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
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
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 Elhabian arXiv:2307.03275
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