Measurement of Infarct Volume in Stroke Patients Using Adaptive Segmentation of Diffusion Weighted MR Images. - Anne L. Martel; Steven J. Allder; Gota S. Delay; Paul S. Morgan; Alan R. Moody (MICCAI, 1999)

Extracting parametric images from dynamic contrast-enhanced MRI studies of the brain using factor analysis. - Anne L. Martel; Alan R. Moody; Steven J. Allder; Gota S. Delay; Paul S. Morgan (Medical Image Anal., 2001)

Piecewise-Quadrilateral Registration by Optical Flow - Applications in Contrast-Enhanced MR Imaging of the Breast. - Michael S. Froh; David C. Barber; Kristy K. Brock; Donald B. Plewes; Anne L. Martel (MICCAI (2), 2006)

Data Weighting for Principal Component Noise Reduction in Contrast Enhanced Ultrasound. - Gord Lueck; Peter N. Burns; Anne L. Martel (MICCAI (2), 2006)

A Fast Method of Generating Pharmacokinetic Maps from Dynamic Contrast-Enhanced Images of the Breast. - Anne L. Martel (MICCAI (2), 2006)

Can Bilateral Asymmetry Analysis of Breast MR Images Provide Additional Information for Detection of Breast Diseases? - Ricardo José Ferrari; Kimberley A. Hill; Donald B. Plewes; Anne L. Martel (SIBGRAPI, 2008)

Classification of Dynamic Contrast-Enhanced Magnetic Resonance Breast Lesions by Support Vector Machines. - Jacob E. D. Levman; Tony Leung; Petrina Causer; Donald B. Plewes; Anne L. Martel (IEEE Trans. Medical Imaging, 2008)

Hepatic Perfusion Imaging Using Factor Analysis of Contrast Enhanced Ultrasound. - Gord Lueck; T. K. Kim; Peter N. Burns; Anne L. Martel (IEEE Trans. Medical Imaging, 2008)

A PDE Approach to Coupled Super-Resolution with Non-parametric Motion. - Mehran Ebrahimi; Anne L. Martel (EMMCVPR, 2009)

Image Registration under Varying Illumination: Hyper-Demons Algorithm. - Mehran Ebrahimi; Anne L. Martel (EMMCVPR, 2009)

A General PDE-Framework for Registration of Contrast Enhanced Images. - Mehran Ebrahimi; Anne L. Martel (MICCAI (1), 2009)

Multi-Modality fiducial marker for validation of registration of medical images with histology. - Rushin Shojaii; Anne L. Martel (Image Processing, 2010)

Image registration for abdominal dynamic contrast-enhanced magnetic resonance images. - Anthony Lausch; Mehran Ebrahimi; Anne L. Martel (ISBI, 2011)

Automatic mask generation using independent component analysis in dynamic contrast enhanced-MRI. - Hatef Mehrabian; Ian Pang; Chaitanya Chandrana; Rajiv Chopra; Anne L. Martel (ISBI, 2011)

Automatic model-based 3D segmentation of the breast in MRI. - Cristina Gallego-Ortiz; Anne L. Martel (Image Processing, 2011)

Validation of histology image registration. - Rushin Shojaii; Tigran Karavardanyan; Martin J. Yaffe; Anne L. Martel (Image Processing, 2011)

Increasing specimen coverage using digital whole-mount breast pathology: Implementation, clinical feasibility and application in research. - Gina M. Clarke; Chris Peressotti; Paul Constantinou; Danoush Hosseinzadeh; Anne L. Martel; Martin J. Yaffe (Comput. Medical Imaging Graph., 2011)

An adaptive complex independent component analysis to analyze dynamic contrast enhanced-MRI. - Hatef Mehrabian; Ian Pang; Rajiv Chopra; Anne L. Martel (ISBI, 2012)

Editorial for the MEDIA Special Issue on MICCAI 2011. - Gabor Fichtinger; Anne L. Martel; Terry M. Peters (Medical Image Anal., 2012)

