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  1. Article ; Online: MAUI (MBI Analysis User Interface)-An image processing pipeline for Multiplexed Mass Based Imaging.

    Alex Baranski / Idan Milo / Shirley Greenbaum / John-Paul Oliveria / Dunja Mrdjen / Michael Angelo / Leeat Keren

    PLoS Computational Biology, Vol 17, Iss 4, p e

    2021  Volume 1008887

    Abstract: Mass Based Imaging (MBI) technologies such as Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and Imaging Mass Cytometry (IMC) allow for the simultaneous measurement of the expression levels of 40 or more proteins in biological tissue, ... ...

    Abstract Mass Based Imaging (MBI) technologies such as Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and Imaging Mass Cytometry (IMC) allow for the simultaneous measurement of the expression levels of 40 or more proteins in biological tissue, providing insight into cellular phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. Here, we present MBI Analysis User Interface (MAUI), a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. Our software streamlines these steps and accelerates processing by enabling real-time and interactive parameter tuning across multiple images.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: An optimized protocol for phenotyping human granulocytes by mass cytometry

    Nora Vivanco Gonzalez / John-Paul Oliveria / Dmitry Tebaykin / Geoffrey T. Ivison / Kaori Mukai / Mindy M. Tsai / Luciene Borges / Kari C. Nadeau / Stephen J. Galli / Albert G. Tsai / Sean C. Bendall

    STAR Protocols, Vol 3, Iss 2, Pp 101280- (2022)

    2022  

    Abstract: Summary: Granulocytes encompass diverse roles, from fighting off pathogens to regulating inflammatory processes in allergies. These roles are represented by distinct cellular phenotypes that we captured with mass cytometry (CyTOF). Our protocol enables ... ...

    Abstract Summary: Granulocytes encompass diverse roles, from fighting off pathogens to regulating inflammatory processes in allergies. These roles are represented by distinct cellular phenotypes that we captured with mass cytometry (CyTOF). Our protocol enables simultaneous evaluation of human basophils, eosinophils, and neutrophils under homeostasis and upon immune activation by anti-Immunoglobulin E (anti-IgE) or interleukin-3 (IL-3). Granulocyte integrity and detection of protein markers were optimized so that rare granulocyte populations could be deeply characterized by single cell mass cytometry.For complete details on the use and execution of this protocol, please refer to Vivanco Gonzalez et al. (2020).
    Keywords Cell isolation ; Single Cell ; Flow Cytometry/Mass Cytometry ; Health Sciences ; Immunology ; Antibody ; Science (General) ; Q1-390
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology

    Yunhao Bai / Bokai Zhu / John-Paul Oliveria / Bryan J. Cannon / Dorien Feyaerts / Marc Bosse / Kausalia Vijayaragavan / Noah F. Greenwald / Darci Phillips / Christian M. Schürch / Samuel M. Naik / Edward A. Ganio / Brice Gaudilliere / Scott J. Rodig / Michael B. Miller / Michael Angelo / Sean C. Bendall / Xavier Rovira-Clavé / Garry P. Nolan /
    Sizun Jiang

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 18

    Abstract: Abstract Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand ... ...

    Abstract Abstract Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
    Keywords Science ; Q
    Subject code 616
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Mass Cytometry Phenotyping of Human Granulocytes Reveals Novel Basophil Functional Heterogeneity

    Nora Vivanco Gonzalez / John-Paul Oliveria / Dmitry Tebaykin / Geoffrey T. Ivison / Kaori Mukai / Mindy M. Tsai / Luciene Borges / Kari C. Nadeau / Stephen J. Galli / Albert G. Tsai / Sean C. Bendall

    iScience, Vol 23, Iss 11, Pp 101724- (2020)

    2020  

    Abstract: Summary: Basophils, the rarest granulocyte, play critical roles in parasite- and allergen-induced inflammation. We applied mass cytometry (CyTOF) to simultaneously asses 44 proteins to phenotype and functionally characterize neutrophils, eosinophils, and ...

    Abstract Summary: Basophils, the rarest granulocyte, play critical roles in parasite- and allergen-induced inflammation. We applied mass cytometry (CyTOF) to simultaneously asses 44 proteins to phenotype and functionally characterize neutrophils, eosinophils, and basophils from 19 healthy donors. There was minimal heterogeneity seen in eosinophils and neutrophils, but data-driven analyses revealed four unique subpopulations within phenotypically basophilic granulocytes (PBG; CD45+HLA-DR−CD123+). Through CyTOF and fluorescence-activated cell sorting (FACS), we classified these four PBG subpopulations as (I) CD16lowFcεRIhighCD244high (88.5 ± 1.2%), (II) CD16highFcεRIhighCD244high (9.1 ± 0.4%), (III) CD16lowFcεRIlowCD244low (2.3 ± 1.3), and (IV) CD16highFcεRIlowCD244low (0.4 ± 0.1%). Prospective isolation confirmed basophilic-morphology of PBG I–III, but neutrophilic-morphology of PBG IV. Functional interrogation via IgE-crosslinking or IL-3 stimulation demonstrated that PBG I–II had significant increases in CD203c expression, whereas PBG III–IV remained unchanged compared with media-alone conditions. Thus, PBG III–IV could serve roles in non-IgE-mediated immunity. Our findings offer new perspectives in human basophil heterogeneity and the varying functional potential of these new subsets in health and disease.
    Keywords Immunology ; Systems Biology ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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