BIN LI (Ben) | University of Oxford

About Me

I obtained my PhD in Biomedical Engineering from the University of Wisconsin-Madison, where I was supervised by Dr Kevin Eliceiri. My research focuses on developing computational approaches to analyzing complex biological/histological image data for precision medicine. Currently, I am a postdoctoral researcher in the Dr Jens Rittscher group at the Institute of Biomedical Engineering, University of Oxford. I work closely with Dr Matthias Friedrich on characterizing image biomarkers for Inflammatory Bowel Disease.

Research Interests

Digital Pathology: whole slide image analysis, computational histopathology
Machine Learning: self-supervised learning, weakly-supervised learning, generative models
Tissue Imaging: tumor microenvironment, multiphoton microscopy, whole slide imaging

News

[Aug. 2023] Our paper about collagen fiber analysis and sythetic training data generation is accepted to Medical Image Analysis.

Publications

Collagen fiber centerline tracking in fibrotic tissue via deep neural networks with variational autoencoder-based synthetic training data generation

Hyojoon Park, Bin Li, Yuming Liu, Michael S Nelson, Helen M Wilson, Eftychios Sifakis, Kevin W Eliceiri

Medical Image Analysis, 2023.

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Detection of crystals in joint fluid aspirates with polychromatic polarisation microscopy

Husam Jum'ah, Michael Shribak, Adib Keikhosravi, Bin Li, Yuming Liu, Deya Obaidat, Kevin W Eliceiri, Agnes Loeffler, Salman Ayub

Annals of the Rheumatic Diseases, 2023.

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Hardware-software co-design of an open-source automatic multimodal whole slide histopathology imaging system

Bin Li, Michael S Nelson, Jenu V Chacko, Nathan Cudworth, Kevin W Eliceiri

Journal of Biomedical Optics, 2023.

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Computationally efficient adaptive decompression for whole slide image processing

Zheyu Li, Bin Li, Kevin W Eliceiri, Vijaykrishnan Narayanan

Biomedical Optics Express, 2023.

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Differentiation of pancreatic ductal adenocarcinoma and chronic pancreatitis using graph neural networks on histopathology and collagen fiber features

Bin Li, Michael S Nelson, Omid Savari, Agnes G Loeffler, Kevin W Eliceiri

Journal of Biomedical Optics, 2022.

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Mat - Processing in-memory acceleration for long-sequence attention

Minxuan Zhou, Yunhui Guo, Weihong Xu, Bin Li, Kevin W Eliceiri, Tajana Rosing

58th ACM/IEEE Design Automation Conference (DAC), 2022.

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Real-time polarization microscopy of fibrillar collagen in histopathology

Adib Keikhosravi, Michael Shribak, Matthew W Conklin, Yuming Liu, Bin Li, Agnes Loeffler, Richard M Levenson, Kevin W Eliceiri

Scientific reports, 2021.

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Pycro-Manager - open-source software for customized and reproducible microscope control

Henry Pinkard, Nico Stuurman, Ivan E Ivanov, Nicholas M Anthony, Wei Ouyang, Bin Li, Bin Yang, Mark A Tsuchida, Bryant Chhun, Grace Zhang, Ryan Mei, Michael Anderson, Douglas P Shepherd, Ian Hunt-Isaak, Raymond L Dunn, Wiebke Jahr, Saul Kato, Loïc A Royer, Jay R Thiagarajah, Kevin W Eliceiri, Emma Lundberg, Shalin B Mehta, Laura Waller

Nature methods, 2021.

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Single image super-resolution for whole slide image using convolutional neural networks and self-supervised color normalization

Bin Li, Adib Keikhosravi, Agnes G Loeffler, Kevin W Eliceiri

Medical Image Analysis, 2021.

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Dual-stream multiple instance learning network for whole slide image classification with self-supervised contrastive learning

Bin Li, Yin Li, Kevin W Eliceiri

Proceedings of the IEEE/CVF conference on computer vision and pattern recognition (CVPR), 2021.

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Services

Conference Reviewers

IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) 2021