).
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Mizuno, T., E. Hase, T. Minamikawa, Y. Tokizane, R. Oe, H. Koresawa, H. Yamamoto, and T. Yasui. "Full-field fluorescence lifetime dual-comb microscopy using spectral mapping and frequency multiplexing of dual-comb optical beats." Science Advances 7, no. 1 (January 2021): eabd2102. http://dx.doi.org/10.1126/sciadv.abd2102.

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Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool for quantitative fluorescence imaging because fluorescence lifetime is independent of concentration of fluorescent molecules or excitation/detection efficiency and is robust to photobleaching. However, since most FLIMs are based on point-to-point measurements, mechanical scanning of a focal spot is needed for forming an image, which hampers rapid imaging. Here, we demonstrate scan-less full-field FLIM based on a one-to-one correspondence between two-dimensional (2D) image pixels and frequency-multiplexed radio frequency (RF) signals. A vast number of dual-comb optical beats between dual optical frequency combs are effectively adopted for 2D spectral mapping and high-density frequency multiplexing in the RF region. Bimodal images of fluorescence amplitude and lifetime are obtained with high quantitativeness from amplitude and phase spectra of fluorescence RF comb modes without the need for mechanical scanning. The parallelized FLIM will be useful for rapid quantitative fluorescence imaging in life science.
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Xu, Jian, Tianyue Zhang, Shenyu Yang, Ziwei Feng, Haoying Li, Dejiao Hu, Fei Qin, et al. "Plasmonic Nanoprobes for Multiplexed Fluorescence-Free Super-Resolution Imaging." Advanced Optical Materials 6, no. 20 (August 5, 2018): 1800432. http://dx.doi.org/10.1002/adom.201800432.

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Lv, Yanlu, Jiulou Zhang, Dong Zhang, Wenjuan Cai, Nanguang Chen, and Jianwen Luo. "In vivosimultaneous multispectral fluorescence imaging with spectral multiplexed volume holographic imaging system." Journal of Biomedical Optics 21, no. 6 (June 3, 2016): 060502. http://dx.doi.org/10.1117/1.jbo.21.6.060502.

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Keshri, Puspam, Bin Zhao, Tianfa Xie, Yousef Bagheri, James Chambers, Yubing Sun, and Mingxu You. "Quantitative and Multiplexed Fluorescence Lifetime Imaging of Intercellular Tensile Forces." Angewandte Chemie 133, no. 28 (June 10, 2021): 15676–83. http://dx.doi.org/10.1002/ange.202103986.

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Dissertations / Theses on the topic "Multiplexed fluorescence imaging"

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Chouket, Raja. "New dimensions for multiplexed fluorescence imaging." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS606.

