Automating liver biopsy segmentation with a robust, open-source tool for pathology research: the HOTSPoT model.

Journal: NPJ digital medicine
Published Date:

Abstract

Artificial intelligence applications in liver pathology remain limited, with existing tools either narrowly focused or lacking external validation. This study introduces HOTSPoT, an open-source, validated transformer-based model for automated segmentation of portal tracts in H&E-stained liver biopsy whole slide images. A multi-institutional dataset of 223 cases was used, with annotations by expert hepatopathologists. HOTSPoT achieved high performance with mean Dice scores of 0.92 (train/val) and 0.91 (test), and mean IoUs of 0.86, 0.85, and 0.84, respectively, showing minimal domain shift. Automated portal tract quantification showed strong concordance with manual assessments (κ up to 0.90), and portal area correlated with fibrosis stage (r = 0.87, p < 0.001). The model is available as a TorchScript file with a modified WSInfer library, enabling efficient WSI-level inference and integration with QuPath for advanced pathology analysis.

Authors

  • Giorgio Cazzaniga
    Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, Università di Milano-Bicocca, Monza, Italy. giorgio9cazzaniga@gmail.com.
  • Vincenzo L'Imperio
    Department of Medicine and Surgery, ASST Monza, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy.
  • Emanuela Bonoldi
    Unit of Surgical Pathology and Cytogenetics, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy.
  • María-Carlota Londoño
    Liver Unit, Hospital Clínic Barcelona, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Universitat de Barcelona, Centro de investigación biomédica en red Enfermedades Hepáticas y Digestivas (CIBEREHD), European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Barcelona, Spain.
  • João Madaleno
    Liver Disease Unit, Department of Internal Medicine, Unidade Local de Saúde de Coimbra - Hospitais da Universidade de Coimbra, Coimbra, Portugal; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Coimbra, Portugal.
  • Augusta Cipriano
    Pathology Department, Unidade Local de Saúde de Coimbra - Hospitais da Universidade de Coimbra, Coimbra, Portugal; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Coimbra, Portugal.
  • Tom J G Gevers
    Department of Gastroenterology and Hepatology, Maastricht University Medical Center, Maastricht, The Netherlands.
  • Iryna V Samarska
    Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands.
  • Özgür M Koc
    Department of Gastroenterology and Hepatology, Maastricht University Medical Center, Maastricht, The Netherlands.
  • Alejandra Villamil
    Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
  • Maria Florencia Sanchez
    Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
  • Vincenza Calvaruso
    Section of Gastroenterology and Hepatology, PROMISE, University of Palermo, Palermo, Italy.
  • Alberto Quattrocchi
    Dipartimento Di Promozione Della Salute, Materno Infantile, Medicina Interna e Specialistica Di Eccellenza (PROMISE), Palermo, Italy.
  • Daniela Cabibi
    Dipartimento Di Promozione Della Salute, Materno Infantile, Medicina Interna e Specialistica Di Eccellenza (PROMISE), Palermo, Italy.
  • Bastian Engel
    Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany.
  • Federica Malinverno
    Division of Gastroenterology, Center for Autoimmune Liver Diseases, European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy.
  • Elisa Merelli
    Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
  • Laura Cristoferi
    Division of Gastroenterology, Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy. Electronic address: Laura.cristoferi@unimi.it.
  • Marco Carbone
    Division of Gastroenterology, Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy; Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom. Electronic address: marco.carbone@unimib.it.
  • Fabio Pagni
    Department of Medicine and Surgery, ASST Monza, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy.
  • Pietro Invernizzi
    Division of Gastroenterology, Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy. Electronic address: Pietro.invernizzi@unimib.it.
  • Alessio Gerussi
    Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy.

Keywords

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