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  1. Article ; Online: Gos: a declarative library for interactive genomics visualization in Python.

    Manz, Trevor / L'Yi, Sehi / Gehlenborg, Nils

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 1

    Abstract: Summary: Gos is a declarative Python library designed to create interactive multiscale visualizations of genomics and epigenomics data. It provides a consistent and simple interface to the flexible Gosling visualization grammar. Gos hides technical ... ...

    Abstract Summary: Gos is a declarative Python library designed to create interactive multiscale visualizations of genomics and epigenomics data. It provides a consistent and simple interface to the flexible Gosling visualization grammar. Gos hides technical complexities involved with configuring web-based genome browsers and integrates seamlessly within computational notebooks environments to enable new interactive analysis workflows.
    Availability and implementation: Gos is released under the MIT License and available on the Python Package Index (PyPI). The source code is publicly available on GitHub (https://github.com/gosling-lang/gos), and documentation with examples can be found at https://gosling-lang.github.io/gos.
    MeSH term(s) Animals ; Computational Biology ; Geese ; Genomics ; Genome ; Gene Library ; Software
    Language English
    Publishing date 2023-01-23
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad050
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Chromoscope: interactive multiscale visualization for structural variation in human genomes.

    L'Yi, Sehi / Maziec, Dominika / Stevens, Victoria / Manz, Trevor / Veit, Alexander / Berselli, Michele / Park, Peter J / Głodzik, Dominik / Gehlenborg, Nils

    Nature methods

    2023  Volume 20, Issue 12, Page(s) 1834–1835

    Language English
    Publishing date 2023-11-01
    Publishing country United States
    Document type Letter
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-023-02056-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web.

    Manz, Trevor / Gold, Ilan / Patterson, Nathan Heath / McCallum, Chuck / Keller, Mark S / Herr, Bruce W / Börner, Katy / Spraggins, Jeffrey M / Gehlenborg, Nils

    Nature methods

    2022  Volume 19, Issue 5, Page(s) 515–516

    Language English
    Publishing date 2022-05-13
    Publishing country United States
    Document type Letter
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01482-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies.

    Moore, Josh / Allan, Chris / Besson, Sébastien / Burel, Jean-Marie / Diel, Erin / Gault, David / Kozlowski, Kevin / Lindner, Dominik / Linkert, Melissa / Manz, Trevor / Moore, Will / Pape, Constantin / Tischer, Christian / Swedlow, Jason R

    Nature methods

    2021  Volume 18, Issue 12, Page(s) 1496–1498

    Abstract: The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 ... ...

    Abstract The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.
    MeSH term(s) Benchmarking ; Computational Biology/instrumentation ; Computational Biology/methods ; Computational Biology/standards ; Data Compression ; Databases, Factual ; Information Storage and Retrieval ; Internet ; Metadata ; Microscopy/instrumentation ; Microscopy/methods ; Microscopy/standards ; Programming Languages ; SARS-CoV-2 ; Software
    Language English
    Publishing date 2021-11-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-021-01326-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Periphery Plots for Contextualizing Heterogeneous Time-Based Charts

    Morrow, Bryce / Manz, Trevor / Chung, Arlene E. / Gehlenborg, Nils / Gotz, David

    2019  

    Abstract: Patterns in temporal data can often be found across different scales, such as days, weeks, and months, making effective visualization of time-based data challenging. Here we propose a new approach for providing focus and context in time-based charts to ... ...

    Abstract Patterns in temporal data can often be found across different scales, such as days, weeks, and months, making effective visualization of time-based data challenging. Here we propose a new approach for providing focus and context in time-based charts to enable interpretation of patterns across time scales. Our approach employs a focus zone with a time and a second axis, that can either represent quantities or categories, as well as a set of adjacent periphery plots that can aggregate data along the time, value, or both dimensions. We present a framework for periphery plots and describe two use cases that demonstrate the utility of our approach.

    Comment: To Appear in IEEE VIS 2019 Short Papers. Open source software and other materials available on github: https://github.com/PrecisionVISSTA/PeripheryPlots Video figure available on Vimeo: https://vimeo.com/349678146
    Keywords Computer Science - Human-Computer Interaction
    Publishing date 2019-06-18
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: OME-Zarr: a cloud-optimized bioimaging file format with international community support.

