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Peer-reviewed Review Papers for Digital Pathology and Microscopy Image Analysis

  1. Deep Learning in Microscopy Image Analysis: A Survey
    Fuyong Xing, Yuanpu Xie, Hai Su, Fujun Liu, Lin Yang
    IEEE Transactions on Neural Networks and Learning Systems, vol. 29, no. 10, pp. 4550-4568, 2018
  2. Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review
    Fuyong Xing, Lin Yang
    IEEE Reviews in Biomedical Engineering, vol. 9, pp. 234-263, 2016
    The 2nd Place Prize in the 2019 IEEE Engineering in Medicine and Biology Prize Paper Award


Book Chapters

  1. Artificial Intelligence for Pathology
    Fuyong Xing, XuhongZhang, Toby C.Cornish
    Book Chapter in Artificial Intelligence in Medicine: Technical Basis and Clinical Applications, pp. 183-221, Chapter 11, Elsevier, 2020
  2. Pancreas Segmentation in CT and MRI via Task-Specific Network Design and Recurrent Neural Contextual Learning
    Jinzhen Cai, Le Lu, Fuyong Xing, Lin Yang
    Book Chapter in Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics, pp. 3-21, Chapter 1, Springer, 2019
  3. Deep Learning for Muscle Pathology Image Analysis
    Yuanpu Xie, Fujun Liu, Fuyong Xing, Lin Yang
    Book Chapter in Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics, pp. 23-41, Chapter 2, Springer, 2019
  4. Deep Voting and Beyond Classification for Microscopy Image Analysis
    Yuanpu Xie, Fuyong Xing, Lin Yang
    Book Chapter in Deep Learning for Medical Image Analysis, pp. 155-175, Chapter 7, Elsevier, 2017
  5. Robust Cell Detection and Segmentation in Histopathological Images using Sparse Reconstruction and Stacked Denoising Autoencoders
    Hai Su, Fuyong Xing, Xiangfei Kong, Yuanpu Xie, Shaoting Zhang, Lin Yang
    Book Chapter in Deep Learning and Convolutional Neural Networks for Medical Image Computing, pp. 257-278, Chapter 15, Springer, 2017
  6. Review of Deep Learning Methods in Mammography, Cardiovascular, and Microscopy Image Analysis
    Gustavo Carneiro, Yefeng Zheng, Fuyong Xing, Lin Yang
    Book Chapter in Deep Learning and Convolutional Neural Networks for Medical Image Computing, pp. 11-32, Chapter 2, Springer, 2017
  7. Machine Learning and Its Applications in Microscopic Image Analysis
    Fuyong Xing, Lin Yang
    Book Chapter in Machine Learning and Medical Imaging, pp. 97-127, Chapter 4, Elsevier, 2016

