Allphin, Alex J., Rohan Nadkarni, Zay Y. Han, Darin P. Clark, Ketan B. Ghaghada, Alexandra Badea, and Cristian T. Badea. “Assessing the cardioprotective effects of exercise in APOE mouse models using deep learning and photon-counting micro-CT.” PLoS One 20, no. 4 (2025): e0320892. https://doi.org/10.1371/journal.pone.0320892.

Devkota, Laxman, Rohan Bhavane, Cristian T. Badea, Eric A. Tanifum, Ananth V. Annapragada, and Ketan B. Ghaghada. “Nanoparticle Contrast Agents for Photon-Counting Computed Tomography: Recent Developments and Future Opportunities.” Wiley Interdiscip Rev Nanomed Nanobiotechnol 17, no. 1 (2025): e70004. https://doi.org/10.1002/wnan.70004.

Nadkarni, Rohan, Darin P. Clark, Alex Jeffrey Allphin, and Cristian T. Badea. “Investigating deep learning strategies for fast denoising of 5D cardiac photon-counting micro-CT images.” Phys Med Biol, September 25, 2024. https://doi.org/10.1088/1361-6560/ad7fc6.

Allphin, A. J., R. Nadkarni, D. P. Clark, C. J. Gil, M. L. Tomov, V. Serpooshan, and C. T. Badea. “Turn-table micro-CT scanner for dynamic perfusion imaging in mice: design, implementation, and evaluation.” Phys Med Biol 69, no. 17 (August 23, 2024). https://doi.org/10.1088/1361-6560/ad6edd.

Badea, Cristian T., Ashlyn Rickard, Alex Allphin, Darin P. Clark, Ketan B. Ghaghada, S. Ridwan, Henry M. Smilowitz, James Hainfeld, and Yvonne M. Mowery. “Enhancing in vivo preclinical studies with VivoVist™ and photon-counting micro-CT imaging.” In Medical Imaging 2024: Clinical and Biomedical Imaging, edited by Barjor S. Gimi and Andrzej Krol, 29–29. SPIE, 2024. https://doi.org/10.1117/12.3005892.

Badea, Cristian T., Rohan Bhavane, Alex Allphin, Rohan Nadkarni, Darin P. Clark, Ananth Annapragada, and Ketan Ghaghada. “Photon counting micro-CT imaging of Bi2WO6 nanoparticles.” In Medical Imaging 2024: Clinical and Biomedical Imaging, edited by Barjor S. Gimi and Andrzej Krol, 43–43. SPIE, 2024. https://doi.org/10.1117/12.3005891.

Nadkarni, Rohan, Zay Yar Han, Robert J. Anderson, Alex J. Allphin, Darin P. Clark, Alexandra Badea, and Cristian T. Badea. “High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry.” PLoS One 19, no. 5 (2024): e0303288. https://doi.org/10.1371/journal.pone.0303288.

Moon, H. S., A. Mahzarnia, J. Stout, R. J. Anderson, Z. Y. Han, C. T. Badea, and A. Badea. “Predicting brain age and associated structural networks in mouse models with humanized APOE alleles using integrative and interpretable graph neural networks.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12927, 2024. https://doi.org/10.1117/12.3005695.

Allphin, A. J., R. Nadkarni, D. P. Clark, and C. T. Badea. “An Acquisition-Based Approach for High-Fidelity Infilling of Photon-Counting X-ray Detector Pixel Gaps.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12925, 2024. https://doi.org/10.1117/12.3006850.

Nadkarni, R., D. P. Clark, A. Allphin, and C. T. Badea. “Deep Learning Models for Rapid Denoising of 5D Cardiac Photon-Counting Micro-CT Images.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12925, 2024. https://doi.org/10.1117/12.3006902.

Clark, D. P., F. R. Schwartz, J. Y. Cao, and C. T. Badea. “Denoising pediatric cardiac photon-counting CT data using volumetric vision transformers and unpaired training data.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12925, 2024. https://doi.org/10.1117/12.3006863.

