A Novel Stochastic Combination of 3D Texture Features for Automated Segmentation of Prostatic Adenocarcinoma from High Resolution MRI. - Anant Madabhushi; Michael D. Feldman; Dimitris N. Metaxas; Deborah Chute; John Tomaszewski 001 (MICCAI (1), 2003)

Graph Embedding to Improve Supervised Classification and Novel Class Detection: Application to Prostate Cancer. - Anant Madabhushi; Jianbo Shi; Mark Rosen; John Tomaszewski 001; Michael D. Feldman (MICCAI, 2005)

Automated detection of prostatic adenocarcinoma from high-resolution ex vivo MRI. - Anant Madabhushi; Michael D. Feldman; Dimitris N. Metaxas; John Tomaszewski 001; Deborah Chute (IEEE Trans. Medical Imaging, 2005)

Comparing Ensembles of Learners: Detecting Prostate Cancer from High Resolution MRI. - Anant Madabhushi; Jianbo Shi; Michael D. Feldman; Mark Rosen; John Tomaszewski 001 (CVAMIA, 2006)

Detecting Prostatic Adenocarcinoma From Digitized Histology Using a Multi-Scale Hierarchical Classification Approach. - Scott Doyle; Carlos Rodriguez; Anant Madabhushi; John Tomaszewski 001; Michael D. Feldman (EMBC, 2006)

A Boosting Cascade for Automated Detection of Prostate Cancer from Digitized Histology. - Scott Doyle; Anant Madabhushi; Michael D. Feldman; John Tomaszewski 001 (MICCAI (2), 2006)

Registering Histological and MR Images of Prostate for Image-Based Cancer Detection. - Yiqiang Zhan; Michael D. Feldman; John Tomaszewski 001; Christos Davatzikos; Dinggang Shen (MICCAI (2), 2006)

A Combined Feature Ensemble Based Mutual Information Scheme for Robust Inter-Modal, Inter-Protocol Image Registration. - Jonathan Chappelow; Anant Madabhushi; Mark Rosen; John Tomaszewski 001; Michael D. Feldman (ISBI, 2007)

Automated Grading of Prostate Cancer Using Architectural and Textural Image Features. - Scott Doyle; Mark I. Hwang; Kinsuk Shah; Anant Madabhushi; Michael D. Feldman; John Tomaszewski 001 (ISBI, 2007)

Multimodal image registration of ex vivo 4 Tesla MRI with whole mount histology for prostate cancer detection. - Jonathan Chappelow; Anant Madabhushi; Mark Rosen; John Tomaszewski 001; Michael D. Feldman (Image Processing, 2007)

Automated grading of breast cancer histopathology using spectral clusteringwith textural and architectural image features. - Scott Doyle; Shannon Agner; Anant Madabhushi; Michael D. Feldman; John Tomaszewski 001 (ISBI, 2008)

Automated gland and nuclei segmentation for grading of prostate and breast cancer histopathology. - Shivang Naik; Scott Doyle; Shannon Agner; Anant Madabhushi; Michael D. Feldman; John Tomaszewski 001 (ISBI, 2008)

Improving supervised classification accuracy using non-rigid multimodal image registration: detecting prostate cancer. - Jonathan Chappelow; Satish Viswanath; James Monaco; Mark Rosen; John Tomaszewski 001; Michael D. Feldman; Anant Madabhushi (Computer-Aided Diagnosis, 2008)

Non-rigid registration between histological and MR images of the prostate: A joint segmentation and registration framework. - Yangming Ou; Dinggang Shen; Michael D. Feldman; John Tomaszewski 001; Christos Davatzikos (CVPR Workshops, 2009)

Segmentation and Classification of Triple Negative Breast Cancers Using DCE-MRI. - Shannon Agner; Jun Xu 005; Hussain Fatakdawala; Shridar Ganesan; Anant Madabhushi; Sarah Englander; Mark Rosen; Kathleen Thomas; Mitchell D. Schnall; Michael D. Feldman; John Tomaszewski 001 (ISBI, 2009)