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Notre groupe de recherche avait déjà mis au point les protocoles OPIOM pour l’imagerie par fluorescence. En exploitant les sections efficaces de photoswiching de fluorescence, OPIOM permet d’extraire sélectivement la réponse des fluorophores réversiblement photoswitchables (RSFs) en présence de fluorophores interférant spectralement. Cependant, OPIOM nous a permis de ne distinguer que 3 RSFPs spectralement similaires. L’objectif de cette thèse était d’augmenter ce nombre. Pour atteindre cet objectif, un nouvel instrument automatisé appelée photoswichomètre a été mis au point pour cribler la signature photochimique de 22 RSFP en analysant leur réponse de fluorescence aux sauts de lumière dont l’intensité couvre 5 ordres de grandeur. Cette signature a d’abord été exploitée dans un nouveau protocole d’imagerie par fluorescence appelé HIGHLIGHT, qui a capitalisé sur OPIOM et amélioré encore sa sélectivité. Dans HIGHLIGHT, les RSFs sont soumis à une modulation harmonique de la lumière et leur contribution aux signaux d’émission de fluorescence globale est sélectivement récupérée en exploitant leur réponse non linéaire singulière dans des conditions optimisées. HIGHLIGHLIGHT a été implémenté pour l’imagerie des RSFPs dans les cellules sans interférence d’autofluorescence, pour réaliser l’imagerie multiplexée de 3 RSFPs qui ne pouvaient pas être discriminés avec OPIOM, aussi pour améliorer l’effet de sectionnement optique. La signature des RSF a ensuite été utilisée dans un deuxième protocole d’imagerie par fluorescence appelé LIGHTNING. Contrairement à OPIOM et HIGHLIGHT qui exploitent les sections efficaces de la photoswitching en régime permanent de faible intensité lumineuse, LIGHTNING exploite le régime transitoire des RSFs sous de multiples illuminations impliquant diverses gammes d’intensités lumineuses pour la discrimination RSF. Ainsi, LIGHTNING nous a permis d’améliorer le degré de multiplexage du contraste dynamique en imagerie de fluorescence jusqu’à 20 RSFP sur 22 RSFP étudiés
Our research group had previously developed the OPIOM protocols for fluorescence imaging. By exploiting their cross sections of fluorescence photoswiching, OPIOM can selectively extract the response of reversibly photoswitchable fluorophores (RSFs) in the presence of spectrally interfering fluorophores. However, OPIOM allowed us to discriminate only 3 spectrally similar reversibly photoswitchable fluorescent proteins (RSFPs). The goal of this PhD was to augment this number. To reach this goal, a new automated instrumental setup called photoswichometer was first developed to express and screen the rich photochemical signature of 22 RSFPs by analyzing their fluorescence response to light jumps with intensities covering 5 orders of magnitude. This signature has been first exploited in a new fluorescence imaging protocol called HIGHLIGHT, which capitalized on OPIOM and further improved its selectivity. In HIGHLIGHT, the RSFs are submitted to harmonic light modulation and their contribution to the overall fluorescence emission signals is selectively retrieved from exploiting their singular non-linear response under optimized conditions. HIGHLIGHT has been implemented to image RSFPs in cells without interference of autofluorescence, to perform multiplexed imaging of 3 RSFPs which could not be discriminated with OPIOM, and used for its intrinsic optical sectioning. The RSF signature has been then used in a second fluorescence imaging protocol called LIGHTNING. In contrast to OPIOM and HIGHLIGHT which exploit the cross sections of fluorescence photoswitching in a steady-state regime of low light intensity, LIGHTNING exploits the transient time fluorescence response of RSFs under multiple illuminations involving various ranges of light intensities for RSF discrimination. Thus, LIGHTNING allowed us to improve the multiplexing degree of dynamic contrast in fluorescence imaging up to 20 RSFP among 22 studied RSFPs
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Behrooz, Ali. "Multiplexed fluorescence diffuse optical tomography." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/50401.

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Fluorescence tomography (FT) is an emerging non-invasive in vivo molecular imaging modality that aims at quantification and three-dimensional (3D) localization of fluorescent tagged inclusions, such as cancer lesions and drug molecules, buried deep in human and animal subjects. Depth-resolved 3D reconstruction of fluorescent inclusions distributed over the volume of optically turbid biological tissue using the diffuse fluorescent photons detected on the skin poses a highly ill-conditioned problem, as depth information must be extracted from boundary data. Due to this ill-posed nature of FT reconstructions, noise and errors in the data can severely impair the accuracy of the 3D reconstructions. Consequently, improvements in the signal-to-noise ratio (SNR) of the data significantly enhance the quality of the FT reconstructions. Furthermore, enhancing the SNR of the FT data can greatly contribute to the speed of FT scans. The pivotal factor in the SNR of the FT data is the power of the radiation illuminating the subject and exciting the administered fluorescent agents. In existing single-point illumination FT systems, the illumination power level is limited by the skin maximum radiation exposure levels. In this research, a multiplexed architecture governed by the Hadamard transform was conceptualized, developed, and experimentally implemented for orders-of-magnitude enhancement of the SNR and the robustness of FT reconstructions. The multiplexed FT system allows for Hadamard-coded multi-point illumination of the subject while maintaining the maximal information content of the FT data. The significant improvements offered by the multiplexed FT system were validated by numerical and experimental studies carried out using a custom-built multiplexed FT system developed exclusively in this work. The studies indicate that Hadamard multiplexing offers significantly enhanced robustness in reconstructing deep fluorescent inclusions from low-SNR FT data.
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Luthman, Anna Siri Naemi. "Spectrally resolved detector arrays for multiplexed biomedical fluorescence imaging." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274904.

