Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma

• Lucas Sancéré ,

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: lsancere@uni-koeln.de (LS); johannes.braegelmann@uni-koeln.de (JB); k.bozek@uni-koeln.de (KB)

  Affiliations Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, North Rhine-Westphalia, Germany, Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, North Rhine-Westphalia, Germany, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, North Rhine-Westphalia, Germany

  https://orcid.org/0009-0000-3857-5641

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• Carina Lorenz,

  Roles Conceptualization, Data curation, Investigation, Visualization, Writing – review & editing

  Affiliations Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, North Rhine-Westphalia, Germany, University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany, University of Cologne, Faculty of Medicine and University Hospital Cologne, Mildred Scheel School of Oncology, Cologne, Germany

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• Doris Helbig,

  Roles Data curation, Project administration, Resources

  Affiliation Department for Dermatology, University Hospital Cologne, Cologne, Germany

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• Oana-Diana Persa,

  Roles Resources

  Affiliation Department of Dermatology and Allergy, School of Medicine, Technical University of Munich, Bavarian Cancer Research Center (BZKF), Munich, Germany

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• Sonja Dengler,

  Roles Resources

  Affiliation Department of Dermatology, Dortmund Hospital gGmbH, University Witten/Herdecke, Dortmund, Germany

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• Alexander Kreuter,

  Roles Resources

  Affiliation Department of Dermatology, Venereology and Allergology, Helios St. Elisabeth Hospital Oberhausen, University Witten/Herdecke, Oberhausen, Germany

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• Martim Laimer,

  Roles Resources

  Affiliation Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria

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• Roland Lang,

  Roles Resources

  Affiliation Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria

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• Anne Fröhlich,

  Roles Resources

  Affiliation Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany

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• Jennifer Landsberg,

  Roles Resources

  Affiliation Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany

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• Johannes Brägelmann ,

  Contributed equally to this work with: Johannes Brägelmann, Katarzyna Bozek

  Roles Conceptualization, Data curation, Funding acquisition, Project administration, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: lsancere@uni-koeln.de (LS); johannes.braegelmann@uni-koeln.de (JB); k.bozek@uni-koeln.de (KB)

  Affiliations Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, North Rhine-Westphalia, Germany, University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany, University of Cologne, Faculty of Medicine and University Hospital Cologne, Mildred Scheel School of Oncology, Cologne, Germany, Medical Clinic III for Oncology, Hematology, Immune-Oncology and Rheumatology, University Hospital Bonn (UKB), Bonn, Germany

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• Katarzyna Bozek

  Contributed equally to this work with: Johannes Brägelmann, Katarzyna Bozek

  Roles Conceptualization, Funding acquisition, Project administration, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: lsancere@uni-koeln.de (LS); johannes.braegelmann@uni-koeln.de (JB); k.bozek@uni-koeln.de (KB)

  Affiliations Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, North Rhine-Westphalia, Germany, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, North Rhine-Westphalia, Germany, Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, North Rhine-Westphalia, Germany

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