Allphin, A. J., D. P. Clark, C. J. Gil, M. L. Tomov, V. Serpooshan, and C. T. Badea. “Advancing Preclinical Micro-Photon Counting CT Perfusion Imaging: From Phantom Experiments to In Vivo Applications.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12925, 2024. https://doi.org/10.1117/12.3006836.

Blocker, Stephanie J., Yvonne M. Mowery, Jeffrey I. Everitt, James Cook, Gary Price Cofer, Yi Qi, Alex M. Bassil, et al. “MR histology reveals tissue features beneath heterogeneous MRI signal in genetically engineered mouse models of sarcoma.” Front Oncol 14 (2024): 1287479. https://doi.org/10.3389/fonc.2024.1287479.

Clark, D. P., A. Allphin, R. Nadkarni, and C. T. Badea. “Multi-Channel Reconstruction (MCR) Toolkit v2.0: open-source Python-based tools for X-ray CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12925, 2024. https://doi.org/10.1117/12.3006978.

Moon, Hae Sol, Ali Mahzarnia, Jacques Stout, Robert J. Anderson, Cristian T. Badea, and Alexandra Badea. “Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer's disease.,” December 14, 2023. https://doi.org/10.1101/2023.12.13.571574.

Gil, Carmen J., Connor J. Evans, Lan Li, Alex J. Allphin, Martin L. Tomov, Linqi Jin, Merlyn Vargas, et al. “Leveraging 3D Bioprinting and Photon-Counting Computed Tomography to Enable Noninvasive Quantitative Tracking of Multifunctional Tissue Engineered Constructs.” Adv Healthc Mater 12, no. 31 (December 2023): e2302271. https://doi.org/10.1002/adhm.202302271.

Schwartz, Fides R., Darin P. Clark, Francesca Rigiroli, Kevin Kalisz, Benjamin Wildman-Tobriner, Sarah Thomas, Joshua Wilson, Cristian T. Badea, and Daniele Marin. “Evaluation of the impact of a novel denoising algorithm on image quality in dual-energy abdominal CT of obese patients.” Eur Radiol 33, no. 10 (October 2023): 7056–65. https://doi.org/10.1007/s00330-023-09644-7.

Clark, Darin P., and Cristian T. Badea. “MCR toolkit: A GPU-based toolkit for multi-channel reconstruction of preclinical and clinical x-ray CT data.” Med Phys 50, no. 8 (August 2023): 4775–96. https://doi.org/10.1002/mp.16532.

Nadkarni, Rohan, Darin P. Clark, Alex J. Allphin, and Cristian T. Badea. “A Deep Learning Approach for Rapid and Generalizable Denoising of Photon-Counting Micro-CT Images.” Tomography 9, no. 4 (July 2, 2023): 1286–1302. https://doi.org/10.3390/tomography9040102.

Moore, Stephen M., James D. Quirk, Andrew W. Lassiter, Richard Laforest, Gregory D. Ayers, Cristian T. Badea, Andriy Y. Fedorov, et al. “Co-Clinical Imaging Metadata Information (CIMI) for Cancer Research to Promote Open Science, Standardization, and Reproducibility in Preclinical Imaging.” Tomography 9, no. 3 (May 11, 2023): 995–1009. https://doi.org/10.3390/tomography9030081.

Allphin, A. J., D. P. Clark, T. Thuering, P. Bhandari, K. B. Ghaghada, and C. T. Badea. “Micro-CT imaging of multiple K-edge elements using GaAs and CdTe photon counting detectors.” Phys Med Biol 68, no. 8 (April 12, 2023). https://doi.org/10.1088/1361-6560/acc77e.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS2 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523190.v1.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS4 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523184.v1.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Data from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.c.6543630.v1.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary table TS1 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523181.v1.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS1 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523193.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS2 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523190.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS3 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523187.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS1 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523193.v1.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary table TS1 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523181.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS3 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523187.v1.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Supplementary figure FS4 from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.22523184.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Data from Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma,” April 3, 2023. https://doi.org/10.1158/1535-7163.c.6543630.