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The ability to resolve multiple fluorescent emissions from different biological targets in video rate applications, such as endoscopy and intraoperative imaging, has traditionally been limited by the use of filter-based imaging systems. Hyper and multispectral imaging facilitate the detection of both spatial and spectral information in a single data acquisition, however, instrumentation for spatiospectral data acquisition is typically complex, bulky and expensive. This thesis seeks to overcome these limitations by using recently commercialised compact and robust hyper/multispectral cameras based on spectrally resolved detector arrays. Following sensor calibrations, which devoted particular attention to the angular sensitivity of the sensors, we integrated spectrally resolved detector arrays into a wide-field and an endoscopic imaging platform. This allowed multiplexed reflectance and fluorescence imaging with spectrally resolved detector array technology in vitro, in tissue mimicking phantoms, in an ex vivo oesophageal model and in vivo in a mouse model. A hyperspectral linescan sensor was first integrated in a wide-field near-infrared reflectance based imaging set-up to assess the suitability of spectrally resolved detector arrays for in vivo imaging of exogenous fluorescent contrast agents. Using this fluorescence hyperspectral imaging system, we could accurately resolve the presence and concentration of seven fluorescent dyes in solution. We also demonstrated high spectral unmixing precision, signal linearity with dye concentration, at depth in tissue mimicking phantoms, and delineation of four fluorescent dyes in vivo. After the successful demonstration of multiplexed fluorescence imaging in a wide-field set-up, we proceeded to combine near-infrared multiplexed fluorescence imaging with visible light spectral reflectance imaging in an endoscopic set-up. A multispectral endoscopic imaging system, capable of simultaneous reflectance and fluorescence imaging, was developed around two snapshot spectrally resolved detector arrays. In the process of system integration and characterisation, methods to characterise and predict the imaging performance of spectral endoscopes were developed. With the endoscope we demonstrated simultaneous imaging and spectral unmixing of chemically oxy/deoxygenated blood and three fluorescent dyes in a tissue mimicking phantom, and of two fluorescent dyes in an ex vivo oesophageal porcine model. With further developments, this technology has the potential to become applicable in medical imaging for detection of diseases such as gastrointestinal cancers.
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Warren, Sean. "Development and application of multiplexed fluorescence imaging to chemotaxis signalling pathways." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/25117.

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This thesis discusses the development of time resolved fluorescence imaging techniques and their use in the study of cellular signalling pathways, in particular the ability to perform multiplexed imaging of a number of pathways in live cells. These techniques are applied to investigate chemotaxis, the ability of cells to migrate directionally in response to a chemoattractant gradient, which requires precise spatiotemporal coordination of signalling events. Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) biosensors to map protein-protein interactions in live cells. The development of a software tool for the global analysis of large FLIM datasets is presented which allows simultaneous analysis of hundreds of FLIM images in minutes and the use of complex models, for example a four-exponential model of an ECFP FRET system, with relatively low photon-count data. Live cell imaging with optimised FRET biosensors is used to investigate the role of Phospholipase C epsilon (PLCε) in fibroblast chemotaxis. It is demonstrated that PLCε-null fibroblasts show a compromised chemotactic response to platelet derived growth factor and spatial defects in Rac1 activation and phosphoinositide signalling. The ability to image multiple functional reporters simultaneously in a single cell is desirable when investigating complex signalling networks with significant cross-talk such as chemotaxis. A number of approaches for multiplexed measurements are investigated, in particular using homo-FRET between two spectrally identical fluorophores, which presents a promising approach to reduce the spectral bandwidth compared to conventional hetero-FRET biosensors. The optimisation and automation of a to perform multiplexed time-resolved fluorescence anisotropy imaging of homo-FRET biosensors is discussed. The development and multiplexed imaging of homo-FRET reporters for phosphoinositide signalling using a polarisation resolved confocal time correlated single photon counting (TCSPC) microscope is presented. Potential approaches for multiplexed imaging three functional reporters are discussed.
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Watabe, Tetsuya. "Booster, a Red－Shifted Genetically Encoded Förster Resonance Energy Transfer (FRET) Biosensor Compatible with Cyan Fluorescent Protein/Yellow Fluorescent Protein-Based FRET Biosensors and Blue Light-Responsive Optogenetic Tools." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263527.