    Moore, Josh / Basurto-Lozada, Daniela / Besson, Sébastien / Bogovic, John / Bragantini, Jordão / Brown, Eva M / Burel, Jean-Marie / Moreno, Xavier Casas / de Medeiros, Gustavo / Diel, Erin E / Gault, David / Ghosh, Satrajit S / Gold, Ilan / Halchenko, Yaroslav O / Hartley, Matthew / Horsfall, Dave / Keller, Mark S / Kittisopikul, Mark / Kovacs, Gabor /
    Yoldaş, Aybüke Küpcü / Kyoda, Koji / de la Villegeorges, Albane le Tournoulx / Li, Tong / Liberali, Prisca / Lindner, Dominik / Linkert, Melissa / Lüthi, Joel / Maitin-Shepard, Jeremy / Manz, Trevor / Marconato, Luca / McCormick, Matthew / Lange, Merlin / Mohamed, Khaled / Moore, William / Norlin, Nils / Ouyang, Wei / Özdemir, Bugra / Palla, Giovanni / Pape, Constantin / Pelkmans, Lucas / Pietzsch, Tobias / Preibisch, Stephan / Prete, Martin / Rzepka, Norman / Samee, Sameeul / Schaub, Nicholas / Sidky, Hythem / Solak, Ahmet Can / Stirling, David R / Striebel, Jonathan / Tischer, Christian / Toloudis, Daniel / Virshup, Isaac / Walczysko, Petr / Watson, Alan M / Weisbart, Erin / Wong, Frances / Yamauchi, Kevin A / Bayraktar, Omer / Cimini, Beth A / Gehlenborg, Nils / Haniffa, Muzlifah / Hotaling, Nathan / Onami, Shuichi / Royer, Loic A / Saalfeld, Stephan / Stegle, Oliver / Theis, Fabian J / Swedlow, Jason R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing ...

    Abstract A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.
    Language English
    Publishing date 2023-05-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.17.528834
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: OME-Zarr: a cloud-optimized bioimaging file format with international community support.

    Moore, Josh / Basurto-Lozada, Daniela / Besson, Sébastien / Bogovic, John / Bragantini, Jordão / Brown, Eva M / Burel, Jean-Marie / Casas Moreno, Xavier / de Medeiros, Gustavo / Diel, Erin E / Gault, David / Ghosh, Satrajit S / Gold, Ilan / Halchenko, Yaroslav O / Hartley, Matthew / Horsfall, Dave / Keller, Mark S / Kittisopikul, Mark / Kovacs, Gabor /
    Küpcü Yoldaş, Aybüke / Kyoda, Koji / le Tournoulx de la Villegeorges, Albane / Li, Tong / Liberali, Prisca / Lindner, Dominik / Linkert, Melissa / Lüthi, Joel / Maitin-Shepard, Jeremy / Manz, Trevor / Marconato, Luca / McCormick, Matthew / Lange, Merlin / Mohamed, Khaled / Moore, William / Norlin, Nils / Ouyang, Wei / Özdemir, Bugra / Palla, Giovanni / Pape, Constantin / Pelkmans, Lucas / Pietzsch, Tobias / Preibisch, Stephan / Prete, Martin / Rzepka, Norman / Samee, Sameeul / Schaub, Nicholas / Sidky, Hythem / Solak, Ahmet Can / Stirling, David R / Striebel, Jonathan / Tischer, Christian / Toloudis, Daniel / Virshup, Isaac / Walczysko, Petr / Watson, Alan M / Weisbart, Erin / Wong, Frances / Yamauchi, Kevin A / Bayraktar, Omer / Cimini, Beth A / Gehlenborg, Nils / Haniffa, Muzlifah / Hotaling, Nathan / Onami, Shuichi / Royer, Loic A / Saalfeld, Stephan / Stegle, Oliver / Theis, Fabian J / Swedlow, Jason R

    Histochemistry and cell biology

    2023  Volume 160, Issue 3, Page(s) 223–251

    Abstract: A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing ...

    Abstract A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.
    MeSH term(s) Humans ; Software ; Microscopy ; Community Support
    Language English
    Publishing date 2023-07-10
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1222930-1
    ISSN 1432-119X ; 0301-5564 ; 0948-6143
    ISSN (online) 1432-119X
    ISSN 0301-5564 ; 0948-6143
    DOI 10.1007/s00418-023-02209-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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