Peer-reviewed Journal Publications

  1. Loss-based Attention for Interpreting Image-level Prediction of Convolutional Neural Networks
    Xiaoshuang Shi, Fuyong Xing, Kaidi Xu, Pingjun Chen, Yun Liang, Zhiyong Lu, Zhenhua Guo
    accepted to IEEE Transactions on Image Processing, 2020
  2. Bidirectional Mapping-Based Domain Adaptation for Nucleus Detection in Cross-Modality Microscopy Images
    Fuyong Xing, Toby C. Cornish, Tellen D. Bennett, Debashis Ghosh
    accepted to IEEE Transactions on Medical Imaging, 2020
  3. A Scalable Optimization Mechanism for Pairwise Based Discrete Hashing
    Xiaoshuang Shi, Fuyong Xing, Zizhao Zhang, Manish Sapkota, Zhenhua Guo, Lin Yang
    IEEE Transactions on Image Processing, vol. 30, pp. 1130-1142, 2020
  4. Generative Adversarial Domain Adaptation for Nucleus Quantification in Images of Tissue Immunohistochemically Stained for Ki-67
    Xuhong Zhang, Toby C. Cornish, Lin Yang, Tellen D. Bennett, Debashis Ghosh, Fuyong Xing
    JCO Clinical Cancer Informatics, vol. 4, pp. 666-679, 2020
  5. Anchor-Based Self-Ensembling for Semi-Supervised Deep Pairwise Hashing
    Xiaoshuang Shi, Zhenhua Guo, Fuyong Xing, Yun Liang, Lin Yang
    International Journal of Computer Vision, vol. 128, pp. 2307-2324, 2020
  6. Graph Temporal Ensembling based Semi-supervised Convolutional Neural Network with Noisy Labels for Histopathology Image Analysis
    Xiaoshuang Shi, Hai Su, Fuyong Xing, Yun Liang, Gang Qu, Lin Yang
    Medical Image Analysis, vol. 60, pp. 101624, 2020
  7. Towards Pixel-to-pixel Deep Nucleus Detection in Microscopy Images
    Fuyong Xing, Yuanpu Xie, Xiaoshuang Shi, Pingjun Chen, Zizhao Zhang, Lin Yang
    BMC Bioinformatics, 20:472, 2019
  8. Pathologist-level Interpretable Whole-slide Cancer Diagnosis with Deep Learning
    Zizhao Zhang, Pingjun Chen, Mason McGough, Fuyong Xing, Chunbao Wang, Marilyn Bui, Yuanpu Xie, Manish Sapkota, Lei Cui, Jasreman Dhillon, Nazeel Ahmad, Farah K. Khalil, Shohreh I. Dickinson, Xiaoshuang Shi, Fujun Liu, Hai Su, Jinzheng Cai, Lin Yang
    Nature Machine Intelligence, vol. 1, pp. 236-245, 2019
  9. Pixel-to-pixel Learning with Weak Supervision for Single-stage Nucleus Recognition in Ki67 Images
    Fuyong Xing, Toby C. Cornish, Tell Bennett, Debashis Ghosh, Lin Yang
    IEEE Transactions on Biomedical Engineering, vol. 66, no. 11, pp. 3088-3097, 2019
  10. Texture Analysis for Muscular Dystrophy Classification in MRI with Improved Class Activation Mapping
    Jinzheng Cai, Fuyong Xing, Abhinandan Batra, Fujun Liu, Glenn A Walter, Krista Vandenborne, Lin Yang
    Pattern Recognition, vol. 86, pp. 368-375, 2019
  11. Deep Convolutional Hashing for Low Dimensional Binary Embedding of Histopathological Images
    Manish Sapkota, Xiaoshuang Shi, Fuyong Xing, Lin Yang
    IEEE Journal of Biomedical and Health Informatics, vol. 23, no. 2, pp. 805-816, 2019
  12. Pairwise Based Deep Ranking Hashing for Histopathology Image Classification and Retrieval
    Xiaoshuang Shi, Manish Sapkota, Fuyong Xing, Fujun Liu, Lei Cui, Lin Yang
    Pattern Recognition, vol. 81, pp. 14-22, 2018
  13. Self-learning for Face Clustering
    Xiaoshuang Shi, Zhenhua Guo, Fuyong Xing, Jinzheng Cai, Lin Yang
    Pattern Recognition, vol. 79, pp. 279-289, 2018
  14. Revisiting Graph Construction for Fast Image Segmentation
    Zizhao Zhang, Fuyong Xing, Hanzi Wang, Yan Yan, Ying Huang, Xiaoshuang Shi, Lin Yang
    Pattern Recognition, vol. 78, pp. 344-357, 2018
