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  1. Article ; Online: High-density volumetric super-resolution microscopy.

    Daly, Sam / Ferreira Fernandes, João / Bruggeman, Ezra / Handa, Anoushka / Peters, Ruby / Benaissa, Sarah / Zhang, Boya / Beckwith, Joseph S / Sanders, Edward W / Sims, Ruth R / Klenerman, David / Davis, Simon J / O'Holleran, Kevin / Lee, Steven F

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1940

    Abstract: Volumetric super-resolution microscopy typically encodes the 3D position of single-molecule fluorescence into a 2D image by changing the shape of the point spread function (PSF) as a function of depth. However, the resulting large and complex PSF spatial ...

    Abstract Volumetric super-resolution microscopy typically encodes the 3D position of single-molecule fluorescence into a 2D image by changing the shape of the point spread function (PSF) as a function of depth. However, the resulting large and complex PSF spatial footprints reduce biological throughput and applicability by requiring lower labeling densities to avoid overlapping fluorescent signals. We quantitatively compare the density dependence of single-molecule light field microscopy (SMLFM) to other 3D PSFs (astigmatism, double helix and tetrapod) showing that SMLFM enables an order-of-magnitude speed improvement compared to the double helix PSF by resolving overlapping emitters through parallax. We demonstrate this optical robustness experimentally with high accuracy ( > 99.2 ± 0.1%, 0.1 locs μm
    MeSH term(s) Microscopy/methods ; Imaging, Three-Dimensional/methods ; Single Molecule Imaging/methods ; Nanotechnology
    Language English
    Publishing date 2024-03-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45828-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Comparative Study of High-Contrast Fluorescence Lifetime Probes for Imaging Amyloid in Tissue.

    Gorka, Felix / Daly, Sam / Pearson, Colin M / Bulovaite, Edita / Zhang, Yu P / Handa, Anoushka / Grant, Seth G N / Snaddon, Thomas N / Needham, Lisa-Maria / Lee, Steven F

    The journal of physical chemistry. B

    2021  Volume 125, Issue 50, Page(s) 13710–13717

    Abstract: Optical imaging of protein aggregates in living and post-mortem tissue can often be impeded by unwanted fluorescence, prompting the need for novel methods to extract meaningful signal in complex biological environments. Historically, benzothiazolium ... ...

    Abstract Optical imaging of protein aggregates in living and post-mortem tissue can often be impeded by unwanted fluorescence, prompting the need for novel methods to extract meaningful signal in complex biological environments. Historically, benzothiazolium derivatives, prominently Thioflavin T, have been the state-of-the-art fluorescent probes for amyloid aggregates, but their optical, structural, and binding properties typically limit them to
    MeSH term(s) Amyloid ; Amyloid beta-Peptides ; Amyloidogenic Proteins ; Benzothiazoles ; Fluorescent Dyes ; Optical Imaging ; Spectrometry, Fluorescence ; alpha-Synuclein
    Chemical Substances Amyloid ; Amyloid beta-Peptides ; Amyloidogenic Proteins ; Benzothiazoles ; Fluorescent Dyes ; alpha-Synuclein
    Language English
    Publishing date 2021-12-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.1c07762
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: A Comparative Study of High-Contrast Fluorescence Lifetime Probes for Imaging Amyloid in Tissue

    Gorka, Felix / Daly, Sam / Pearson, Colin M. / Bulovaite, Edita / Zhang, Yu P. / Handa, Anoushka / Grant, Seth G. N. / Snaddon, Thomas N. / Needham, Lisa-Maria / Lee, Steven F.

    Journal of physical chemistry. 2021 Dec. 09, v. 125, no. 50

    2021  

    Abstract: Optical imaging of protein aggregates in living and post-mortem tissue can often be impeded by unwanted fluorescence, prompting the need for novel methods to extract meaningful signal in complex biological environments. Historically, benzothiazolium ... ...

    Abstract Optical imaging of protein aggregates in living and post-mortem tissue can often be impeded by unwanted fluorescence, prompting the need for novel methods to extract meaningful signal in complex biological environments. Historically, benzothiazolium derivatives, prominently Thioflavin T, have been the state-of-the-art fluorescent probes for amyloid aggregates, but their optical, structural, and binding properties typically limit them to in vitro applications. This study compares the use of novel uncharged derivative, PAP_1, with parent Thioflavin T as a fluorescence lifetime imaging probe. This is applied specifically to imaging recombinant α-synuclein aggregates doped into brain tissue. Despite the 100-fold lower brightness of PAP_1 compared to that of Thioflavin T, PAP_1 binds to α-synuclein aggregates with an affinity several orders of magnitude greater than Thioflavin T; thus, we observe a specific decrease in the fluorescence lifetime of PAP_1 bound to α-synuclein aggregates, resulting in a separation of >1.4 standard deviations between PAP_1-stained brain tissue background and α-synuclein aggregates that is not observed with Thioflavin T. This enables contrast between highly fluorescent background tissue and amyloid fibrils that is attributed to the greater affinity of PAP_1 for α-synuclein aggregates, avoiding the substantial off-target staining observed with Thioflavin T.
    Keywords amyloid ; brain ; comparative study ; fluorescence ; physical chemistry
    Language English
    Dates of publication 2021-1209
    Size p. 13710-13717.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.1c07762
    Database NAL-Catalogue (AGRICOLA)

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  4. Book ; Online: 3DMaterialGAN

    Jangid, Devendra K. / Brodnik, Neal R. / Khan, Amil / Echlin, McLean P. / Pollock, Tresa M. / Daly, Sam / Manjunath, B. S.

    Learning 3D Shape Representation from Latent Space for Materials Science Applications

    2020  

    Abstract: In the field of computer vision, unsupervised learning for 2D object generation has advanced rapidly in the past few years. However, 3D object generation has not garnered the same attention or success as its predecessor. To facilitate novel progress at ... ...

    Abstract In the field of computer vision, unsupervised learning for 2D object generation has advanced rapidly in the past few years. However, 3D object generation has not garnered the same attention or success as its predecessor. To facilitate novel progress at the intersection of computer vision and materials science, we propose a 3DMaterialGAN network that is capable of recognizing and synthesizing individual grains whose morphology conforms to a given 3D polycrystalline material microstructure. This Generative Adversarial Network (GAN) architecture yields complex 3D objects from probabilistic latent space vectors with no additional information from 2D rendered images. We show that this method performs comparably or better than state-of-the-art on benchmark annotated 3D datasets, while also being able to distinguish and generate objects that are not easily annotated, such as grain morphologies. The value of our algorithm is demonstrated with analysis on experimental real-world data, namely generating 3D grain structures found in a commercially relevant wrought titanium alloy, which were validated through statistical shape comparison. This framework lays the foundation for the recognition and synthesis of polycrystalline material microstructures, which are used in additive manufacturing, aerospace, and structural design applications.
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Image and Video Processing
    Subject code 004
    Publishing date 2020-07-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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