A constrained independent component analysis technique for artery-vein separation of two-photon laser scanning microscopy images of the cerebral microvasculature. - Hatef Mehrabian; Liis Lindvere; Bojana Stefanovic; Anne L. Martel (Medical Image Anal., 2012)

Using independent components analysis to calculate intravascular contrast agent concentration in prostate cancer. - Hatef Mehrabian; Masoom A. Haider; Anne L. Martel (ISBI, 2013)

A Gauss-Newton approach to joint image registration and intensity correction. - Mehran Ebrahimi; Anthony Lausch; Anne L. Martel (Comput. Methods Programs Biomed., 2013)

Feature Selection in Computer-Aided Breast Cancer Diagnosis via Dynamic Contrast-Enhanced Magnetic Resonance Images. - Megan Rakoczy; Donald McGaughey; Michael J. Korenberg; Jacob E. D. Levman; Anne L. Martel (J. Digit. Imaging, 2013)

Calculation of Intravascular Signal in Dynamic Contrast Enhanced-MRI Using Adaptive Complex Independent Component Analysis. - Hatef Mehrabian; Rajiv Chopra; Anne L. Martel (IEEE Trans. Medical Imaging, 2013)

Classification of breast lesions presenting as mass and non-mass lesions. - Cristina Gallego-Ortiz; Anne L. Martel (Computer-Aided Diagnosis, 2014)

A Vector Machine Formulation with Application to the Computer-Aided Diagnosis of Breast Cancer from DCE-MRI Screening Examinations. - Jacob E. D. Levman; Ellen Warner; Petrina Causer; Anne L. Martel (J. Digit. Imaging, 2014)

Semi-Automatic Region-of-Interest Segmentation Based Computer-Aided Diagnosis of Mass Lesions from Dynamic Contrast-Enhanced Magnetic Resonance Imaging Based Breast Cancer Screening. - Jacob E. D. Levman; Ellen Warner; Petrina Causer; Anne L. Martel (J. Digit. Imaging, 2014)

Clustering Analysis for Semi-supervised Learning Improves Classification Performance of Digital Pathology. - Mohammad Peikari; Judit T. Zubovits; Gina M. Clarke; Anne L. Martel (MLMI, 2015)

Automated Segmentation of Breast in 3-D MR Images Using a Robust Atlas. - Farzad Khalvati; Cristina Gallego-Ortiz; Sharmila Balasingham; Anne L. Martel (IEEE Trans. Medical Imaging, 2015)

Automated metastatic brain lesion detection: a computer aided diagnostic and clinical research tool. - Jeremy Devine; Arjun Sahgal; Irene Karam; Anne L. Martel (Computer-Aided Diagnosis, 2016)

Automatic cell detection and segmentation from H and E stained pathology slides using colorspace decorrelation stretching. - Mohammad Peikari; Anne L. Martel (Digital Pathology, 2016)

Breast segmentation in MRI using Poisson surface reconstruction initialized with random forest edge detection. - Anne L. Martel; Cristina Gallego-Ortiz; YingLi Lu (Image Processing, 2016)

Interpreting extracted rules from ensemble of trees: Application to computer-aided diagnosis of breast MRI. - Cristina Gallego-Ortiz; Anne L. Martel (CoRR, 2016)

A Metric for Reducing False Positives in the Computer-Aided Detection of Breast Cancer from Dynamic Contrast-Enhanced Magnetic Resonance Imaging Based Screening Examinations of High-Risk Women. - Jacob E. D. Levman; Cristina Gallego-Ortiz; Ellen Warner; Petrina Causer; Anne L. Martel (J. Digit. Imaging, 2016)

Triaging Diagnostically Relevant Regions from Pathology Whole Slides of Breast Cancer: A Texture Based Approach. - Mohammad Peikari; Mehrdad J. Gangeh; Judit T. Zubovits; Gina M. Clarke; Anne L. Martel (IEEE Trans. Medical Imaging, 2016)