A Knowledge Representation Framework for Integration, Classification of Multi-Scale Imaging and Non-Imaging Data: Preliminary Results in Predicting Prostate Cancer Recurrence by Fusing Mass Spectrometry and Histology. - George Lee 002; Scott Doyle; James Monaco; Michael D. Feldman; Stephen R. Master; John Tomaszewski 001; Anant Madabhushi (ISBI, 2009)

A boosted distance metric: application to content based image retrieval and classification of digitized histopathology. - Jay Naik; Scott Doyle; Ajay Basavanhally; Shridar Ganesan; Michael D. Feldman; John Tomaszewski 001; Anant Madabhushi (Computer-Aided Diagnosis, 2009)

Probabilistic pairwise Markov models: application to prostate cancer detection. - James Monaco; John Tomaszewski 001; Michael D. Feldman; Mehdi Moradi; Parvin Mousavi; Alexander Boag; Chris Davidson; Purang Abolmaesumi; Anant Madabhushi (Image Processing, 2009)

Evaluation of effects of jpeg2000 compression on a computer-aided detection system for prostate cancer on digitized histopathology. - Scott Doyle; James Monaco; Anant Madabhushi; Stefan Lindholm; Patric Ljung; Lance Ladic; John Tomaszewski 001; Michael D. Feldman (ISBI, 2010)

HistoCAD: Machine Facilitated Quantitative Histoimaging with Computer Assisted Diagnosis. - John E. Tomaszewski (Prostate Cancer Imaging, 2010)

High-Throughput Prostate Cancer Gland Detection, Segmentation, and Classification from Digitized Needle Core Biopsies. - Jun Xu 005; Rachel Sparks; Andrew Janowczyk; John Tomaszewski 001; Michael D. Feldman; Anant Madabhushi (Prostate Cancer Imaging, 2010)

Computer-assisted targeted therapy (CATT) for prostate radiotherapy planning by fusion of CT and MRI. - Jonathan Chappelow; Stefan Both; Satish Viswanath; Stephen Hahn 002; Michael D. Feldman; Mark Rosen; John Tomaszewski 001; Neha Vapiwala; Pratik Patel; Anant Madabhushi (Image-Guided Procedures, 2010)

High-throughput detection of prostate cancer in histological sections using probabilistic pairwise Markov models. - James Monaco; John Tomaszewski 001; Michael D. Feldman; Ian S. Hagemann; Mehdi Moradi; Parvin Mousavi; Alexander Boag; Chris Davidson; Purang Abolmaesumi; Anant Madabhushi (Medical Image Anal., 2010)

Computerized Image-Based Detection and Grading of Lymphocytic Infiltration in HER2+ Breast Cancer Histopathology. - Ajay Basavanhally; Shridar Ganesan; Shannon Agner; James Monaco; Michael D. Feldman; John Tomaszewski 001; Gyan Bhanot; Anant Madabhushi (IEEE Trans. Biomed. Eng., 2010)

Expectation-Maximization-Driven Geodesic Active Contour With Overlap Resolution (EMaGACOR): Application to Lymphocyte Segmentation on Breast Cancer Histopathology. - Hussain Fatakdawala; Jun Xu 005; Ajay Basavanhally; Gyan Bhanot; Shridar Ganesan; Michael D. Feldman; John Tomaszewski 001; Anant Madabhushi (IEEE Trans. Biomed. Eng., 2010)

Supervised regularized canonical correlation analysis: Integrating histologic and proteomic data for predicting biochemical failures. - Abhishek Golugula; George Lee 002; Stephen R. Master; Michael D. Feldman; John Tomaszewski 001; Anant Madabhushi (EMBC, 2011)

