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  1. Article ; Online: Experimental imaging and Monte Carlo modeling of ultrafast pulse propagation in thin scattering slabs.

    Pattelli, Lorenzo / Mazzamuto, Giacomo

    Journal of biomedical optics

    2022  Volume 27, Issue 8

    Abstract: Significance: Most radiative transport problems in turbid media are typically associated with mm or cm scales, leading to typical time scales in the range of hundreds of ps or more. In certain cases, however, much thinner layers can also be relevant, ... ...

    Abstract Significance: Most radiative transport problems in turbid media are typically associated with mm or cm scales, leading to typical time scales in the range of hundreds of ps or more. In certain cases, however, much thinner layers can also be relevant, which can dramatically alter the overall transport properties of a scattering medium. Studying scattering in these thin layers requires ultrafast detection techniques and adaptations to the common Monte Carlo (MC) approach.
    Aim: We aim to discuss a few relevant aspects for the simulation of light transport in thin scattering membranes, and compare the obtained numerical results with experimental measurements based on an all-optical gating technique.
    Approach: A thin membrane with controlled scattering properties based on polymer-dispersed TiO2 nanoparticles is fabricated for experimental validation. Transmittance measurements are compared against a custom open-source MC implementation including specific pulse profiles for tightly focused femtosecond laser pulses.
    Results: Experimental transmittance data of ultrafast pulses through a thin scattering sample are compared with MC simulations in the spatiotemporal domain to retrieve its scattering properties. The results show good agreement also at short distances and time scales.
    Conclusions: When simulating light transport in scattering membranes with thicknesses in the orders of tens of micrometer, care has to be taken when describing the temporal, spatial, and divergence profiles of the source term, as well as the possible truncation of step length distributions, which could be introduced by simple strategies for the generation of random exponentially distributed variables.
    MeSH term(s) Computer Simulation ; Diagnostic Imaging ; Heart Rate ; Monte Carlo Method ; Nanoparticles
    Language English
    Publishing date 2022-06-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1309154-2
    ISSN 1560-2281 ; 1083-3668
    ISSN (online) 1560-2281
    ISSN 1083-3668
    DOI 10.1117/1.JBO.27.8.083020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy.

    Sorelli, Michele / Costantini, Irene / Bocchi, Leonardo / Axer, Markus / Pavone, Francesco Saverio / Mazzamuto, Giacomo

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 4160

    Abstract: Fluorescence microscopy can be exploited for evaluating the brain's fiber architecture with unsurpassed spatial resolution in combination with different tissue preparation and staining protocols. Differently from state-of-the-art polarimetry-based ... ...

    Abstract Fluorescence microscopy can be exploited for evaluating the brain's fiber architecture with unsurpassed spatial resolution in combination with different tissue preparation and staining protocols. Differently from state-of-the-art polarimetry-based neuroimaging modalities, the quantification of fiber tract orientations from fluorescence microscopy volume images entails the application of specific image processing techniques, such as Fourier or structure tensor analysis. These, however, may lead to unreliable outcomes as they do not isolate myelinated fibers from the surrounding tissue. In this work, we describe a novel image processing pipeline that enables the computation of accurate 3D fiber orientation maps from both grey and white matter regions, exploiting the selective multiscale enhancement of tubular structures of varying diameters provided by a 3D implementation of the Frangi filter. The developed software tool can efficiently generate orientation distribution function maps at arbitrary spatial scales which may support the histological validation of modern diffusion-weighted magnetic resonance imaging tractography. Despite being tested here on two-photon scanning fluorescence microscopy images, acquired from tissue samples treated with a label-free technique enhancing the autofluorescence of myelinated fibers, the presented pipeline was developed to be employed on all types of 3D fluorescence images and fiber staining.
    MeSH term(s) Brain/diagnostic imaging ; Algorithms ; Image Processing, Computer-Assisted/methods ; Diffusion Magnetic Resonance Imaging/methods ; Microscopy, Fluorescence
    Language English
    Publishing date 2023-03-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-30953-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Mapping brain state-dependent sensory responses across the mouse cortex.

    Montagni, Elena / Resta, Francesco / Tort-Colet, Núria / Scaglione, Alessandro / Mazzamuto, Giacomo / Destexhe, Alain / Pavone, Francesco Saverio / Allegra Mascaro, Anna Letizia

    iScience

    2024  Volume 27, Issue 5, Page(s) 109692

    Abstract: Sensory information must be integrated across a distributed brain network for stimulus processing and perception. Recent studies have revealed specific spatiotemporal patterns of cortical activation for the early and late components of sensory-evoked ... ...