Gammon, Seth T., Allison S. Cohen, Adrienne L. Lehnert, Daniel C. Sullivan, Dariya Malyarenko, Henry Charles Manning, David A. Hormuth, et al. “An Online Repository for Pre-Clinical Imaging Protocols (PIPs).” Tomography 9, no. 2 (March 27, 2023): 750–58. https://doi.org/10.3390/tomography9020060.

Peehl, Donna M., Cristian T. Badea, Thomas L. Chenevert, Heike E. Daldrup-Link, Li Ding, Lacey E. Dobrolecki, A McGarry Houghton, et al. “Animal Models and Their Role in Imaging-Assisted Co-Clinical Trials.” Tomography 9, no. 2 (March 16, 2023): 657–80. https://doi.org/10.3390/tomography9020053.

Patel, Rutulkumar, Yvonne M. Mowery, Yi Qi, Alex M. Bassil, Matt Holbrook, Eric S. Xu, Cierra S. Hong, et al. “Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma.” Mol Cancer Ther 22, no. 1 (January 3, 2023): 112–22. https://doi.org/10.1158/1535-7163.MCT-21-0991.

Allphin, Alex J., Ali Mahzarnia, Darin P. Clark, Yi Qi, Zay Y. Han, Prajwal Bhandari, Ketan B. Ghaghada, Alexandra Badea, and Cristian T. Badea. “Advanced photon counting CT imaging pipeline for cardiac phenotyping of apolipoprotein E mouse models.” PLoS One 18, no. 10 (2023): e0291733. https://doi.org/10.1371/journal.pone.0291733.

Clark, D. P., F. R. Schwartz, A. Euler, V. Mergen, H. Alkadhi, D. Marin, and C. T. Badea. “Unsupervised learning of robust models for cardiac and photon-counting x-ray CT denoising.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12463, 2023. https://doi.org/10.1117/12.2653640.

Allphin, A. J., R. Nadkarni, D. P. Clark, and C. T. Badea. “Ex vivo high-resolution hybrid micro-CT imaging using photon counting and energy integrating detectors.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12468, 2023. https://doi.org/10.1117/12.2654370.

Allphin, A. J., D. P. Clark, T. Thuering, P. Bhandari, K. B. Ghaghada, and C. T. Badea. “Spectral micro-CT imaging of multiple K-edge elements using GaAs and CdTe photon counting detectors.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12463, 2023. https://doi.org/10.1117/12.2654262.

Moon, Hae Sol, Lindsay Heffron, Ali Mahzarnia, Barnabas Obeng-Gyasi, Matthew Holbrook, Cristian T. Badea, Wuwei Feng, and Alexandra Badea. “Automated multimodal segmentation of acute ischemic stroke lesions on clinical MR images.” Magn Reson Imaging 92 (October 2022): 45–57. https://doi.org/10.1016/j.mri.2022.06.001.

Nadkarni, Rohan, Alex Allphin, Darin P. Clark, and Cristian T. Badea. “Material decomposition from photon-counting CT using a convolutional neural network and energy-integrating CT training labels.” Phys Med Biol 67, no. 15 (July 18, 2022). https://doi.org/10.1088/1361-6560/ac7d34.

Allphin, Alex J., Yvonne M. Mowery, Kyle J. Lafata, Darin P. Clark, Alex M. Bassil, Rico Castillo, Diana Odhiambo, Matthew D. Holbrook, Ketan B. Ghaghada, and Cristian T. Badea. “Photon Counting CT and Radiomic Analysis Enables Differentiation of Tumors Based on Lymphocyte Burden.” Tomography 8, no. 2 (March 10, 2022): 740–53. https://doi.org/10.3390/tomography8020061.