Spatially weighted mutual information (SWMI) for registration of digitally reconstructed ex vivo whole mount histology and in vivo prostate MRI. - Pratik Patel; Jonathan Chappelow; John Tomaszewski 001; Michael D. Feldman; Mark Rosen; Natalie Shih; Anant Madabhushi (EMBC, 2011)

Detection of prostate cancer on histopathology using color fractals and Probabilistic Pairwise Markov models. - Elaine Yu; James P. Monaco; John Tomaszewski 001; Natalie Shih; Michael D. Feldman; Anant Madabhushi (EMBC, 2011)

A boosted classifier for integrating multiple fields of view: Breast cancer grading in histopathology. - Ajay Basavanhally; Shridar Ganesan; Natalie Shih; Carolyn Mies; Michael D. Feldman; John Tomaszewski 001; Anant Madabhushi (ISBI, 2011)

Cascaded multi-class pairwise classifier (CascaMPa) for normal, cancerous, and cancer confounder classes in prostate histology. - Scott Doyle; Michael D. Feldman; John Tomaszewski 001; Natalie Shih; Anant Madabhushi (ISBI, 2011)

Incorporating domain knowledge for tubule detection in breast histopathology using O'Callaghan neighborhoods. - Ajay Basavanhally; Elaine Yu; Jun Xu 005; Shridar Ganesan; Michael D. Feldman; John Tomaszewski 001; Anant Madabhushi (Computer-Aided Diagnosis, 2011)

An Active Learning Based Classification Strategy for the Minority Class Problem: Application to Histopathology Annotation. - Scott Doyle; James Monaco; Michael D. Feldman; John Tomaszewski 001; Anant Madabhushi (BMC Bioinform., 2011)

Supervised Regularized Canonical Correlation Analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery. - Abhishek Golugula; George Lee 002; Stephen R. Master; Michael D. Feldman; John Tomaszewski 001; David W. Speicher; Anant Madabhushi (BMC Bioinform., 2011)

HistoStitcher©: An interactive program for accurate and rapid reconstruction of digitized whole histological sections from tissue fragments. - Jonathan Chappelow; John Tomaszewski 001; Michael D. Feldman; Natalie Shih; Anant Madabhushi (Comput. Medical Imaging Graph., 2011)

Determining histology-MRI slice correspondences for defining MRI-based disease signatures of prostate cancer. - Gaoyu Xiao; B. Nicolas Bloch; Jonathan Chappelow; Elizabeth Genega; Neil Rofsky; Robert E. Lenkinski; John Tomaszewski 001; Michael D. Feldman; Mark Rosen; Anant Madabhushi (Comput. Medical Imaging Graph., 2011)

Incorporating the whole-mount prostate histology reconstruction program Histostitcher into the extensible imaging platform (XIP) framework. - Robert Toth; Jonathan Chappelow; Christoph Vetter; Oliver Kutter; Christoph Russ; Michael D. Feldman; John Tomaszewski 001; Natalie Shih; Anant Madabhushi (Computer-Aided Diagnosis, 2012)

Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer. - Scott Doyle; Michael D. Feldman; Natalie Shih; John Tomaszewski 001; Anant Madabhushi (BMC Bioinform., 2012)

A Boosted Bayesian Multiresolution Classifier for Prostate Cancer Detection From Digitized Needle Biopsies. - Scott Doyle; Michael D. Feldman; John Tomaszewski 001; Anant Madabhushi (IEEE Trans. Biomed. Eng., 2012)

Co-occurring gland tensors in localized cluster graphs: Quantitative histomorphometry for predicting biochemical recurrence for intermediate grade prostate cancer. - George Lee 002; Rachel Sparks; Sahirzeeshan Ali; Anant Madabhushi; Michael D. Feldman; Stephen R. Master; Natalie Shih; John Tomaszewski 001 (ISBI, 2013)