    Abstract Sensory information must be integrated across a distributed brain network for stimulus processing and perception. Recent studies have revealed specific spatiotemporal patterns of cortical activation for the early and late components of sensory-evoked responses, which are associated with stimulus features and perception, respectively. Here, we investigated how the brain state influences the sensory-evoked activation across the mouse cortex. We utilized isoflurane to modulate the brain state and conducted wide-field calcium imaging of Thy1-GCaMP6f mice to monitor distributed activation evoked by multi-whisker stimulation. Our findings reveal that the level of anesthesia strongly shapes the spatiotemporal features and the functional connectivity of the sensory-activated network. As anesthesia levels decrease, we observe increasingly complex responses, accompanied by the emergence of the late component within the sensory-evoked response. The persistence of the late component under anesthesia raises new questions regarding the potential existence of perception during unconscious states.
    Language English
    Publishing date 2024-04-09
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.109692
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Optical Clearing and Labeling for Light-sheet Fluorescence Microscopy in Large-scale Human Brain Imaging.

    Di Meo, Danila / Ramazzotti, Josephine / Scardigli, Marina / Cheli, Franco / Pesce, Luca / Brady, Niamh / Mazzamuto, Giacomo / Costantini, Irene / Pavone, Francesco S

    Journal of visualized experiments : JoVE

    2024  , Issue 203

    Abstract: Despite the numerous clearing techniques that emerged in the last decade, processing postmortem human brains remains a challenging task due to its dimensions and complexity, which make imaging with micrometer resolution particularly difficult. This paper ...

    Abstract Despite the numerous clearing techniques that emerged in the last decade, processing postmortem human brains remains a challenging task due to its dimensions and complexity, which make imaging with micrometer resolution particularly difficult. This paper presents a protocol to perform the reconstruction of volumetric portions of the human brain by simultaneously processing tens of sections with the SHORT (SWITCH - H2O2 - Antigen Retrieval - 2,2'-thiodiethanol [TDE]) tissue transformation protocol, which enables clearing, labeling, and sequential imaging of the samples with light-sheet fluorescence microscopy (LSFM). SHORT provides rapid tissue clearing and homogeneous multi-labeling of thick slices with several neuronal markers, enabling the identification of different neuronal subpopulations in both white and grey matter. After clearing, the slices are imaged via LSFM with micrometer resolution and in multiple channels simultaneously for a rapid 3D reconstruction. By combining SHORT with LSFM analysis within a routinely high-throughput protocol, it is possible to obtain the 3D cytoarchitecture reconstruction of large volumetric areas at high resolution in a short time, thus enabling comprehensive structural characterization of the human brain.
    MeSH term(s) Humans ; Hydrogen Peroxide ; Microscopy, Fluorescence/methods ; Brain/diagnostic imaging ; Neurons ; Neuroimaging/methods ; Imaging, Three-Dimensional ; Optical Imaging/methods
    Chemical Substances Hydrogen Peroxide (BBX060AN9V)
    Language English
    Publishing date 2024-01-26
    Publishing country United States
    Document type Journal Article ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/65960
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A Guide to Perform 3D Histology of Biological Tissues with Fluorescence Microscopy.

    Laurino, Annunziatina / Franceschini, Alessandra / Pesce, Luca / Cinci, Lorenzo / Montalbano, Alberto / Mazzamuto, Giacomo / Sancataldo, Giuseppe / Nesi, Gabriella / Costantini, Irene / Silvestri, Ludovico / Pavone, Francesco Saverio

    International journal of molecular sciences

    2023  Volume 24, Issue 7

    Abstract: The analysis of histological alterations in all types of tissue is of primary importance in pathology for highly accurate and robust diagnosis. Recent advances in tissue clearing and fluorescence microscopy made the study of the anatomy of biological ... ...