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Wu, Juwell Wendy. "Near-infrared emitting quantum dots for cellular and vascular fluorescent labeling in in vivo multiplexed imaging studies." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/68460.

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Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 199-217).
In vivo multimodal, multiplexed microscopy allows real-time observation of hematopoietic cells, their stem and progenitor cells and metastatic cancer cells in their native bone marrow (BM) environment. Multiplexing has made possible detailed studies of the BM's microarchitecture, which helps define the niche of these cells; it has nonetheless been limited by the paucity of suitable probes fluorescent in the near-infrared spectrum that is favored by tissue optics. This project attempts to address this problem by developing cellular and vascular fluorescent imaging probes comprised of semiconductor nanocrystals, or quantum dots (QDs), with tunable fluorescence between 65o-8oonm and exhibiting photostability, robust quantum yield and narrow fluorescence profiles that are critical for such applications. The synthesis of alloyed CdTexSe1 x QDs will be detailed in the thesis. Reproducibility and workability in subsequent steps are emphasized in the methods. Special attention is also paid to the difference between working with alloyed versus single semiconductor QDs, especially the need to achieve physical and spectral uniformity when composition and its gradient are also variable. The steps for creating biological probes from these QD fluorophores are also described. They include overcoating, water solubilization and functionalization for cellular uptake and vascular retention. Finally, the thesis returns to its motivation and reports novel methods, developed using NIR QD vascular imaging probes, for visualizing in vivo 3-D imaging data of the murine BM and characterizing the tissue's architecture. Measuring the Euclidean distance between BM osteoblasts and blood vessels is presented to exemplify a potential platform for describing the geographic relationships between cells, molecules and structural components in any tissue.
by Juwell Wendy Wu.
Ph.D.
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Fries, Maximilian Werner. "Multiplexed biochemical imaging reveals the extent and complexity of non-genetic heterogeneity in DNA damage-induced caspase dynamics." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/273868.