Identifying in vivo DCE MRI parameters correlated with ex vivo quantitative microvessel architecture: A radiohistomorphometric approach. - Asha Singanamalli; Rachel Sparks; Mirabela Rusu; Natalie Shih; Amy Ziober; John Tomaszewski 001; Mark Rosen; Michael D. Feldman; Anant Madabhushi (Digital Pathology, 2013)

Multi-Field-of-View Framework for Distinguishing Tumor Grade in ER+ Breast Cancer From Entire Histopathology Slides. - Ajay Basavanhally; Shridar Ganesan; Michael D. Feldman; Natalie Shih; Carolyn Mies; John Tomaszewski 001; Anant Madabhushi (IEEE Trans. Biomed. Eng., 2013)

Automatic detection of invasive ductal carcinoma in whole slide images with convolutional neural networks. - Angel Cruz-Roa; Ajay Basavanhally; Fabio A. González 001; Hannah Gilmore; Michael D. Feldman; Shridar Ganesan; Natalie Shih; John Tomaszewski 001; Anant Madabhushi (Digital Pathology, 2014)

Cascaded ensemble of convolutional neural networks and handcrafted features for mitosis detection. - Haibo Wang; Angel Cruz-Roa; Ajay Basavanhally; Hannah Gilmore; Natalie Shih; Mike Feldman; John Tomaszewski 001; Fabio A. González 001; Anant Madabhushi (Digital Pathology, 2014)

Spectral embedding-based registration (SERg) for multimodal fusion of prostate histology and MRI. - Eileen Hwuang; Mirabela Rusu; Sudha Karthigeyan; Shannon Agner; Rachel Sparks; Natalie Shih; John Tomaszewski 001; Mark Rosen; Michael D. Feldman; Anant Madabhushi (Image Processing, 2014)

Supervised Multi-View Canonical Correlation Analysis (sMVCCA): Integrating Histologic and Proteomic Features for Predicting Recurrent Prostate Cancer. - George Lee 002; Asha Singanamalli; Haibo Wang; Michael D. Feldman; Stephen R. Master; Natalie N. C. Shih; Elaine Spangler; Timothy R. Rebbeck; John Tomaszewski 001; Anant Madabhushi (IEEE Trans. Medical Imaging, 2015)

Quantification of tumor morphology via 3D histology: application to oral cavity cancers. - Scott Doyle; Margaret Brandwein-Gensler; John Tomaszewski 001 (Digital Pathology, 2016)

Automated renal histopathology: digital extraction and quantification of renal pathology. - Pinaki Sarder; Brandon Ginley; John Tomaszewski 001 (Digital Pathology, 2016)

Automatic computational labeling of glomerular textural boundaries. - Brandon Ginley; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2017)

Leveraging unsupervised training sets for multi-scale compartmentalization in renal pathology. - Brendon Lutnick; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2017)

Data-driven sampling method for building 3D anatomical models from serial histology. - Snehal Ulhas Salunke; Tova Ablove; Theresa Danforth; John Tomaszewski 001; Scott Doyle (Digital Pathology, 2017)

Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. - Metin N. Gurcan; John Tomaszewski 001; James A. Overton; Scott Doyle; Alan Ruttenberg; Barry Smith 001 (J. Biomed. Informatics, 2017)

Computational analysis of the structural progression of human glomeruli in diabetic nephropathy. - Brandon G. Ginley; John Tomaszewski 001; Kuang-Yu Jen; Agnes B. Fogo; Sanjay Jain 006; Pinaki Sarder (Digital Pathology, 2018)

Glomerular detection and segmentation from multimodal microscopy images using a Butterworth band-pass filter. - Darshana Govind; Brandon Ginley; Brendon Lutnick; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2018)

Deep variational auto-encoders for unsupervised glomerular classification. - Brendon Lutnick; Rabi Yacoub; Kuang-Yu Jen; John Tomaszewski 001; Sanjay Jain 006; Pinaki Sarder (Digital Pathology, 2018)