    Abstract The analysis of histological alterations in all types of tissue is of primary importance in pathology for highly accurate and robust diagnosis. Recent advances in tissue clearing and fluorescence microscopy made the study of the anatomy of biological tissue possible in three dimensions. The combination of these techniques with classical hematoxylin and eosin (H&E) staining has led to the birth of three-dimensional (3D) histology. Here, we present an overview of the state-of-the-art methods, highlighting the optimal combinations of different clearing methods and advanced fluorescence microscopy techniques for the investigation of all types of biological tissues. We employed fluorescence nuclear and eosin Y staining that enabled us to obtain hematoxylin and eosin pseudo-coloring comparable with the gold standard H&E analysis. The computational reconstructions obtained with 3D optical imaging can be analyzed by a pathologist without any specific training in volumetric microscopy, paving the way for new biomedical applications in clinical pathology.
    MeSH term(s) Hematoxylin ; Eosine Yellowish-(YS) ; Microscopy, Fluorescence/methods ; Staining and Labeling ; Imaging, Three-Dimensional/methods ; Microscopy, Confocal
    Chemical Substances Hematoxylin (YKM8PY2Z55) ; Eosine Yellowish-(YS) (TDQ283MPCW)
    Language English
    Publishing date 2023-04-04
    Publishing country Switzerland
    Document type Review ; Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24076747
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Brain-wide neuron quantification toolkit reveals strong sexual dimorphism in the evolution of fear memory.

    Franceschini, Alessandra / Mazzamuto, Giacomo / Checcucci, Curzio / Chicchi, Lorenzo / Fanelli, Duccio / Costantini, Irene / Passani, Maria Beatrice / Silva, Bianca Ambrogina / Pavone, Francesco Saverio / Silvestri, Ludovico

    Cell reports

    2023  Volume 42, Issue 8, Page(s) 112908

    Abstract: Fear responses are functionally adaptive behaviors that are strengthened as memories. Indeed, detailed knowledge of the neural circuitry modulating fear memory could be the turning point for the comprehension of this emotion and its pathological states. ... ...

    Abstract Fear responses are functionally adaptive behaviors that are strengthened as memories. Indeed, detailed knowledge of the neural circuitry modulating fear memory could be the turning point for the comprehension of this emotion and its pathological states. A comprehensive understanding of the circuits mediating memory encoding, consolidation, and retrieval presents the fundamental technological challenge of analyzing activity in the entire brain with single-neuron resolution. In this context, we develop the brain-wide neuron quantification toolkit (BRANT) for mapping whole-brain neuronal activation at micron-scale resolution, combining tissue clearing, high-resolution light-sheet microscopy, and automated image analysis. The robustness and scalability of this method allow us to quantify the evolution of activity patterns across multiple phases of memory in mice. This approach highlights a strong sexual dimorphism in recruited circuits, which has no counterpart in the behavior. The methodology presented here paves the way for a comprehensive characterization of the evolution of fear memory.
    MeSH term(s) Mice ; Animals ; Sex Characteristics ; Brain/physiology ; Fear/physiology ; Neurons/physiology
    Language English
    Publishing date 2023-07-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2023.112908
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Fast whole-brain imaging of seizures in zebrafish larvae by two-photon light-sheet microscopy.

    de Vito, Giuseppe / Turrini, Lapo / Müllenbroich, Caroline / Ricci, Pietro / Sancataldo, Giuseppe / Mazzamuto, Giacomo / Tiso, Natascia / Sacconi, Leonardo / Fanelli, Duccio / Silvestri, Ludovico / Vanzi, Francesco / Pavone, Francesco Saverio

    Biomedical optics express

    2022  Volume 13, Issue 3, Page(s) 1516–1536

    Abstract: Light-sheet fluorescence microscopy (LSFM) enables real-time whole-brain functional imaging in zebrafish larvae. Conventional one-photon LSFM can however induce undesirable visual stimulation due to the use of visible excitation light. The use of two- ... ...

    Abstract Light-sheet fluorescence microscopy (LSFM) enables real-time whole-brain functional imaging in zebrafish larvae. Conventional one-photon LSFM can however induce undesirable visual stimulation due to the use of visible excitation light. The use of two-photon (2P) excitation, employing near-infrared invisible light, provides unbiased investigation of neuronal circuit dynamics. However, due to the low efficiency of the 2P absorption process, the imaging speed of this technique is typically limited by the signal-to-noise-ratio. Here, we describe a 2P LSFM setup designed for non-invasive imaging that enables quintuplicating state-of-the-art volumetric acquisition rate of the larval zebrafish brain (5 Hz) while keeping low the laser intensity on the specimen. We applied our system to the study of pharmacologically-induced acute seizures, characterizing the spatial-temporal dynamics of pathological activity and describing for the first time the appearance of caudo-rostral ictal waves (CRIWs).
    Language English
    Publishing date 2022-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2572216-5
    ISSN 2156-7085
    ISSN 2156-7085
    DOI 10.1364/BOE.434146
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: 3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy.