Transitioning Between Convolutional and Fully Connected Layers in Neural Networks. - Shazia Akbar; Mohammad Peikari; Sherine Salama; Sharon Nofech-Mozes; Anne L. Martel (DLMIA/ML-CDS@MICCAI, 2017)

Motion Corruption Detection in Breast DCE-MRI. - Sylvester Chiang; Sharmila Balasingham; Lara Richmond; Belinda Curpen; Mia Skarpathiotakis; Anne L. Martel (MLMI@MICCAI, 2017)

Determining tumor cellularity in digital slides using ResNet. - Shazia Akbar; Mohammad Peikari; Sherine Salama; Sharon Nofech-Mozes; Anne L. Martel (Digital Pathology, 2018)

Localization and classification of cell nuclei in post-neoadjuvant breast cancer surgical specimen using fully convolutional networks. - Rene Bidart; Mehrdad J. Gangeh; Mohammad Peikari; Sherine Salama; Sharon Nofech-Mozes; Anne L. Martel; Ali Ghodsi 001 (Digital Pathology, 2018)

Cluster-Based Learning from Weakly Labeled Bags in Digital Pathology. - Shazia Akbar; Anne L. Martel (CoRR, 2018)

Deformable Registration for Longitudinal Breast MRI Screening. - Hatef Mehrabian; Lara Richmond; YingLi Lu; Anne L. Martel (J. Digit. Imaging, 2018)

Automated Segmentation of DCIS in Whole Slide Images. - Nikhil Seth; Shazia Akbar; Sharon Nofech-Mozes; Sherine Salama; Anne L. Martel (ECDP, 2019)

Use of convolutional neural networks to predict risk of masking by mammographic density. - Theo Cleland; James G. Mainprize; Olivier Alonzo-Proulx; Jennifer A. Harvey; Roberta A. Jong; Anne L. Martel; Martin J. Yaffe (Computer-Aided Diagnosis, 2019)

Unsupervised Clustering of Quantitative Imaging Phenotypes Using Autoencoder and Gaussian Mixture Model. - Jianan Chen 001; Laurent Milot; Helen M. C. Cheung; Anne L. Martel (MICCAI (4), 2019)

Multi-layer Domain Adaptation for Deep Convolutional Networks. - Ozan Ciga; Jianan Chen 001; Anne L. Martel (DART/MIL3ID@MICCAI, 2019)

Metastatic Vertebrae Segmentation for Use in a Clinical Pipeline. - Geoff Klein; Anne L. Martel; Arjun Sahgal; Cari M. Whyne; Michael R. Hardisty (CSI@MICCAI, 2019)

Co-registered Cardiac ex vivo DT Images and Histological Images for Fibrosis Quantification. - Peter Lin; Anne L. Martel; Susan Camilleri; Mihaela Pop (STACOM@MICCAI, 2019)

The transition module: a method for preventing overfitting in convolutional neural networks. - Shazia Akbar; Mohammad Peikari; Sherine Salama; Sharon Nofech-Mozes; Anne L. Martel (Comput. methods Biomech. Biomed. Eng. Imaging Vis., 2019)

Intensity augmentation for domain transfer of whole breast segmentation in MRI. - Linde S. Hesse; Grey Kuling; Mitko Veta; Anne L. Martel (CoRR, 2019)

A graph-based lesion characterization and deep embedding approach for improved computer-aided diagnosis of nonmass breast MRI lesions. - Cristina Gallego-Ortiz; Anne L. Martel (Medical Image Anal., 2019)

Self supervised contrastive learning for digital histopathology. - Ozan Ciga; Anne L. Martel; Tony Xu (CoRR, 2020)

Overcoming the limitations of patch-based learning to detect cancer in whole slide images. - Ozan Ciga; Tony Xu; Sharon Nofech-Mozes; Shawna Noy; Fang-I Lu; Anne L. Martel (CoRR, 2020)

AMINN: Autoencoder-based Multiple Instance Neural Network for Outcome Prediction of Multifocal Liver Metastases. - Jianan Chen 001; Helen M. C. Cheung; Laurent Milot; Anne L. Martel (CoRR, 2020)