  15. Deep Learning in Microscopy Image Analysis: A Survey
    Fuyong Xing, Yuanpu Xie, Hai Su, Fujun Liu, Lin Yang
    IEEE Transactions on Neural Networks and Learning Systems, vol. 29, no. 10, pp. 4550-4568, 2018
  16. Efficient and Robust Cell Detection: A Structured Regression Approach
    Yuanpu Xie, Fuyong Xing, Xiaoshuang Shi, Xiangfei Kong, Hai Su, Lin Yang
    Medical Image Analysis, vol. 44, pp. 245-254, 2018
  17. AIIMD: An Integrated Framework of Automatic Idiopathic Inflammatory Myopathy Diagnosis for Muscle
    Manish Sapkota, Fujun Liu, Yuanpu Xie, Hai Su, Fuyong Xing, Lin Yang
    IEEE Journal of Biomedical and Health Informatics, vol. 22, no. 3, pp. 942-954, 2018
  18. Supervised Graph Hashing for Histopathology Image Retrieval and Classification
    Xiaoshuang Shi, Fuyong Xing, Kaidi Xu, Yuanpu Xie, Hai Su, Lin Yang
    Medical Image Analysis, vol. 22, pp. 117-128, 2017
  19. An Automatic Learning-Based Framework for Robust Nucleus Segmentation
    Fuyong Xing, Yuanpu Xie, Lin Yang
    IEEE Transactions on Medical Imaging, vol. 35, no. 2, pp. 550-566, 2016
  20. Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review
    Fuyong Xing, Lin Yang
    IEEE Reviews in Biomedical Engineering, vol. 9, pp. 234-263, 2016
    The 2nd Place Prize in the 2019 IEEE Engineering in Medicine and Biology Prize Paper Award
  21. Robust Cell Detection of Histopathological Brain Tumor Images Using Sparse Reconstruction and Adaptive Dictionary Selection
    Hai Su, Fuyong Xing, Lin Yang
    IEEE Transactions on Medical Imaging, vol. 35, no. 6, pp. 1575-1586, 2016
  22. High-throughput Histopathological Image Analysis via Robust Cell Segmentation and Hashing
    Xiaofan Zhang, Fuyong Xing, Hai Su, Lin Yang, Shaoting Zhang
    Medical Image Analysis, vol. 26, no. 1, pp. 306-315, 2015
  23. Automatic Ki-67 Counting Using Robust Cell Detection and Online Dictionary Learning
    Fuyong Xing, Hai Su, Janna Neltner, Lin Yang
    IEEE Transactions on Biomedical Engineering, vol. 61, no. 3, pp. 859-870, 2014
  24. Automatic Myonuclear Detection in Isolated Single Muscle Fibers Using Robust Ellipse Fitting and Sparse Representation
    Hai Su, Fuyong Xing, Jonah Lee, Charlotte Peterson, Lin Yang
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 11, no. 4, pp. 714-726, 2014
  25. Novel Image Markers for Non-small Cell Lung Cancer Classification and Survival Prediction
    Hongyuan Wang, Fuyong Xing, Hai Su, Arnold Stromberg, Lin Yang
    BMC Bioinformatics 15:310, 2014
  26. Content-based Histopathology Image Retrieval Using CometCloud
    Xin Qi, Daihou Wang, Ivan Rodero, Javier Diaz-Montes, Rebekah H. Gensure, Fuyong Xing, Hua Zhong, Lauri Goodell, Manish Parashar, David J. Foran, Lin Yang
    BMC Bioinformatics 15:287, 2014
  27. Parallel Content Based Sub-Image Retrieval Using Hierarchical Searching
    Lin Yang, Xin Qi, Fuyong Xing, Tahsin Kurc, Joel Saltz, David J. Foran
    Bioinformatics, vol. 30, no. 7, pp. 996-1002, 2014
  28. Robust Segmentation of Overlapping Cells in Histopathology Specimens Using Parallel Seed Detection and Repulsive Level Set
    Xin Qi, Fuyong Xing, David J. Foran, Lin Yang
    IEEE Transactions on Biomedical Engineering, vol. 59, no. 3, pp. 754-765, 2012
  29. The Analysis of Image Feature Robustness Using CometCloud
    Xin Qi, Hyunjoo Kim, Fuyong Xing, Manish Parashar, David J. Foran, Lin Yang
    Journal of Pathology Informatics 3:33, 2012