Clark, D. P., A. J. Allphin, Y. M. Mowery, and C. T. Badea. “Photon-counting X-ray CT perfusion imaging in animal models of cancer.” In Proceedings of SPIE - The International Society for Optical Engineering, Vol. 12304, 2022. https://doi.org/10.1117/12.2646403.

Badea, C. T., D. P. Clark, A. Alphin, J. C. Ramirez-Giraldo, P. Bhandari, Y. M. Mowery, and K. B. Ghaghada. “Co-clinical photon counting CT research for multi-contrast imaging.” In Proceedings of SPIE - The International Society for Optical Engineering, Vol. 12304, 2022. https://doi.org/10.1117/12.2646399.

Clark, D. P., E. Abadi, N. Felice, W. P. Segars, E. Samei, and C. T. Badea. “Cardiac CT reconstruction for vendor-neutral virtual imaging trials.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12031, 2022. https://doi.org/10.1117/12.2612950.

Badea, C. T., D. P. Clark, A. Alphin, K. B. Ghaghada, and Y. M. Mowery. “Photon Counting Micro-CT for Imaging Cisplatin.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12036, 2022. https://doi.org/10.1117/12.2612574.

Allphin, A. J., Y. Mowery, K. J. Lafata, D. P. Clark, A. Basil, R. Castillo, M. D. Holbrook, K. B. Ghaghada, and C. T. Badea. “Spectral micro-CT and nanoradiomic analysis for classification of tumors based on lymphocytic burden in cancer therapy studies.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12036, 2022. https://doi.org/10.1117/12.2611519.

Clark, D. P., and C. T. Badea. “Volumetric, dual-domain x-ray CT reconstruction with deep learning.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12031, 2022. https://doi.org/10.1117/12.2611771.

Allphin, A. J., D. P. Clark, A. Badea, and C. T. Badea. “Anatomical and functional cardiac PCCT imaging pipeline for characterization of Apolipoprotein E mouse models.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12036, 2022. https://doi.org/10.1117/12.2611806.

Nadkarni, R., A. Allphin, D. P. Clark, and C. T. Badea. “Material Decomposition from Photon-Counting CT using a Convolutional Neural Network and Energy-Integrating CT Training Labels.” In Proceedings of SPIE - The International Society for Optical Engineering, Vol. 12304, 2022. https://doi.org/10.1117/12.2646405.

Badea, Cristian. “Principles of Micro X-ray Computed Tomography.” In Molecular Imaging Principles and Practice, edited by Brian Ross and Sanjiv Sam Gambir, 1:47–64. Academic Press, 2021. https://doi.org/10.1016/B978-0-12-816386-3.00006-5.

Holbrook, Matthew D., Darin P. Clark, Rutulkumar Patel, Yi Qi, Alex M. Bassil, Yvonne M. Mowery, and Cristian T. Badea. “Detection of Lung Nodules in Micro-CT Imaging Using Deep Learning.” Tomography 7, no. 3 (August 7, 2021): 358–72. https://doi.org/10.3390/tomography7030032.

Clark, D. P., and C. T. Badea. “Advances in micro-CT imaging of small animals.” Phys Med 88 (August 2021): 175–92. https://doi.org/10.1016/j.ejmp.2021.07.005.

Schwartz, Fides R., Darin P. Clark, Yuqin Ding, Juan Carlos Ramirez-Giraldo, Cristian T. Badea, and Daniele Marin. “Evaluating renal lesions using deep-learning based extension of dual-energy FoV in dual-source CT-A retrospective pilot study.” Eur J Radiol 139 (June 2021): 109734. https://doi.org/10.1016/j.ejrad.2021.109734.

