Three-Dimensional Shape-Motion Analysis of the Left Anterior Descending Coronary Artery in EBCT Images. - Ioannis A. Kakadiaris; Amol Pednekar; Alberto Santamaría-Pang (MICCAI (2), 2004)

Automatic Reconstruction of Dendrite Morphology from Optical Section Stacks. - S. Urban; Sean M. O'Malley; B. Walsh; Alberto Santamaría-Pang; Peter Saggau; Costa M. Colbert; Ioannis A. Kakadiaris (CVAMIA, 2006)

Adaptive Frames-Based Denoising of Confocal Microscopy Data. - Alberto Santamaría-Pang; Teodor Stefan Bildea; Ioannis Konstantinidis 001; Ioannis A. Kakadiaris (ICASSP (2), 2006)

Automatic Centerline Extraction of Irregular Tubular Structures Using Probability Volumes from Multiphoton Imaging. - Alberto Santamaría-Pang; Costa M. Colbert; Peter Saggau; Ioannis A. Kakadiaris (MICCAI (2), 2007)

Denoising for 3-D Photon-Limited Imaging Data Using Nonseparable Filterbanks. - Alberto Santamaría-Pang; Teodor Stefan Bildea; Tan Shan; Ioannis A. Kakadiaris (IEEE Trans. Image Process., 2008)

Automated liver lesion characterization using fast kVp switching dual energy computed tomography imaging. - Alberto Santamaría-Pang; Sandeep Dutta; Sokratis Makrogiannis; Amy K. Hara; William Pavlicek; Alvin C. Silva; Brian Thomsen; Scott Robertson; Darin Okerlund; David A. Langan; Rahul Bhotika (Computer-Aided Diagnosis, 2010)

Functional Morphology Analysis of the Left Anterior Descending Coronary Artery in EBCT Images. - Ioannis A. Kakadiaris; Alberto Santamaría-Pang; Amol Pednekar (IEEE Trans. Biomed. Eng., 2010)

Tissue segmentation and classification using graph-based unsupervised clustering. - Daniel Margolis; Alberto Santamaría-Pang; Jens Rittscher (ISBI, 2012)

Cell segmentation and classification via unsupervised shape ranking. - Alberto Santamaría-Pang; Yuchi Huang; Jens Rittscher (ISBI, 2013)

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue. - Michael J. Gerdes; Christopher J. Sevinsky; Anup Sood; Sudeshna Adak; Musodiq O. Bello; Alexander Bordwell; Ali Can; Alex Corwin; Sean Dinn; Robert Filkins; Denise Hollman; Vidya Kamath; et al. (Proc. Natl. Acad. Sci. USA, 2013)

Mapping for tissue based cytometry. - Jens Rittscher; Alberto Santamaría-Pang (ISBI, 2014)

Cell segmentation and classification by hierarchical supervised shape ranking. - Alberto Santamaría-Pang; Jens Rittscher; Michael J. Gerdes; Dirk Ryan Padfield (ISBI, 2015)

Automatic Morphological Reconstruction of Neurons from Multiphoton and Confocal Microscopy Images Using 3D Tubular Models. - Alberto Santamaría-Pang; Paul Hernandez-Herrera; Manos Papadakis; Peter Saggau; Ioannis A. Kakadiaris (Neuroinformatics, 2015)

Multi-channel algorithm for segmentation of tumor blood vessels using multiplexed image data. - Yousef Al-Kofahi; Christopher Sevinsky; Alberto Santamaría-Pang; Fiona Ginty; Anup Sood; Qing Li (ISBI, 2016)

Robust single cell quantification of immune cell subtypes in histological samples. - Alberto Santamaría-Pang; Raghav K. Padmanabhan; Anup Sood; Michael J. Gerdes; Christopher Sevinsky; Qing Li; Nicole LaPlante; Fiona Ginty (BHI, 2017)

Blood vessel characterization using virtual 3D models and convolutional neural networks in fluorescence microscopy. - Aritra Chowdhury; Dmitry V. Dylov; Qing Li; Michael MacDonald; Dan E. Meyer; Michael Marino; Alberto Santamaría-Pang (ISBI, 2017)

A computational study on convolutional feature combination strategies for grade classification in colon cancer using fluorescence microscopy data. - Aritra Chowdhury; Christopher J. Sevinsky; Alberto Santamaría-Pang; Bülent Yener (Digital Pathology, 2017)

Towards Semantic Action Analysis via Emergent Language. - Alberto Santamaría-Pang; James R. Kubricht; Chinmaya Devaraj; Aritra Chowdhury; Peter H. Tu (AIVR, 2019)

A Learning Approach to Interactive Advertising. - Peter H. Tu; Donald Hamilton; Tao Gao; Alex Chen; Justin Foehner; Alberto Santamaría-Pang; James Kubricht (AVSS, 2019)

Automated Phenotyping via Cell Auto Training (CAT) on the Cell DIVE Platform. - Alberto Santamaría-Pang; Anup Sood; Dan E. Meyer; Aritra Chowdhury; Fiona Ginty (BIBM, 2019)

From Symbols to Signals: Symbolic Variational Autoencoders. - Chinmaya Devaraj; Aritra Chowdhury; Arpit Jain; James R. Kubricht; Peter H. Tu; Alberto Santamaría-Pang (ICASSP, 2020)

Escell: Emergent Symbolic Cellular Language. - Aritra Chowdhury; James R. Kubricht; Anup Sood; Peter H. Tu; Alberto Santamaría-Pang (ISBI, 2020)

