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Bringing Open Data to Whole Slide Imaging

  • Conference paper
  • First Online:
Digital Pathology (ECDP 2019)

Abstract

Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or “pyramidal”) representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs.

S. Besson, R. Leigh and M. Linkert—These authors contributed equally to this work.

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Acknowledgements

This work was funded by grants from the BBSRC (Ref: BB/P027032/1, BB/R015384/1) and the Wellcome Trust (Ref: 202908/Z/16/Z).

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Correspondence to Jason R. Swedlow .

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Besson, S. et al. (2019). Bringing Open Data to Whole Slide Imaging. In: Reyes-Aldasoro, C., Janowczyk, A., Veta, M., Bankhead, P., Sirinukunwattana, K. (eds) Digital Pathology. ECDP 2019. Lecture Notes in Computer Science(), vol 11435. Springer, Cham. https://doi.org/10.1007/978-3-030-23937-4_1

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  • DOI: https://doi.org/10.1007/978-3-030-23937-4_1

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-23936-7

  • Online ISBN: 978-3-030-23937-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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