WSI2ML – An Open-Source Whole Slide Image Annotation Software for Machine Learning Applications

  • Luan V. C. Martins USP
  • Adriana Passos Bueno CIPE/A.C. Camargo Cancer Center
  • Alexandre Defelicibus CIPE/A.C. Camargo Cancer Center
  • Rodrigo D. Drummond CIPE/A.C. Camargo Cancer Center
  • Renan Valieris CIPE/A.C. Camargo Cancer Center
  • Yu-Tao Zhu China Branch of BRICS Institute of Future Networks
  • Israel Tojal Da Silva CIPE/A.C. Camargo Cancer Center
  • Liang Zhao USP


Machine learning (ML) has emerged as a powerful tool for improving the clinical pathology routine; however, developing novel ML research requires a complex multidisciplinary team effort. Therefore, a software for tackling the challenges of effectively annotating, building, and validating ML models is desirable. In this work we present WSI2ML, a web-based platform that provides a friendly interface suited for ML computational pathology research to be easily performed. Compared to similar tools currently available, the proposed software provides a complete toolset for each stage of ML workflow. We demonstrate the usefulness and functionality of WSI2ML by analyzing the performance results obtained in a tissue recognition task using a novel gastric cancer research dataset that is currently being developed with the tool. The software, documentation, installation instructions and related annotation handling library is freely available at

Palavras-chave: bioinformatics, image tagging, whole slide image


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MARTINS, Luan V. C.; BUENO, Adriana Passos; DEFELICIBUS, Alexandre; DRUMMOND, Rodrigo D.; VALIERIS, Renan; ZHU, Yu-Tao; DA SILVA, Israel Tojal; ZHAO, Liang. WSI2ML – An Open-Source Whole Slide Image Annotation Software for Machine Learning Applications. In: SIMPÓSIO BRASILEIRO DE SISTEMAS MULTIMÍDIA E WEB (WEBMEDIA), 29. , 2023, Ribeirão Preto/SP. Anais [...]. Porto Alegre: Sociedade Brasileira de Computação, 2023 . p. 104–109.