Description of Research Expertise

My research portfolio combines theoretical work on statistical shape characterization using a symmetry-based representation of shape with applied and translational research in multiple areas of biomedical image analysis. I am particularly interested in analysis techniques that are tailored to specific anatomical structures. My key work in this area involves automatic segmentation and morphometry of the hippocampal formation (HF) in magnetic resonance imaging (MRI). The HF plays a central role in memory function and is a site of early neurodegeneration in Alzheimer’s disease. In a broad effort to develop more detailed imaging-based biomarkers for Alzheimer’s disease, my team has developed a first of its kind detailed computational atlas of the HF from postmortem MRI microscopy. With NIH R01 funding, we are now integrating this atlas with histology, leveraging it for the analysis of the HF and its subfields in in vivo MRI, and evaluating MRI-derived subfield-specific as alternative imaging biomarkers in dementia. We recently published a pioneering technique for automatic segmentation of HF subfields in high-resolution, HF-focused T2-weighted in vivo MRI, showing excellent agreement with manual segmentation. Concurrently, we developed and evaluated a strategy for improving the accuracy of general-purpose segmentation techniques using machine learning as a corrective wrapper method. Other recent publications include a surface-based tract-specific strategy for diffusion MRI analysis, for which open-source software is currently being developed, and an automatic cardiac MRI segmentation method with an explicit prior on heart wall thickness.

Selected Publications

Ravikumar S, Denning AE, Lim S, Chung E, Sadeghpour N, Ittyerah R, Wisse LEM, Das SR, Xie L, Robinson JL, Schuck T, Lee EB, Detre JA, Tisdall MD, Prabhakaran K, Mizsei G, de Onzono Martin MMI, Arroyo Jiménez MDM, Mũnoz M, Marcos Rabal MDP, Cebada Sánchez S, Delgado González JC, de la Rosa Prieto C, Irwin DJ, Wolk DA, Insausti R, Yushkevich PA.: Postmortem imaging reveals patterns of medial temporal lobe vulnerability to tau pathology in Alzheimer's disease Nat Commun 15 : 4803,2024.

Dong, Mengjin, Xie, Long, Das, Sandhitsu R, Wang, Jiancong, Wisse, Laura EM, deFlores, Robin, Wolk, David A, Yushkevich, Paul A: Regional Deep Atrophy: Using Temporal Information to Automatically Identify Regions Associated with Alzheimer’s Disease Progression from Longitudinal MRI Imaging Neuroscience : 2024.

Lyu X, Duong MT, Xie L, de Flores R, Richardson H, Hwang G, Wisse LEM, DiCalogero M, McMillan CT, Robinson JL, Xie SX, Lee EB, Irwin DJ, Dickerson BC, Davatzikos C, Nasrallah IM, Yushkevich PA, Wolk DA, Das SR; Alzheimer's Disease Neuroimaging Initiative.: Tau-neurodegeneration mismatch reveals vulnerability and resilience to comorbidities in Alzheimer's continuum Alzheimers Dement : 2024.

Herz C, Vergnet N, Tian S, Aly AH, Jolley MA, Tran N, Arenas G, Lasso A, Schwartz N, O'Neill KE, Yushkevich PA, Pouch AM.: Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis J Med Imaging (Bellingham) : 2024.

Brown, Christopher, Das, Sandhitsu, Xie, Long, Nasrallah, Ilya, Detre, John, Chen‐Plotkin, Alice, Shaw, Leslie, McMillan, Corey, Yushkevich, Paul, Wolk, David: Medial temporal lobe gray matter microstructure in preclinical Alzheimer''s disease Alzheimer's & Dementia : 2024.

Taghvaei, Mohammad, Mechanic-Hamilton, Dawn J., Sadaghiani, Shokufeh, Shakibajahromi, Banafsheh, Dolui, Sudipto, Das, Sandhitsu, Brown, Christopher, Tackett, William, Khandelwal, Pulkit, Cook, Philip, Shinohara, Russell T., Yushkevich, Paul, Bassett, Danielle S., Wolk, David A., Detre, John A.: Impact of white matter hyperintensities on structural connectivity and cognition in cognitively intact ADNI participants Neurobiology of Aging 135 : 79-90,2024.