Blocker, Stephanie J., James Cook, Yvonne M. Mowery, Jeffrey I. Everitt, Yi Qi, Kathryn J. Hornburg, Gary P. Cofer, et al. “Ex Vivo MR Histology and Cytometric Feature Mapping Connect Three-dimensional in Vivo MR Images to Two-dimensional Histopathologic Images of Murine Sarcomas.” Radiol Imaging Cancer 3, no. 3 (May 2021): e200103. https://doi.org/10.1148/rycan.2021200103.

Lee, Chang-Lung, Jessica W. Lee, Andrea R. Daniel, Matt Holbrook, Stephanie Hasapis, Ato O. Wright, Jeremy Brownstein, et al. “Characterization of cardiovascular injury in mice following partial-heart irradiation with clinically relevant dose and fractionation.” Radiother Oncol 157 (April 2021): 155–62. https://doi.org/10.1016/j.radonc.2021.01.023.

Badea, Alexandra, Robert Schmalzigaug, Woojoo Kim, Pamela Bonner, Umer Ahmed, G Allan Johnson, Gary Cofer, et al. “Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging.” Magn Reson Imaging 76 (February 2021): 26–38. https://doi.org/10.1016/j.mri.2020.09.023.

Holbrook, M. D., D. P. Clark, and C. T. Badea. “Deep learning based spectral distortion correction and decomposition for photon counting ct using calibration provided by an energy integrated detector.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11595, 2021. https://doi.org/10.1117/12.2581124.

Clark, D. P., and C. T. Badea. “A constrained bregman framework for unsupervised convolutional denoising of multi-channel x-ray ct data.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11595, 2021. https://doi.org/10.1117/12.2581832.

Holbrook, M. D., D. P. Clark, R. Patel, Y. Qi, Y. M. Mowery, and C. T. Badea. “Towards deep learning detection of lung nodules using micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11600, 2021. https://doi.org/10.1117/12.2581120.

Holbrook, M. D., D. P. Clark, and C. T. Badea. “Dual source hybrid spectral micro-CT using an energy-integrating and a photon-counting detector.” Phys Med Biol 65, no. 20 (October 21, 2020): 205012. https://doi.org/10.1088/1361-6560/aba8b2.

Shoghi, Kooresh I., Cristian T. Badea, Stephanie J. Blocker, Thomas L. Chenevert, Richard Laforest, Michael T. Lewis, Gary D. Luker, et al. “Co-Clinical Imaging Resource Program (CIRP): Bridging the Translational Divide to Advance Precision Medicine.” Tomography 6, no. 3 (September 2020): 273–87. https://doi.org/10.18383/j.tom.2020.00023.

Clark, Darin P., Fides R. Schwartz, Daniele Marin, Juan C. Ramirez-Giraldo, and Cristian T. Badea. “Deep learning based spectral extrapolation for dual-source, dual-energy x-ray computed tomography.” Med Phys 47, no. 9 (September 2020): 4150–63. https://doi.org/10.1002/mp.14324.

Holbrook, M. D., S. J. Blocker, Y. M. Mowery, A. Badea, Y. Qi, E. S. Xu, D. G. Kirsch, G. A. Johnson, and C. T. Badea. “MRI-Based Deep Learning Segmentation and Radiomics of Sarcoma in Mice.” Tomography 6, no. 1 (March 2020): 23–33. https://doi.org/10.18383/j.tom.2019.00021.

Blocker, S. J., M. D. Holbrook, Y. M. Mowery, D. C. Sullivan, and C. T. Badea. “The impact of respiratory gating on improving volume measurement of murine lung tumors in micro-CT imaging.” PLoS One 15, no. 2 (2020): e0225019. https://doi.org/10.1371/journal.pone.0225019.

Badea, C. T., K. Ghaghada, M. D. Holbrook, P. Bhandari, D. P. Clark, Y. Qi, and Y. Mowery. “A spectral CT study on iodine augmentation of radiation therapy and its potential for combination with chemotherapy.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11317, 2020. https://doi.org/10.1117/12.2549583.