Towards Emergent Language Symbolic Semantic Segmentation and Model Interpretability. - Alberto Santamaría-Pang; James Kubricht; Aritra Chowdhury; Chitresh Bhushan; Peter H. Tu (MICCAI (1), 2020)

Symbolic Semantic Segmentation and Interpretation of COVID-19 Lung Infections in Chest CT volumes based on Emergent Languages. - Aritra Chowdhury; Alberto Santamaría-Pang; James R. Kubricht; Jianwei Qiu; Peter H. Tu (CoRR, 2020)

Emergent Languages from Pretrained Embeddings Characterize Latent Concepts in Dynamic Imagery. - James R. Kubricht; Alberto Santamaría-Pang; Chinmaya Devaraj; Aritra Chowdhury; Peter H. Tu (Int. J. Semantic Comput., 2020)

Emergent Symbolic Language Based Deep Medical Image Classification. - Aritra Chowdhury; Alberto Santamaría-Pang; James R. Kubricht; Peter H. Tu (ISBI, 2021)

Adversarial Attacks with Time-Scale Representations. - Alberto Santamaría-Pang; Jianwei Qiu; Aritra Chowdhury; James Kubricht; Peter H. Tu; Naresh Iyer; Nurali Virani (CoRR, 2021)

Deep Labeling of fMRI Brain Networks Using Cloud Based Processing. - Sejal Ghate; Alberto Santamaría-Pang; Ivan Tarapov; Haris I. Sair; Craig K. Jones (ISVC (1), 2022)

Deep Labeling of fMRI Brain Networks. - Ammar Ahmed Pallikonda Latheef; Sejal Ghate; Zhipeng Hui; Alberto Santamaría-Pang; Ivan Tarapov; Haris I. Sair; Craig K. Jones (CoRR, 2023)

Region-based Contrastive Pretraining for Medical Image Retrieval with Anatomic Query. - Ho Hin Lee; Alberto Santamaría-Pang; Jameson Merkow; Ozan Oktay; Fernando Pérez-García; Javier Alvarez-Valle; Ivan Tarapov (CoRR, 2023)

3D-MIR: A Benchmark and Empirical Study on 3D Medical Image Retrieval in Radiology. - Asma Ben Abacha; Alberto Santamaría-Pang; Ho Hin Lee; Jameson Merkow; Qin Cai; Surya Teja Devarakonda; Abdullah Islam; Julia Gong; Matthew P. Lungren; Thomas Lin; Noel C. F. Codella; Ivan Tarapov (CoRR, 2023)

Atlas-Based Labeling of Resting-State fMRI. - Hrishikesh Kambli; Alberto Santamaría-Pang; Ivan Tarapov; Elham Beheshtian; Licia P. Luna; Haris I. Sair; Craig K. Jones (Brain Connect., 2024)

Foundation Models for Biomedical Image Segmentation: A Survey. - Ho Hin Lee; Yu Gu 017; Theodore Zhao; Yanbo Xu; Jianwei Yang; Naoto Usuyama; Cliff Wong; Mu Wei; Bennett A. Landman; Yuankai Huo; Alberto Santamaría-Pang; Hoifung Poon (CoRR, 2024)

Emergent Language Symbolic Autoencoder (ELSA) with Weak Supervision to Model Hierarchical Brain Networks. - Ammar Ahmed Pallikonda Latheef; Alberto Santamaría-Pang; Craig K. Jones; Haris I. Sair (CoRR, 2024)

MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging. - Noel C. F. Codella; Ying Jin; Shrey Jain; Yu Gu; Ho Hin Lee; Asma Ben Abacha; Alberto Santamaría-Pang; Will Guyman; Naiteek Sangani; Sheng Zhang; Hoifung Poon; Stephanie L. Hyland; et al. (CoRR, 2024)

OPTIC: Optimizing Patient-Provider Triaging & Improving Communications in Clinical Operations using GPT-4 Data Labeling and Model Distillation. - Alberto Santamaría-Pang; Frank Tuan; Ross Campbell; Cindy Zhang; Ankush Jindal; Roopa Surapur; Brad Holloman; Deanna Hanisch; Rae Buckley; Carisa Cooney; Ivan Tarapov; Kimberly S. Peairs; et al. (CoRR, 2025)

Multi-Modal Mamba Modeling for Survival Prediction (M4Survive): Adapting Joint Foundation Model Representations. - Ho Hin Lee; Alberto Santamaría-Pang; Jameson Merkov; Matthew P. Lungren; Ivan Tarapov (CoRR, 2025)

WaveFormer: A 3D Transformer with Wavelet-Driven Feature Representation for Efficient Medical Image Segmentation. - Md Mahfuz Al Hasan; Mahdi Zaman; Abdul Jawad; Alberto Santamaría-Pang; Ho Hin Lee; Ivan Tarapov; Kyle See; Md Shah Imran; Antika Roy; Yaser Pourmohammadi Fallah; Navid Asadizanjani; Reza Forghani (CoRR, 2025)

From Embeddings to Accuracy: Comparing Foundation Models for Radiographic Classification. - Xue Li; Jameson Merkow; Noel C. F. Codella; Alberto Santamaría-Pang; Naiteek Sangani; Alexander Ersoy; Christopher Burt; John W. Garrett; Richard J. Bruce; Joshua D. Warner; Tyler J. Bradshaw; Ivan Tarapov; et al. (CoRR, 2025)