Khandelwal, Pulkit, Duong, Michael Tran, Sadaghiani, Shokufeh, Lim, Sydney, Denning, Amanda E., Chung, Eunice, Ravikumar, Sadhana, Arezoumandan, Sanaz, Peterson, Claire, Bedard, Madigan, Capp, Noah, Ittyerah, Ranjit, Migdal, Elyse, Choi, Grace, Kopp, Emily, Loja, Bridget, Hasan, Eusha, Li, Jiacheng, Bahena, Alejandra, Prabhakaran, Karthik, Mizsei, Gabor, Gabrielyan, Marianna, Schuck, Theresa, Trotman, Winifred, Robinson, John, Ohm, Daniel T., Lee, Edward B., Trojanowski, John Q., McMillan, Corey, Grossman, Murray, Irwin, David J., Detre, John A., Tisdall, M. Dylan, Das, Sandhitsu R., Wisse, Laura E. M., Wolk, David A., Yushkevich, Paul A.: Automated deep learning segmentation of high-resolution 7 Tesla postmortem MRI for quantitative analysis of structure-pathology correlations in neurodegenerative diseases Imaging Neuroscience 2 : 1-30,2024.

Denning, Amanda E., Ittyerah, Ranjit, Levorse, Lisa M., Sadeghpour, Niyousha, Athalye, Chinmayee, Chung, Eunice, Ravikumar, Sadhana, Dong, Mengjin, Duong, Michael Tran, Li, Yue, Ilesanmi, Ademola, Sreepada, Lasya P., Sabatini, Philip, Lowe, MaKayla, Bahena, Alejandra, Zablah, Jamila, Spencer, Barbara E., Watanabe, Ryohei, Kim, Boram, Sørensen, Maja Højvang, Khandelwal, Pulkit, Brown, Christopher, Hrybouski, Stanislau, Xie, Sharon X., de Flores, Robin, Robinson, John L., Schuck, Theresa, Ohm, Daniel T., Arezoumandan, Sanaz, Porta, Sílvia, Detre, John A., Insausti, Ricardo, Wisse, Laura E. M., Das, Sandhitsu R., Irwin, David J., Lee, Edward B., Wolk, David A., Yushkevich, Paul A.: Association of quantitative histopathology measurements with antemortem medial temporal lobe cortical thickness in the Alzheimer’s disease continuum Acta Neuropathologica 148 (1): 37,2024.

Wuestefeld, Anika, Baumeister, Hannah, Adams, Jenna N., de Flores, Robin, Hodgetts, Carl J., Mazloum-Farzaghi, Negar, Olsen, Rosanna K., Puliyadi, Vyash, Tran, Tammy T., Bakker, Arnold, Canada, Kelsey L., Dalton, Marshall A., Daugherty, Ana M., La Joie, Renaud, Wang, Lei, Bedard, Madigan L., Buendia, Esther, Chung, Eunice, Denning, Amanda, del Mar Arroyo-Jiménez, María, Artacho-Pérula, Emilio, Irwin, David J., Ittyerah, Ranjit, Lee, Edward B., Lim, Sydney, del Pilar Marcos-Rabal, María, Iñiguez de Onzoño Martin, Maria Mercedes, Lopez, Monica Munoz, de la Rosa Prieto, Carlos, Schuck, Theresa, Trotman, Winifred, Vela, Alicia, Yushkevich, Paul, Amunts, Katrin, Augustinack, Jean C., Ding, Song-Lin, Insausti, Ricardo, Kedo, Olga, Berron, David, Wisse, Laura E. M.: Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories Hippocampus 34 (5): 241-260,2024.

Ohm DT, Rhodes E, Bahena A, Capp N, Lowe M, Sabatini P, Trotman W, Olm CA, Phillips J, Prabhakaran K, Rascovsky K, Massimo L, McMillan C, Gee J, Tisdall MD, Yushkevich PA, Lee EB, Grossman M, Irwin DJ.: Neuroanatomical and cellular degeneration associated with a social disorder characterized by new ritualistic belief systems in a TDP-C patient vs. a Pick patient Front Neurol 14 : 1245886,2023.

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Academic Contact Information

Penn Image Computing and Science Laboratory
Richards Building, 6th Floor, D605
3700 Hamilton Walk
Philadelphia, PA 19104
Phone: 215-746-6924