Holbrook, M. D., S. J. Blocker, Y. Mowery, A. Badea, Y. Qi, D. G. Kirsch, and C. T. Badea. “MRI-based radiomics of sarcomas in the preclinical arm of a Co-clinical trial.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11317, 2020. https://doi.org/10.1117/12.2549628.

Holbrook, M. D., D. P. Clark, and C. T. Badea. “Development of a spectral Micro-CT system using a photon counting detector with anti-coincidence corrections.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11312, 2020. https://doi.org/10.1117/12.2549617.

Clark, D. P., and C. T. Badea. “Fast spectral x-ray CT reconstruction with data-adaptive, convolutional regularization.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11312, 2020. https://doi.org/10.1117/12.2549615.

Holbrook, M. D., D. P. Clark, and C. T. Badea. “Hybrid energy integrating and photon counting micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11312, 2020. https://doi.org/10.1117/12.2549603.

Blocker, S. J., M. D. Holbrook, Y. M. Mowery, D. C. Sullivan, and C. T. Badea. “The impact of respiratory gating on improving volume measurement of murine lung tumors in micro-CT imaging,” October 29, 2019. https://doi.org/10.1101/823245.

Lee, Chang-Lung, Andrea R. Daniel, Matt Holbrook, Jeremy Brownstein, Lorraine Da Silva Campos, Stephanie Hasapis, Yan Ma, Luke B. Borst, Cristian T. Badea, and David G. Kirsch. “Sensitization of Vascular Endothelial Cells to Ionizing Radiation Promotes the Development of Delayed Intestinal Injury in Mice.” Radiat Res 192, no. 3 (September 2019): 258–66. https://doi.org/10.1667/RR15371.1.

Clark, Darin, Matthew Holbrook, Chang-Lung Lee, and Cristian Badea. “Photon-counting cine-cardiac CT in the mouse,” June 4, 2019. https://doi.org/10.1101/660100.

Ma, Zhiyuan, Yen-Rei Yu, Cristian T. Badea, Jeffrey J. Kovacs, Xinyu Xiong, Suzy Comhair, Claude A. Piantadosi, and Sudarshan Rajagopal. “Vascular Endothelial Growth Factor Receptor 3 Regulates Endothelial Function Through β-Arrestin 1.” Circulation 139, no. 13 (March 26, 2019): 1629–42. https://doi.org/10.1161/CIRCULATIONAHA.118.034961.

Badea, C. T., D. P. Clark, M. Holbrook, M. Srivastava, Y. Mowery, and K. B. Ghaghada. “Functional imaging of tumor vasculature using iodine and gadolinium-based nanoparticle contrast agents: a comparison of spectral micro-CT using energy integrating and photon counting detectors.” Phys Med Biol 64, no. 6 (March 12, 2019): 065007. https://doi.org/10.1088/1361-6560/ab03e2.

Holbrook, M., S. J. Blocker, Y. M. Mowery, and C. T. Badea. “Multi-modal MRI segmentation of sarcoma tumors using convolutional neural networks.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10948, 2019. https://doi.org/10.1117/12.2512822.

Clark, Darin P., Matthew Holbrook, Chang-Lung Lee, and Cristian T. Badea. “Photon-counting cine-cardiac CT in the mouse.” PLoS One 14, no. 9 (2019): e0218417. https://doi.org/10.1371/journal.pone.0218417.

Clark, D. P., and C. T. Badea. “Spectral data completion for dual-source x-ray CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10948, 2019. https://doi.org/10.1117/12.2512825.

Blocker, S. J., M. Holbrook, Y. M. Mowery, and C. T. Badea. “To gate or not to gate: An evaluation of respiratory gating techniques to improve volume measurement of murine lung tumors in micro-CT imaging.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10953, 2019. https://doi.org/10.1117/12.2512534.