Peer-reviewed Conference Proceeding Publications

  1. Loss-based Attention for Deep Multiple Instance Learning
    Xiaoshuang Shi, Fuyong Xing, Yuanpu Xie, Zizhao Zhang, Lei Cui, Lin Yang
    The 34th AAAI Conference on Artificial Intelligence (AAAI), pp. 5742-5749, 2020
  2. Adversarial Domain Adaptation and Pseudo-Labeling for Cross-Modality Microscopy Image Quantification
    Fuyong Xing, Tell Bennett, Debashis Ghosh
    The 22nd International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 11764, pp.740-749, 2019
  3. MDNet: A Semantically and Visually Interpretable Medical Image Diagnosis Network
    Zizhao Zhang, Yuanpu, Xie, Fuyong Xing, Mason Mcgough, Lin Yang
    IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 6428-6436, 2017
    Oral Presentation
  4. Cell Encoding for Histopathology Image Classification
    Xiaoshuang Shi, Fuyong Xing, Yuanpu Xie, Lin Yang
    The 20th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 10434, pp. 30-38, 2017
  5. Improving Deep Pancreas Segmentation in CT and MRI Image via Recurrent Neural Contextual Learning and Direct Loss Function
    Jinzheng Cai, Le Lu, Yuanpu Xie, Fuyong Xing, Lin Yang
    The 20th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 10435, pp. 674–682, 2017
  6. Asymmetric Discrete Graph Hashing
    Xiaoshuang Shi, Fuyong Xing, Kaidu Xu, Manish Sapkota, Lin Yang
    The Proceedings of 31st AAAI Conference on Artificial Intelligence (AAAI-17), pp. 2541-2547, 2017
  7. Transfer Shape Modeling Towards High-throughput Microscopy Image Segmentation
    Fuyong Xing, Xiaoshuang Shi, Zizhao Zhang, Jinzheng Cai, Yuanpu Xie, Lin Yang
    The 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 9902, pp. 183-190, 2016
    Oral Presentation
  8. Pancreas Segmentation Using Graph based Data Fusion with Convolutional Neural Networks
    Jinzheng Cai, Le Lu, Qian Yin, Zizhao Zhang, Fuyong Xing, Lin Yang
    The 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 9901, pp. 442-450, 2016
  9. Kernel-Based Supervised Discrete Hashing for Image Retrieval
    Xiaoshuang Shi, Fuyong Xing, Jinzheng Cai, Zizhao Zhang, Yuanpu Xie, Lin Yang
    European Conference on Computer Vision (ECCV), pp. 419-433, 2016
  10. SemiContour: A Semi-supervised Learning Approach for Contour Detection
    Zizhao Zhang, Fuyong Xing, Xiaoshuang Shi, Lin Yang
    IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 251-259, 2016
  11. Fast Cell Segmentation Using Scalable Sparse Manifold Learning and Affine Transform-approximated Active Contour
    Fuyong Xing, Lin Yang
    The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 9351, pp. 332-339, 2015
  12. Robust Muscle Cell Quantification Using Structured Edge Detection and Hierarchical Segmentation
    Fujun Liu, Fuyong Xing, Zizhao Zhang, Mason Mcgough, Lin Yang
    The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 9351, pp. 324-331, 2015
  13. Beyond Classification: Structured Regression for Robust Cell Detection Using Convolutional Neural Network
    Yuanpu Xie, Fuyong Xing, Xiangfei Kong, Hai Su, Lin Yang
    The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 9351, pp. 358-365, 2015
    MICCAI Student Travel Awards; Runners Up for Young Scientist Awards
  14. Robust Cell Detection and Segmentation in Histopathological Images Using Sparse Reconstruction and Stacked Denoising Autoencoders
    Hai Su, Fuyong Xing, Xiangfei Kong, Yuanpu Xie, Shaoting Zhang, Lin Yang
    The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 9351, pp. 383-390, 2015
    Oral Presentation; Runners Up for Young Scientist Awards
  15. Deep Voting: A Robust Approach Toward Nucleus Localization in Microscopy Images
    Yuanpu Xie, Xiangfei Kong, Fuyong Xing, Fujun Liu, Hai Su, Lin Yang
    The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 9351, pp. 374-382, 2015
  16. Unsupervised Shape Prior Modeling for Cell Segmentation in Neuroendocrine Tumor
    Fuyong Xing, Lin Yang
    The 12th International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, pp. 1443-1446, 2015
    ISBI National Institutes of Health (NIH) Travel Award
  17. Region Segmentation in Histopathological Breast Cancer Images Using Deep Convolutional Neural Network
    Hai Su, Fujun Liu, Yuanpu Xie, Fuyong Xing, Sreenivasan Meyyappan, Lin Yang
    The 12th International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, pp. 55-58, 2015
  18. Automatic Muscle Perimysium Annotation Using Deep Convolutional Neural Network
    Manish Sapkota, Fuyong Xing, Hai Su, Lin Yang
    The 12th International Symposium on Biomedical Imaging (ISBI): From Nano to Macro pp. 205-208, 2015
  19. Robust Cell Segmentation Using Region Selection with Dynamic Programming
    Fujun Liu, Fuyong Xing, Lin Yang
    The 11th International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, pp. 521-524, 2014
    Oral Presentation
  20. Touching Adipocyte Cells Decomposition Using Combinatorial Optimization
    Fujun Liu, Fuyong Xing, Hai Su, Lin Yang
    The 11th International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, pp. 1340-1343, 2014
    Oral Presentation
  21. Robust Selection-Based Sparse Shape Model for Lung Cancer Image Segmentation
    Fuyong Xing, Lin Yang
    The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 8151, pp. 404-412, 2013
    MICCAI Student Travel Awards
  22. An Integrated Framework for Automatic Ki-67 Scoring in Pancreatic Neuroendocrine Tumor
    Fuyong Xing, Hai Su, Lin Yang
    The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 8149, pp. 436-443, 2013
  23. Robust Cell Segmentation for Non-Small Cell Lung Cancer
    Fuyong Xing, Lin Yang
    The 10th International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, pp. 386-389, 2013
  24. Learning Based Automatic Detection of Myonuclei in Isolated Single Skeletal Muscle Fibers Using Multi-Focus Image Fusion
    Hai Su, Fuyong Xing, Jonah D. Lee, Charlotte A. Peterson, Lin Yang
    The 10th International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, pp. 432-435, 2013