Examining structural changes in diabetic nephropathy using inter-nuclear distances in glomeruli: a comparison of variously automated methods. - Olivier Simon; Rabi Yacoub; Sanjay Jain 006; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2018)

Iterative annotation to ease neural network training: Specialized machine learning in medical image analysis. - Brendon Lutnick; Brandon Ginley; Darshana Govind; Sean D. McGarry; Peter S. LaViolette; Rabi Yacoub; Sanjay Jain 006; John Tomaszewski 001; Kuang-Yu Jen; Pinaki Sarder (CoRR, 2018)

Examining structural patterns and causality in diabetic nephropathy using inter-glomerular distance and Bayesian graphical models. - Aurijoy Majumdar; Kuang-Yu Jen; Sanjay Jain 006; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2019)

An integrated iterative annotation technique for easing neural network training in medical image analysis. - Brendon Lutnick; Brandon Ginley; Darshana Govind; Sean D. McGarry; Peter S. LaViolette; Rabi Yacoub; Sanjay Jain 006; John Tomaszewski 001; Kuang-Yu Jen; Pinaki Sarder (Nat. Mach. Intell., 2019)

Probabilistic modelling of diabetic nephropathy progression. - Samuel P. Border; Kuang-Yu Jen; Washington L. C. dos-Santos; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2020)

The presence and location of podocytes in glomeruli as affected by diabetes mellitus. - Kathryn E. Maraszek; Briana A. Santo; Rabi Yacoub; John Tomaszewski 001; Imtiaz Mohammad; Amber M. Worral; Pinaki Sarder (Digital Pathology, 2020)

Generative modeling for renal microanatomy. - Leema Krishna Murali; Brendon Lutnick; Brandon Ginley; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2020)

Neutrophil Extracellular Traps (NETs): an unexplored territory in renal pathobiology, a pilot computational study. - Briana A. Santo; Brahm H. Segal; John Tomaszewski 001; Imtiaz Mohammad; Amber M. Worral; Sanjay Jain 006; Michelle B. Visser; Pinaki Sarder (Digital Pathology, 2020)

Clot organization on histology is associated with radiomics features that predict treatment outcomes from mechanical thrombectomy. - Tatsat R. Patel; Mohammad Waqas; Sarah Fricano; Adam A. Dmytriw; John Tomaszewski 001; Elad I. Levy; Kenneth V. Snyder; Jason M. Davies; Adnan H. Siddiqui; Vincent M. Tutino (Digital Pathology, 2021)

A distributed system improves inter-observer and AI concordance in annotating interstitial fibrosis and tubular atrophy. - Avinash Kammardi Shashiprakash; Brendon Lutnick; Brandon Ginley; Darshana Govind; Nicholas J. Lucarelli; Kuang-Yu Jen; Avi Z. Rosenberg; Anatoly Urisman; Vighnesh Walavalkar; Jonathan E. Zuckerman; Marco Delsante; Mei Lin Z. Bissonnette; et al. (Digital Pathology, 2021)

HistoLens: a generalizable tool for increasing accessibility and interpretability of quantitative analyses in digital pathology. - Samuel P. Border; Brandon Ginley; John E. Tomaszewski; Pinaki Sarder (Digital and Computational Pathology, 2022)

Integrating image analysis with single cell RNA-seq data to study podocyte-specific changes in diabetic kidney disease. - Darshana Govind; Saber Meamardoost; Rabi Yacoub; Rudiyanto Gunawan; John E. Tomaszewski; Pinaki Sarder (Digital and Computational Pathology, 2022)

Computational integration of renal histology and urinary proteomics using neural networks. - Nicholas J. Lucarelli; Donghwan Yun; Dohyun Han; Brandon Ginley; Kyung Chul Moon; Avi Rosenberg; John Tomaszewski 001; Seung Seok Han; Pinaki Sarder (Digital and Computational Pathology, 2022)