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An ImageJ Plugin for Whole Slide Imaging

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Bildverarbeitung für die Medizin 2014

Part of the book series: Informatik aktuell ((INFORMAT))

Abstract

Whole slide imaging (WSI) has become important in medicine and pathology, and challenges processing and management of high-resolution images with up to 10GB of data. Open source tools such as ImageJ do not sufficiently support high volume data and require manual interaction in otherwise automatic workflows. We present an open source ImageJ plugin for automatic processing of Nanozoomer Digital Pathology Images (NDPI). In a batch-orientated workflow, the plugin provides an image processing pipeline including data conversion, segmentation, tiling, region of interest detection, thresholding, and quantification. The plugin is exemplarily applied to quantitative analysis of renal histology images. However, the general design supports other WSI file formats and analysis tasks.

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Author information

Authors and Affiliations

  1. Department of Medical Informatics, Uniklinik RWTH Aachen, Aachen, Germany

    Daniel Haak, Yusuf Z. Filmwala, Eric Heder, Stephan Jonas & Thomas M. Deserno

  2. Institute of Pathology, Uniklinik RWTH Aachen, Aachen, Germany

    Peter Boor

Authors
  1. Daniel Haak
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  2. Yusuf Z. Filmwala
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  3. Eric Heder
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  4. Stephan Jonas
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  5. Peter Boor
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  6. Thomas M. Deserno
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Corresponding author

Correspondence to Daniel Haak .

Editor information

Editors and Affiliations

  1. Institut für Medizinische Informatik, Uniklinik RWTH Aachen, Aachen, Germany

    Thomas Martin Deserno

  2. Institut für Medizinische Informatik, Universität zu Lübeck, Lübeck, Germany

    Heinz Handels

  3. Abteilung für Medizinische und Biologische Informatik, Deutsches Krebsforschungszentrum, Heidelberg, Germany

    Hans-Peter Meinzer

  4. Institut für Medizinische Informatik, Charité – Universitätsmedizin Berlin, Berlin, Berlin, Germany

    Thomas Tolxdorff

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© 2014 Springer-Verlag Berlin Heidelberg

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Haak, D., Filmwala, Y., Heder, E., Jonas, S., Boor, P., Deserno, T. (2014). An ImageJ Plugin for Whole Slide Imaging. In: Deserno, T., Handels, H., Meinzer, HP., Tolxdorff, T. (eds) Bildverarbeitung für die Medizin 2014. Informatik aktuell. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-54111-7_76

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