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SCI Collaboration

Computational Pathology

We use our knowledge in diagnostic and molecular pathology for the development of computational biomarkers. The algorithms we develop learn unique features of cell differentiation and organization in regular pathology slides. Through  partnership with the Institute of Scientific Computing and Imaging we use images from H&E stained tissue sections to predict disease outcomes and response to treatments. The ultimate goal is to built fast and accurate prediction models from pathology images that can assist with point-of-care decision making and with a patient’s individualized treatment planning.

 

    HistoEM: A Pathologist-Guided and Explainable Workflow Using Histogram Embedding for Gland Classification. 

    Alessandro Ferrero, Elham Ghelichkhan, Hamid Manoochehri, Man Minh Ho, Daniel J. Albertson, Benjamin J. Brintz, Ross T. Whitaker, Beatrice S. Knudsen

     

    KnudsenGlandCancer
    Graphical abstract
    KnudsenMICCAI2022

    Automating Ground Truth Annotations for Gland Segmentation Through Immunohistochemistry
    Tushar Kataria, Saradha Rajamani, Abdul Bari Ayubi, Mary Bronner, Jolanta Jedrzkiewicz, Beatrice S Knudsen, Shireen Y Elhabian. Mod Pathol. 2023 Dec

    Knudsenground
    Graphical abstract:​

    Stain Based Contrastive Co-training for Histopathological Image Analysis
    Authors: Bodong Zhang, Beatrice Knudsen, Deepika Sirohi,
    Alessandro Ferrero, Tolga Tasdizen arXiv:2206.12505

    KnudsenColor
    Graphical abstract:
    KnudsenMICCAI2022

    Structural Cycle GAN for Virtual Immunohistochemistry Staining of Gland Markers in the Colon
    Authors: Shikha Dubey, Tushar Kataria, Beatrice Knudsen, Shireen Y. Elhabian arXiv:2308.13182

    image
    Graphical abstract
    KnudsenMICCAI2023
    KnudsenModel
    Graphical abstract

    SCI Research Publications

    Selected Publications

    HistoEm: A Pathologist-Guided and Explainable Workflow Using Histogram Embedding for Gland Classification 
    Alessandro Ferrero, Elham Ghelichkham, Hamid Manoochehri, Man Minh Ho, Daniel J. Alberston, Benjamin J. Brintz, Ross T. Whitaker, Beatrice S. Knudsen arXiv:2209.13408v1

    Automating Ground Truth Annotations for Gland Segmentation Through Immunohistochemistry
    Authors: Tushar Kataria, Saradha Rajamani, Abdul Bari Ayubi, Mary Bronner, Jolanta Jedrzkiewicz, Beatrice S Knudsen, Shireen Y Elhabian Mod Pathol. 2023 Dec

    Stain Based Contrastive Co-training for Histopathological Image Analysis  
    Authors: Bodong Zhang, Beatrice Knudsen, Deepika Sirohi, Alessandro Ferrero, Tolga Tasdizen arXiv:2206.12505

    Structural Cycle GAN for Virtual Immunohistochemistry Staining of Gland Markers in the Colon 
    Authors: Shikha Dubey, Tushar Kataria, Beatrice Knudsen, Shireen Y. Elhabian arXiv:2308.13182

    To pretrain or not to pretrain? A case study of domain-specific pretraining for semantic segmentation in histopathology 
    Authors: Tushar Kataria, Beatrice Knudsen, Shireen Y. Elhabian arXiv:2307.03275