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Genetically identical cells show a heterogeneous response to a multitude of signals such as growth factors and DNA damage. While this heterogeneity has been shown to be a major determinant of treatment success in several diseases including cancer, little is known about how differences in biochemical signalling networks underlie such heterogeneity. State-of-the-art methodologies to study biochemical networks are often invasive and enable to quantify biochemical events only on cell populations or at a single point in time for a single cell, and therefore, cannot adequately quantify the fast, asynchronous and heterogeneous responses. In order to address these limitations, we have developed a unique sensing platform based on fluorescence lifetime imaging microscopy (FLIM) capable to multiplex at least three biosensors by utilizing Förster Resonance Energy Transfer (FRET) efficiently. After an overall introduction in Chapter 1, I describe the rational design and characterization of novel FRET pairs aiming to utilize the visible spectrum efficiently in combination with FLIM in Chapter 2. We combined blue, green and red donor fluorescent proteins that are excited at the same wavelength (840 nm for two-photon excitation) with genetically encoded quenchers, i.e. non-fluorescent chromoproteins as acceptors. This sensing platform enables the simultaneous detection of three biochemical reactions within single living cells providing new opportunities to characterize and understand non-genetic heterogeneity. In Chapter 3, I will demonstrate the first application of this novel platform by studying the activity of three key enzymes in DNA damage-induced cell death, caspase-2, -3, and -9. We confirm the heterogeneous nature of Cisplatin-induced cell death in genetically identical cells but reveal the existence of at least three subpopulations of cells characterized by distinct caspase dynamics. By combining biochemical and morphological information we infer the existence of different biochemical network topologies that are associated with alternative death phenotypes each cell adopts, such as apoptosis and programmed necrosis. Finally, deconvolution of cellular populations and direct measurement of a three-node caspase network - formerly impossible - permitted us to design perturbations of cell fate choices utilizing clinically relevant inhibitors. These perturbations resulted in changes in cell fate in response to Cisplatin, a clinically desirable outcome that suggests new avenues for combinatorial drugging and a new strategy to reveal cancer vulnerabilities that may be otherwise confounded by typical genetic and non-genetic heterogeneity.
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Deiss, Frédérique. "Développement de réseaux multiplexés de biocapteurs électrochimiques." Thesis, Bordeaux 1, 2009. http://www.theses.fr/2009BOR13883/document.

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Ce travail de thèse a porté sur le développement de réseaux de micro- et nanocapteurs opto-électrochimiques pour la bioanalyse. Ils répondent à la demande grandissante dans le domaine de la recherche et du diagnostic pour des outils permettant de réaliser de multiples analyses simultanément avec des échantillons de faibles volumes. Ces nouvelles biopuces de haute densité sont fabriquées à partir de faisceaux cohérents de fibres optiques. Une des deux faces est micro- ou nanostructurée par une attaque chimique, puis fonctionnalisée avec une sonde biologique. La première biopuce est un réseau de nanocapteurs fluorescents à ADN où les sondes ont été immobilisées grâce aux propriétés d’électropolymérisation du pyrrole. La lecture est réalisée à distance au travers du faisceau d’imagerie. En combinant la technique d’immobilisation avec des microleviers électrochimiques, plusieurs sondes différentes ont pu être adressées sur le même réseau nanostructuré. La seconde biopuce permet d’effectuer des immunodosages multiplexés en utilisant l’imagerie électrochimiluminescente résolue à l’échelle d’une microsphère. Le développement de cette technique permet de combiner les avantages de l’électrochimiluminescence avec des immunodosages multiplexés. L’élaboration de ces réseaux allie différentes techniques physico-chimiques, notamment électrochimiques, pour obtenir des biopuces avec un fort potentiel, grâce à une densité et un degré de multiplexage importants
This work presents the development of optoelectrochemical micro- and nanosensor arrays for bioanalytical applications. These platforms respond to the growing need in research and diagnostic for tools allowing multiple and simultaneous analysis in small-volume samples. These new high density biochips are made from coherent optical fiber bundles: one face is micro- or nanostructured by chemical etching and then functionnalized with biological probes. The first biochip is a fluorescent DNA nanosensor array where probes have been immobilized by electrodeposition of a polypyrrole thin film. The detection of the hybridization is remotely performed through the imaging fiber. Different probes were succesfully addressed onto the same nanostructured array thanks to electrochemical cantilevers. The second biochip allows multiplexed sandwich immunoassays using electrochimiluminescent imaging resolved at the single bead level. In particular, the development of this new readout mechanism allows extending electrochemiluminescent detection for multiplexed immunoassays. Design and implementations of both platforms take advantages of different physical and chemical techniques, especially electrochemical, to obtain biochips with a great potential through high density and high multiplexing level
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Ho, Derek. "CMOS Contact Imagers for Spectrally-multiplexed Fluorescence DNA Biosensing." Thesis, 2013. http://hdl.handle.net/1807/35849.