BIAS: Transparent reporting of biomedical image analysis challenges. - Lena Maier-Hein; Annika Reinke; Michal Kozubek 001; Anne L. Martel; Tal Arbel; Matthias Eisenmann; Allan Hanbury; Pierre Jannin; Henning Müller; Sinan Onogur; Julio Saez-Rodriguez; Bram van Ginneken; et al. (Medical Image Anal., 2020)

Improving Self-supervised Learning with Hardness-aware Dynamic Curriculum Learning: An Application to Digital Pathology. - Chetan L. Srinidhi; Anne L. Martel (ICCVW, 2021)

AMINN: Autoencoder-Based Multiple Instance Neural Network Improves Outcome Prediction in Multifocal Liver Metastases. - Jianan Chen 001; Helen M. C. Cheung; Laurent Milot; Anne L. Martel (MICCAI (5), 2021)

IJCARS: MICCAI 2020 special issue. - Anne L. Martel; Danail Stoyanov; Diana Mateus; Leo Joskowicz; Purang Abolmaesumi (Int. J. Comput. Assist. Radiol. Surg., 2021)

BI-RADS BERT & Using Section Tokenization to Understand Radiology Reports. - Grey Kuling; Belinda Curpen; Anne L. Martel (CoRR, 2021)

Learning to segment images with classification labels. - Ozan Ciga; Anne L. Martel (Medical Image Anal., 2021)

Loss odyssey in medical image segmentation. - Jun Ma 016; Jianan Chen 001; Matthew Ng; Rui Huang; Yu Li 031; Chen Li; Xiaoping Yang 001; Anne L. Martel (Medical Image Anal., 2021)

Deep neural network models for computational histopathology: A survey. - Chetan L. Srinidhi; Ozan Ciga; Anne L. Martel (Medical Image Anal., 2021)

Intensity Augmentation to Improve Generalizability of Breast Segmentation Across Different MRI Scan Protocols. - Linde S. Hesse; Grey Kuling; Mitko Veta; Anne L. Martel (IEEE Trans. Biomed. Eng., 2021)

Head and Neck Tumor Segmentation with 3D UNet and Survival Prediction with Multiple Instance Neural Network. - Jianan Chen 001; Anne L. Martel (HECKTOR@MICCAI, 2022)

Cell phenotyping using unsupervised clustering on multiplexed fluorescence images of breast cancer tissue specimens. - Wenchao Han; Alison M. Cheung; Dan Wang; Kela Liu; Martin J. Yaffe; Anne L. Martel (Digital and Computational Pathology, 2022)

Sparse capsule networks for informative representation learning in digital pathology. - Matthew McNeil; Cem Anil; Anne L. Martel (Digital and Computational Pathology, 2022)

Metastatic Cancer Outcome Prediction with Injective Multiple Instance Pooling. - Jianan Chen 001; Anne L. Martel (CoRR, 2022)

Metrics reloaded: Pitfalls and recommendations for image analysis validation. - Lena Maier-Hein; Annika Reinke; Evangelia Christodoulou; Ben Glocker; Patrick Godau; Fabian Isensee; Jens Kleesiek; Michal Kozubek 001; Mauricio Reyes 001; Michael A. Riegler; Manuel Wiesenfarth; Michael Baumgartner 001; et al. (CoRR, 2022)

Biomedical image analysis competitions: The state of current participation practice. - Matthias Eisenmann; Annika Reinke; Vivienn Weru; Minu Dietlinde Tizabi; Fabian Isensee; Tim J. Adler; Patrick Godau; Veronika Cheplygina; Michal Kozubek 001; Sharib Ali; Anubha Gupta; Jan Kybic; et al. (CoRR, 2022)

BI-RADS BERT and Using Section Segmentation to Understand Radiology Reports. - Grey Kuling; Belinda Curpen; Anne L. Martel (J. Imaging, 2022)

Self-supervised driven consistency training for annotation efficient histopathology image analysis. - Chetan L. Srinidhi; Seung Wook Kim 001; Fu-Der Chen; Anne L. Martel (Medical Image Anal., 2022)