Holbrook, Matthew, Darin P. Clark, and Cristian T. Badea. “Overcoming detector limitations of x-ray photon counting for preclinical microcomputed tomography.” J Med Imaging (Bellingham) 6, no. 1 (January 2019): 011004. https://doi.org/10.1117/1.JMI.6.1.011004.

Blocker, S. J., Y. M. Mowery, M. D. Holbrook, Y. Qi, D. G. Kirsch, G. A. Johnson, and C. T. Badea. “Bridging the translational gap: Implementation of multimodal small animal imaging strategies for tumor burden assessment in a co-clinical trial.” PLoS One 14, no. 4 (2019): e0207555. https://doi.org/10.1371/journal.pone.0207555.

Clark, D. P., and C. T. Badea. “Convolutional regularization methods for 4D, x-ray CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10948, 2019. https://doi.org/10.1117/12.2512816.

Holbrook, M., D. P. Clark, and C. T. Badea. “Low-dose 4D cardiac imaging in small animals using dual source micro-CT.” Phys Med Biol 63, no. 2 (January 9, 2018): 025009. https://doi.org/10.1088/1361-6560/aa9b45.

Badea, C. T. “Small Animal X-ray Computed Tomography.” In Handbook of X-Ray Imaging: Physics and Technology, edited by Paolo Russo, 749–749. CRC Press, 2018.

Holbrook, M., D. P. Clark, W. Barber, and C. T. Badea. “Development of a spectral photon-counting micro-CT system with a translate-rotate geometry.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10573, 2018. https://doi.org/10.1117/12.2293373.

Ashton, Jeffrey R., Katherine D. Castle, Yi Qi, David G. Kirsch, Jennifer L. West, and Cristian T. Badea. “Dual-Energy CT Imaging of Tumor Liposome Delivery After Gold Nanoparticle-Augmented Radiation Therapy.” Theranostics 8, no. 7 (2018): 1782–97. https://doi.org/10.7150/thno.22621.

Clark, D. P., and C. T. Badea. “Data-efficient methods for multi-channel x-ray CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10573, 2018. https://doi.org/10.1117/12.2293628.

Holbrook, M., D. P. Clark, and C. T. Badea. “Multiscale dual energy micro-CT for imaging using iodinated and gold nanoparticles.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10573, 2018. https://doi.org/10.1117/12.2293688.

Clark, D. P., M. Holbrook, and C. T. Badea. “Multi-energy CT decomposition using convolutional neural networks.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10573, 2018. https://doi.org/10.1117/12.2293728.

Badea, C. T., M. Holbrook, D. P. Clark, and K. Ghaghada. “Spectral imaging of iodine and gadolinium nanoparticles using dual-energy CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10573, 2018. https://doi.org/10.1117/12.2293625.

Blocker, S. J., Y. M. Mowery, M. D. Holbrook, Y. Qi, D. G. Kirsch, G. A. Johnson, and C. T. Badea. “Bridging the translational gap: Implementation of multimodal small animal imaging strategies for tumor burden assessment in a co-clinical trial,” 2018. https://doi.org/10.1101/462861.

Ashton, Jeffrey R., Elizabeth B. Gottlin, Edward F. Patz, Jennifer L. West, and Cristian T. Badea. “A comparative analysis of EGFR-targeting antibodies for gold nanoparticle CT imaging of lung cancer.” PLoS One 13, no. 11 (2018): e0206950. https://doi.org/10.1371/journal.pone.0206950.

Clark, Darin P., and Cristian T. Badea. “Hybrid spectral CT reconstruction.” PLoS One 12, no. 7 (2017): e0180324. https://doi.org/10.1371/journal.pone.0180324.

Clark, D. P., and C. T. Badea. “A data-driven regularization strategy for statistical CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10132, 2017. https://doi.org/10.1117/12.2254484.

Clark, D. P., and C. T. Badea. “Localized and efficient cardiac CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10132, 2017. https://doi.org/10.1117/12.2254700.