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Within the realm of biosensing, DNA analysis has become an indispensable research tool in medicine, enabling the investigation of relationships among genes, proteins, and drugs. Conventional DNA microarray technology uses multiple lasers and complex optics, resulting in expensive and bulky systems which are not suitable for point-of-care medical diagnostics. The immobilization of DNA probes across the microarray substrate also results in substantial spatial variation. To mitigate the above shortcomings, this thesis presents a set of techniques developed for the CMOS image sensor for point-of-care spectrally-multiplexed fluorescent DNA sensing and other fluorescence biosensing applications. First, a CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. The CPG exploits the absorption property of a polysilicon gate to form an optical filter, thus the sensor does not require an external color filter. A prototype has been fabricated in a standard 0.35μm digital CMOS technology and demonstrates intensity measurements of blue (450nm), green (520nm), and red (620nm) illumination. Second, a wide dynamic range CMOS multi-color image sensor is presented. An analysis is performed for the wide dynamic-range, asynchronous self-reset with residue readout architecture where photon shot noise is taken into consideration. A prototype was fabricated in a standard 0.35μm CMOS process and is validated in color light sensing. The readout circuit achieves a measured dynamic range of 82dB with a peak SNR of 46.2dB. Third, a low-power CMOS image sensor VLSI architecture for use with comparator based ADCs is presented. By eliminating the in-pixel source follower, power consumption is reduced, compared to the conventional active pixel sensor. A 64×64 prototype with a 10μm pixel pitch has been fabricated in a 0.35μm standard CMOS technology and validated experimentally. Fourth, a spectrally-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem has been quantitatively modeled and validated in the detection of marker gene sequences for spinal muscular atropy disease and the E. coli bacteria. Spectral multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limit of 240nM and 210nM of target concentration at a sample volume of 10μL for the green and red transduction channels, respectively.
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"Identifying and Characterizing Type 1 and Type 2 Eosinophil Subtypes." Doctoral diss., 2020. http://hdl.handle.net/2286/R.I.57159.

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abstract: Eosinophils are innate immune cells that are most commonly associated with parasite infection and allergic responses. Recent studies, though, have identified eosinophils as cells with diverse effector functions at baseline and in disease. Eosinophils in specific tissue immune environments are proposed to promote unique and specific effector functions, suggesting these cells have the capacity to differentiate into unique subtypes. The studies here focus on defining these subtypes using functional, molecular, and genetic analysis as well as using novel techniques to image these subtypes in situ. To characterized these subtypes, an in vitro cytokine induced type 1 (E1) and type 2 (E2) eosinophil model was developed that display features and functions of eosinophils found in vivo. For example, E1 eosinophils secrete type 1 mediators (e.g., IL-12, CXCL9 and CXCL10), express iNOS and express increased levels of the surface molecules PDL1 and MHC-I. Conversely, E2 eosinophils release type 2 mediators (e.g., IL4, IL13, CCL17, and CCL22), degranulate and express increased surface molecules CD11b, ST2 and Siglec-F. Completion of differential expression analysis of RNAseq on these subtypes revealed 500 and 655 unique genes were upregulated in E1 and E2 eosinophils, respectively. Functional enrichment studies showed interferon regulatory factor (IRF) transcription factors were uniquely regulated in both mouse and human E1 and E2 eosinophils. These subtypes are sensitive to their environment, modulating their IRF and cell surface expression when stimulated with opposing cytokines, suggesting plasticity. To identify and study these subtypes in situ, chromogenic and fluorescent eosinophil-specific immunostaining protocols were developed. Methods were created and optimized, here, to identify eosinophils by their granule proteins in formalin fixed mouse tissues. Yet, eosinophil-specific antibodies alone are not enough to identify and study the complex interactions eosinophil subtypes perform within a tissue. Therefore, as part of this thesis, a novel highly-multiplexed immunohistochemistry technique was developed utilizing cleavable linkers to address these concerns. This technique is capable of analyzing up to 22 markers within a single biopsy with single-cell resolution. With this approach, eosinophil subtypes can be studied in situ in routine patient biopsies.
Dissertation/Thesis
Doctoral Dissertation Biochemistry 2020
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Books on the topic "Multiplexed fluorescence imaging"

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Luthman, Anna Siri. Spectrally Resolved Detector Arrays for Multiplexed Biomedical Fluorescence Imaging. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-98255-7.