Self Supervised Multi-view Graph Representation Learning in Digital Pathology. - Vishwesh Ramanathan; Anne L. Martel (GRAIL/OCELOT@MICCAI, 2023)

Masked Image Modeling for Label-Efficient Segmentation in Two-Photon Excitation Microscopy. - Tony Xu; Matthew Rozak; Emmanuel E. Ntiri; Adrienne Dorr; James R. Mester; Bojana Stefanovic; Anne L. Martel; Maged Goubran (MILLanD@MICCAI, 2023)

Integrated image-processing and transcriptomic analysis of cancer-associated fibroblasts (CAFs) in breast cancer subtypes. - Alison M. Cheung; Hassan Besher; Dan Wang; Kela Liu; Yutaka Amemiya; Jianan Chen 001; Anne L. Martel; Arun Seth; Martin J. Yaffe (Digital and Computational Pathology, 2023)

Identification of molecular cell type of breast cancer on digital histopathology images using deep learning and multiplexed fluorescence imaging. - Wenchao Han; Alison M. Cheung; Vishwesh Ramanathan; Dan Wang; Kela Liu; Martin J. Yaffe; Anne L. Martel (Digital and Computational Pathology, 2023)

Ink removal in whole slide images using hallucinated data. - Vishwesh Ramanathan; Wenchao Han; Dina Bassiouny; Eileen Rakovitch; Anne L. Martel (Digital and Computational Pathology, 2023)

Understanding metric-related pitfalls in image analysis validation. - Annika Reinke; Minu Tizabi; Michael Baumgartner 001; Matthias Eisenmann; Doreen Heckmann-Nötzel; A. Emre Kavur; Tim Rädsch; Carole H. Sudre; Laura Ación; Michela Antonelli; Tal Arbel; Spyridon Bakas; et al. (CoRR, 2023)

Cross-Validation Is All You Need: A Statistical Approach To Label Noise Estimation. - Jianan Chen 001; Anne L. Martel (CoRR, 2023)

VertDetect: Fully End-to-End 3D Vertebral Instance Segmentation Model. - Geoff Klein; Michael R. Hardisty; Cari M. Whyne; Anne L. Martel (CoRR, 2023)

ROOD-MRI: Benchmarking the robustness of deep learning segmentation models to out-of-distribution and corrupted data in MRI. - Lyndon Boone; Mahdi Biparva; Parisa Mojiri Forooshani; Joel Ramirez; Mario Masellis; Robert Bartha; Sean Symons; Stephen C. Strother; Sandra E. Black; Chris Heyn; Anne L. Martel; Richard H. Swartz; et al. (NeuroImage, 2023)

Detecting Noisy Labels with Repeated Cross-Validations. - Jianan Chen 001; Vishwesh Ramanathan; Tony Xu; Anne L. Martel (MICCAI (10), 2024)

Ensemble of Prior-guided Expert Graph Models for Survival Prediction in Digital Pathology. - Vishwesh Ramanathan; Pushpak Pati; Matthew McNeil; Anne L. Martel (MICCAI (5), 2024)

A generalizable 3D framework and model for self-supervised learning in medical imaging. - Tony Xu; Sepehr Hosseini; Chris Anderson; Anthony Rinaldi; Rahul G. Krishnan; Anne L. Martel; Maged Goubran (CoRR, 2025)

ModalTune: Fine-Tuning Slide-Level Foundation Models with Multi-Modal Information for Multi-task Learning in Digital Pathology. - Vishwesh Ramanathan; Tony Xu; Pushpak Pati; Faruk Ahmed; Maged Goubran; Anne L. Martel (CoRR, 2025)

Enhancing breast cancer detection on screening mammogram using self-supervised learning and a hybrid deep model of Swin Transformer and Convolutional Neural Network. - Han Chen; Anne L. Martel (CoRR, 2025)

Breast Cancer Detection from Multi-View Screening Mammograms with Visual Prompt Tuning. - Han Chen; Anne L. Martel (CoRR, 2025)