    Pesce, Luca / Scardigli, Marina / Gavryusev, Vladislav / Laurino, Annunziatina / Mazzamuto, Giacomo / Brady, Niamh / Sancataldo, Giuseppe / Silvestri, Ludovico / Destrieux, Christophe / Hof, Patrick R / Costantini, Irene / Pavone, Francesco S

    Communications biology

    2022  Volume 5, Issue 1, Page(s) 447

    Abstract: The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence ... ...

    Abstract The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence contributions of aged tissues. To meet this challenge, we optimized SHORT (SWITCH-H
    MeSH term(s) Adult ; Aged ; Brain/diagnostic imaging ; Fluorescent Antibody Technique ; Humans ; Hydrogen Peroxide ; Imaging, Three-Dimensional/methods ; Microscopy, Fluorescence/methods
    Chemical Substances Hydrogen Peroxide (BBX060AN9V)
    Language English
    Publishing date 2022-05-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-022-03390-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Studying the trafficking of labeled trodusquemine and its application as nerve marker for light-sheet and expansion microscopy.

    Capitini, Claudia / Pesce, Luca / Fani, Giulia / Mazzamuto, Giacomo / Genovese, Massimo / Franceschini, Alessandra / Paoli, Paolo / Pieraccini, Giuseppe / Zasloff, Michael / Chiti, Fabrizio / Pavone, Francesco S / Calamai, Martino

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology

    2022  Volume 36, Issue 12, Page(s) e22655

    Abstract: Trodusquemine is an aminosterol with a variety of biological and pharmacological functions, such as acting as an antimicrobial, stimulating body weight loss and interfering with the toxicity of proteins involved in the development of Alzheimer's and ... ...

    Abstract Trodusquemine is an aminosterol with a variety of biological and pharmacological functions, such as acting as an antimicrobial, stimulating body weight loss and interfering with the toxicity of proteins involved in the development of Alzheimer's and Parkinson's diseases. The mechanisms of interaction of aminosterols with cells are, however, still largely uncharacterized. Here, by using fluorescently labeled trodusquemine (TRO-A594 and TRO-ATTO565), we show that trodusquemine binds initially to the plasma membrane of living cells, that the binding affinity is dependent on cholesterol, and that trodusquemine is then internalized and mainly targeted to lysosomes after internalization. We also found that TRO-A594 is able to strongly and selectively bind to myelinated fibers in fixed mouse brain slices, and that it is a marker compatible with tissue clearing and light-sheet fluorescence microscopy or expansion microscopy. In conclusion, this work contributes to further characterize the biology of aminosterols and provides a new tool for nerve labeling suitable for the most advanced microscopy techniques.
    MeSH term(s) Animals ; Mice ; Cholestanes/pharmacology ; Spermine/pharmacology ; Microscopy, Fluorescence/methods ; Cholesterol
    Chemical Substances 3-N-1(spermine)-7, 24-dihydroxy-5-cholestane 24-sulfate ; Cholestanes ; Spermine (2FZ7Y3VOQX) ; Cholesterol (97C5T2UQ7J)
    Language English
    Publishing date 2022-11-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639186-2
    ISSN 1530-6860 ; 0892-6638
    ISSN (online) 1530-6860
    ISSN 0892-6638
    DOI 10.1096/fj.202201276R
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Semantic Segmentation of Neuronal Bodies in Fluorescence Microscopy Using a 2D+3D CNN Training Strategy with Sparsely Annotated Data

    Castelli, Filippo Maria / Roffilli, Matteo / Mazzamuto, Giacomo / Costantini, Irene / Silvestri, Ludovico / Pavone, Francesco Saverio

    2020  

    Abstract: Semantic segmentation of neuronal structures in 3D high-resolution fluorescence microscopy imaging of the human brain cortex can take advantage of bidimensional CNNs, which yield good results in neuron localization but lead to inaccurate surface ... ...

    Abstract Semantic segmentation of neuronal structures in 3D high-resolution fluorescence microscopy imaging of the human brain cortex can take advantage of bidimensional CNNs, which yield good results in neuron localization but lead to inaccurate surface reconstruction. 3D CNNs, on the other hand, would require manually annotated volumetric data on a large scale and hence considerable human effort. Semi-supervised alternative strategies which make use only of sparse annotations suffer from longer training times and achieved models tend to have increased capacity compared to 2D CNNs, needing more ground truth data to attain similar results. To overcome these issues we propose a two-phase strategy for training native 3D CNN models on sparse 2D annotations where missing labels are inferred by a 2D CNN model and combined with manual annotations in a weighted manner during loss calculation.
    Keywords Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition ; Quantitative Biology - Neurons and Cognition
    Subject code 006
    Publishing date 2020-08-31
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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