IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37224-2.html
   My bibliography  Save this article

Interoperable slide microscopy viewer and annotation tool for imaging data science and computational pathology

Author

Listed:
  • Chris Gorman

    (Massachusetts General Hospital and Harvard Medical School)

  • Davide Punzo

    (Radical Imaging)

  • Igor Octaviano

    (Radical Imaging)

  • Steven Pieper

    (Isomics Inc)

  • William J. R. Longabaugh

    (Institute for Systems Biology)

  • David A. Clunie

    (PixelMed Publishing LLC)

  • Ron Kikinis

    (Brigham and Women’s Hospital and Harvard Medical School)

  • Andrey Y. Fedorov

    (Brigham and Women’s Hospital and Harvard Medical School)

  • Markus D. Herrmann

    (Massachusetts General Hospital and Harvard Medical School)

Abstract

The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and interoperability, which is detrimental to the reproducibility of scientific findings and clinical integration of technological innovations. We introduce Slim, an open-source, web-based slide microscopy viewer that implements the internationally accepted Digital Imaging and Communications in Medicine (DICOM) standard to achieve interoperability with a multitude of existing medical imaging systems. We showcase the capabilities of Slim as the slide microscopy viewer of the NCI Imaging Data Commons and demonstrate how the viewer enables interactive visualization of traditional brightfield microscopy and highly-multiplexed immunofluorescence microscopy images from The Cancer Genome Atlas and Human Tissue Atlas Network, respectively, using standard DICOMweb services. We further show how Slim enables the collection of standardized image annotations for the development or validation of machine learning models and the visual interpretation of model inference results in the form of segmentation masks, spatial heat maps, or image-derived measurements.

Suggested Citation

  • Chris Gorman & Davide Punzo & Igor Octaviano & Steven Pieper & William J. R. Longabaugh & David A. Clunie & Ron Kikinis & Andrey Y. Fedorov & Markus D. Herrmann, 2023. "Interoperable slide microscopy viewer and annotation tool for imaging data science and computational pathology," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37224-2
    DOI: 10.1038/s41467-023-37224-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37224-2
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-37224-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Fabio Crameri & Grace E. Shephard & Philip J. Heron, 2020. "The misuse of colour in science communication," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sarah Westarp & Felix Brandt & Lena Neumair & Christina Betz & Amin Dagane & Sebastian Kemper & Christoph R. Jacob & Peter Neubauer & Anke Kurreck & Felix Kaspar, 2024. "Nucleoside Phosphorylases make N7-xanthosine," Nature Communications, Nature, vol. 15(1), pages 1-7, December.
    2. Magda Dubois & Tobias U. Hauser, 2022. "Value-free random exploration is linked to impulsivity," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Ramon Gao & Michael D. Kelzenberg & Harry A. Atwater, 2024. "Dynamically stable radiation pressure propulsion of flexible lightsails for interstellar exploration," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Grace E. Shephard & Christine Houser & John W. Hernlund & Juan J. Valencia-Cardona & Reidar G. Trønnes & Renata M. Wentzcovitch, 2021. "Seismological expression of the iron spin crossover in ferropericlase in the Earth’s lower mantle," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    5. Alik Ismail-Zadeh & Anne Davaille & Jean Besse & Yuri Volozh, 2024. "East European sedimentary basins long heated by a fading mantle upwelling," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    6. Tiemo Pedergnana & Abel Faure-Beaulieu & Romain Fleury & Nicolas Noiray, 2024. "Loss-compensated non-reciprocal scattering based on synchronization," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    7. Guido Fioravanti & Michela Cameletti & Sara Martino & Giorgio Cattani & Enrico Pisoni, 2022. "A spatiotemporal analysis of NO2 concentrations during the Italian 2020 COVID‐19 lockdown," Environmetrics, John Wiley & Sons, Ltd., vol. 33(4), June.
    8. Shubham Chandra & Chengcheng Wang & Shu Beng Tor & Upadrasta Ramamurty & Xipeng Tan, 2024. "Powder-size driven facile microstructure control in powder-fusion metal additive manufacturing processes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Xiaochuan Tian & Mark D. Behn & Garrett Ito & Jana C. Schierjott & Boris J. P. Kaus & Anton A. Popov, 2024. "Magmatism controls global oceanic transform fault topography," Nature Communications, Nature, vol. 15(1), pages 1-9, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37224-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.