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SCI Collaboration

Cell and Gland
Visualization of Computer Learned Features

Computational Pathology

We use our knowledge in diagnostic and molecular pathology to motivate the development of machine learning algorithms. The algorithms 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.

Meet our collaborators

 

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