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Luthman, Anna Siri. Spectrally Resolved Detector Arrays for Multiplexed Biomedical Fluorescence Imaging. Springer, 2018.

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Luthman, Anna Siri. Spectrally Resolved Detector Arrays for Multiplexed Biomedical Fluorescence Imaging. Springer International Publishing AG, 2019.

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Book chapters on the topic "Multiplexed fluorescence imaging"

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Peng, Leilei. "Fourier Multiplexed Fluorescence Lifetime Imaging." In Methods in Molecular Biology, 157–72. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1593-5_11.

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Chouket, Raja, Ruikang Zhang, Agnès Pellissier-Tanon, Annie Lemarchand, Agathe Espagne, Thomas Le Saux, and Ludovic Jullien. "Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions." In Methods in Molecular Biology, 191–227. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1593-5_13.

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Chouket, Raja, Ruikang Zhang, Agnès Pellissier-Tanon, Annie Lemarchand, Agathe Espagne, Thomas Le Saux, and Ludovic Jullien. "Correction to: Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions." In Methods in Molecular Biology, C1. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1593-5_22.

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Jia, Yunlong, Françoise Bleicher, Jonathan Reboulet, and Samir Merabet. "Bimolecular Fluorescence Complementation (BiFC) and Multiplexed Imaging of Protein–Protein Interactions in Human Living Cells." In Methods in Molecular Biology, 173–90. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1593-5_12.

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Moffitt, J. R., and X. Zhuang. "RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)." In Visualizing RNA Dynamics in the Cell, 1–49. Elsevier, 2016. http://dx.doi.org/10.1016/bs.mie.2016.03.020.

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"Bio-Mediated Synthesis of Quantum Dots for Fluorescent Biosensing and Bio-Imaging Applications." In Materials Research Foundations, 185–223. Materials Research Forum LLC, 2021. http://dx.doi.org/10.21741/9781644901571-7.

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Quantum dots (QDs) have received great attention for development of novel fluorescent nanoprobe with tunable colors towards the near-infrared (NIR) region because of their unique optical and electronic properties such as luminescence characteristics, wide range, continuous absorption spectra and narrow emission spectra with high light stability. Quantum dots are promising materials for biosensing and single molecular bio-imaging application due to their excellent photophysical properties such as strong brightness and resistance to photobleaching. However, the use of quantum dots in biomedical applications is limited due to their toxicity. Recently, the development of novel and safe alternative method, the biomediated greener approach is one of the best aspects for synthesis of quantum dots. In this Chapter, biomediated synthesis of quantum dots by living organisms and biomimetic systems were highlighted. Quantum dots based fluorescent probes utilizing resonance energy transfer (RET), especially Förster resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET) and chemiluminescence resonance energy transfer (CRET) to probe biological phenomena were discussed. In addition, quantum dot nanocomposites are promising ultrasensitive bioimaging probe for in vivo multicolor, multimodal, multiplex and NIR deep tissue imaging. Finally, this chapter provides a conclusion with future perspectives of this field.
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Conference papers on the topic "Multiplexed fluorescence imaging"

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Le, Vu Nam, Huai Dong Yang, Xin Rong Zhang, Guo Fan Jin, and Si Chun Zhang. "Frequency division multiplexed multi-color fluorescence microscope system." In Space Optics and Earth Imaging and Space Navigation, edited by Carl Nardell, Suijian Xue, and Huaidong Yang. SPIE, 2017. http://dx.doi.org/10.1117/12.2307240.

