Icytomine: A User-Friendly Tool for Integrating Workflows on Whole Slide Images

  • Daniel Felipe Gonzalez Obando
  • Diana Mandache
  • Jean-Christophe Olivo-Marin
  • Vannary Meas-YedidEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11435)


We present Icytomine, a user-friendly software platform for processing large images from slide scanners. Icytomine integrates in one unique framework the tools and algorithms that were developed independently on Icy and Cytomine platforms to visualise and process digital pathology images. We illustrate the power of this new platform through the design of a dedicated program that uses convolutional neural network to detect and classify glomeruli in kidney biopsies coming from a multicentric clinical study. We show that by streamlining the analytical capabilities of Icy with the AI tools found in Cytomine, we achieved highly promising results.


Whole slide imaging Reproducible research Open-source plugin Convolutional neural network Fine-tuning Detection of glomeruli 


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Daniel Felipe Gonzalez Obando
    • 1
  • Diana Mandache
    • 1
  • Jean-Christophe Olivo-Marin
    • 1
  • Vannary Meas-Yedid
    • 1
    Email author
  1. 1.Institut Pasteur, Bioimage Analysis Unit-CNRS UMR 3691ParisFrance

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