Peer-reviewed Workshop Publications

  1. Skeletal Muscle Cell Segmentation Using Distributed Convolutional Neural Network
    Manish Sapkota, Fuyong Xing, Fujun Liu, Lin Yang
    High Performance Computing for Biomedical Image Analysis Workshop in conjunction with the 18th International Conference on Medical Image Computing and Computer Assisted Intervention (HPC-MICCAI), Munich, Germany, 2015
  2. High-throughput Automatic Muscle Image Segmentation Using Cloud Computing and Multi-core Programming
    Zizhao Zhang, Fuyong Xing, Fujun Liu, Lin Yang
    High Performance Computing for Biomedical Image Analysis Workshop in conjunction with the 18th International Conference on Medical Image Computing and Computer Assisted Intervention (HPC-MICCAI), Munich, Germany, 2015
  3. Histopathological Lung Cancer Image Mining Using Kd-tree and MapReduce
    Fuyong Xing, Manish Sapkota, Lin Yang
    High Performance Computing for Biomedical Image Analysis Workshop in conjunction with the 17th International Conference on Medical Image Computing and Computer Assisted Intervention (HPC-MICCAI), Boston, USA, 2014
  4. Exploring Online Nuclear Segmentation on Large Fluorescence Brain Tumor Images Using CometCloud
    Xin Qi, Daihou Wang, Javier Diaz-Montes, Ivan Rodero, Tony Pan, Abulimit Aji, Lee Cooper, Fuyong Xing, Manish Parashar, David J. Foran, Lin Yang
    High Performance Computing for Biomedical Image Analysis Workshop in conjunction with the 16th International Conference on Medical Image Computing and Computer Assisted Intervention (HPC-MICCAI), Nagoya, Japan, 2013
  5. Content-based Parallel Sub-image Retrieval
    Fuyong Xing, Xin Qi, David J. Foran, Tahsin Kurc, Joel Saltz, Lin Yang
    Data- and Compute-Intensive Clinical and Translational Imaging Applications Workshop in conjunction with the 15th International Conference on Medical Image Computing and Computer Assisted Intervention (DCICTIA-MICCAI), Nice, France, 2012
  6. Content-based Image Retrieval on Imaged Peripheral Blood Smear Specimens Using High Performance Computation
    Xin Qi, Fuyong Xing, Meghana Ghadge, Ivan Rodero, Moustafa Abdelbaky, Manish Parashar, Evita Sadimin, David J. Foran, Lin Yang
    Data- and Compute-Intensive Clinical and Translational Imaging Applications Workshop in conjunction with the 15th International Conference on Medical Image Computing and Computer Assisted Intervention (DCICTIA-MICCAI), Nice, France, 2012
  7. The Analysis of Image Texture Feature Robustness Using CometCloud
    Xin Qi, Hyunjoo Kim, Fuyong Xing, Manish Parashar, David J. Foran, Lin Yang
    High Performance Computing for Biomedical Image Analysis Workshop in conjunction with the 14th International Conference on Medical Image Computing and Computer Assisted Intervention (HPC-MICCAI), Toronto, Canada, 2011
  8. GPU Enabled Parallel Touching Cell Segmentation Using Mean Shift Based Seed Detection and Repulsive Level Set
    Xin Qi, Fuyong Xing, David J. Foran, Lin Yang
    High Performance Computing for Biomedical Image Analysis Workshop in conjunction with the 14th International Conference on Medical Image Computing and Computer Assisted Intervention (HPC-MICCAI), Beijing, China, 2010

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