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Jo, YoungJu, Hyungjoo Cho, Wei Sun Park, Geon Kim, DongHun Ryu, Young Seo Kim, Moosung Lee, et al. "Label-free multiplexed microtomography of endogenous subcellular dynamics using generalizable deep learning." In CLEO: Applications and Technology. Washington, D.C.: Optica Publishing Group, 2022. http://dx.doi.org/10.1364/cleo_at.2022.ath2i.6.

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We report a deep-learning-based imaging technique to predict 3D multiplexed fluorescence signals based on label-free refractive index measurements. We demonstrate the retrieval of specific subcellular information without exogenous labeling or staining, enabling multiplexed molecular imaging across various spatiotemporal scales.
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Cheng, Shiyi, Sipei Fu, Yumi Mun Kim, Ji Yi, and Lei Tian. "Multiplexed virtual fluorescence labeling from multi-contrast microscopy by deep learning." In High-Speed Biomedical Imaging and Spectroscopy VI, edited by Keisuke Goda and Kevin K. Tsia. SPIE, 2021. http://dx.doi.org/10.1117/12.2578439.

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Rudkouskaya, A., S. Chen, N. Sinsuebphon, J. E. Mazurkiewicz, M. Ochoa, X. Intes, and M. Barroso. "Multiplexed Fluorescence Lifetime in vivo FRET Imaging using a Dark Quencher." In Optical Molecular Probes, Imaging and Drug Delivery. Washington, D.C.: OSA, 2019. http://dx.doi.org/10.1364/omp.2019.ow5d.4.

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Chen, Kun, Rui Yan, Limin Xiang, and Ke Xu. "Excitation spectral microscopy for highly multiplexed fluorescence imaging and quantitative biosensing." In High-Speed Biomedical Imaging and Spectroscopy VII, edited by Keisuke Goda and Kevin K. Tsia. SPIE, 2022. http://dx.doi.org/10.1117/12.2612265.

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Lv, Yanlu, Chuangjian Cai, Jing Bai, and Jianwen Luo. "Compact multispectral fluorescence imaging system with spectral multiplexed volume holographic grating." In SPIE BioPhotonics Australasia, edited by Mark R. Hutchinson and Ewa M. Goldys. SPIE, 2016. http://dx.doi.org/10.1117/12.2239925.

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Pera, Vivian, Dana H. Brooks, and Mark Niedre. "A sparse nonnegative demixing algorithm with intrinsic regularization for multiplexed fluorescence tomography." In 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI 2015). IEEE, 2015. http://dx.doi.org/10.1109/isbi.2015.7164050.

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Chan, Antony C. S., Edmund Y. Lam, and Kevin K. Tsia. "Signal reduction in fluorescence imaging using radio frequency-multiplexed excitation by compressed sensing." In SPIE/COS Photonics Asia, edited by Bahram Jalali, Ming Li, Keisuke Goda, and Mohammad H. Asghari. SPIE, 2014. http://dx.doi.org/10.1117/12.2072016.

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Jiang, Yang, David Cooper, Matthew D. Carson, and Eric J. Seibel. "Custom bile duct phantom for first-in-human multiplexed NIR fluorescence peptide imaging." In Design and Quality for Biomedical Technologies XII, edited by Rongguang Liang, T. Joshua Pfefer, and Jeeseong Hwang. SPIE, 2019. http://dx.doi.org/10.1117/12.2509893.

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Zhang, Ruikang, Raja Chouket, Jérome Quérard, Marie-Aude Plamont, Zsolt Kelemen, Agathe Espagne, Alison G. Tebo, et al. "Out-of-Phase Imaging after Optical Modulation for Micro-and Macro-scale Multiplexed Fluorescence Imaging Against Autofluorescence and Ambient Light." In Novel Techniques in Microscopy. Washington, D.C.: OSA, 2019. http://dx.doi.org/10.1364/ntm.2019.ns2b.4.

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