Clark, D. P., and C. T. Badea. “Low-dose 4D myocardial perfusion with x-ray micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 10132, 2017. https://doi.org/10.1117/12.2254548.

Touch, Mengheng, Darin P. Clark, William Barber, and Cristian T. Badea. “A neural network-based method for spectral distortion correction in photon counting x-ray CT.” Phys Med Biol 61, no. 16 (August 21, 2016): 6132–53. https://doi.org/10.1088/0031-9155/61/16/6132.

Spiliopoulos, D., G. C. Kagadis, D. Karnabatidis, G. A. Johnson, and C. T. Badea. “Digital Subtracted Angiography of Small Animals (Accepted).” In Handbook of Small Animal Imaging: Preclinical Imaging, Therapy, and Applications, edited by G. C. Kagadis, N. L. Ford, G. K. Loudos, and D. Karnabatidis, 67–75. Taylor & Francis Books, Inc., CRC Press, 2016.

Touch, M., D. P. Clark, W. Barber, and C. T. Badea. “Novel approaches to address spectral distortions in photon counting x-ray CT using artificial neural networks.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9783, 2016. https://doi.org/10.1117/12.2217037.

Clark, D. P., and C. T. Badea. “Joint regularization for spectrooral CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9783, 2016. https://doi.org/10.1117/12.2217091.

Clark, D. P., and C. T. Badea. “Resolution-enhancing hybrid, spectral CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9783, 2016. https://doi.org/10.1117/12.2216935.

Ashton, J. R., J. Hoye, K. Deland, M. Whitley, Y. Qi, E. Moding, D. G. Kirsch, J. West, and C. T. Badea. “A dual energy CT study on vascular effects of gold nanoparticles in radiation therapy.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9788, 2016. https://doi.org/10.1117/12.2217012.

Clark, Darin P., Chang-Lung Lee, David G. Kirsch, and Cristian T. Badea. “Spectrotemporal CT data acquisition and reconstruction at low dose.” Med Phys 42, no. 11 (November 2015): 6317–36. https://doi.org/10.1118/1.4931407.

Liu, Y., C. Badea, N. Mistry, and W. D’Souza. “SU-C-303-07: Influence of Image Registration Algorithms and Noise Levels On the Accuracy of Fractional Regional Ventilation.” Med Phys 42, no. 6 (June 2015): 3198. https://doi.org/10.1118/1.4923824.

Clark, D. P., M. Touch, W. Barber, and C. T. Badea. “Simultaneous imaging of multiple contrast agents using full-spectrum micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9412, 2015. https://doi.org/10.1117/12.2081049.

Liu, Yang, Jeffrey R. Ashton, Everett J. Moding, Hsiangkuo Yuan, Janna K. Register, Andrew M. Fales, Jaeyeon Choi, et al. “A Plasmonic Gold Nanostar Theranostic Probe for In Vivo Tumor Imaging and Photothermal Therapy.” Theranostics 5, no. 9 (2015): 946–60. https://doi.org/10.7150/thno.11974.

Clark, D. P., and C. T. Badea. “Rank-sparsity constrained atlas construction and phenotyping.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9413, 2015. https://doi.org/10.1117/12.2081415.

Clark, D. P., and C. T. Badea. “Spectral deblurring: An algorithm for high-resolution, hybrid spectral CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9412, 2015. https://doi.org/10.1117/12.2081249.

Clark, D. P., C. L. Lee, D. G. Kirsch, and C. T. Badea. “Rank-sparsity constrained, spectro-temporal reconstruction for retrospectively gated, dynamic CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9412, 2015. https://doi.org/10.1117/12.2081379.

Ashton, Jeffrey R., Jennifer L. West, and Cristian T. Badea. “In vivo small animal micro-CT using nanoparticle contrast agents.” Front Pharmacol 6 (2015): 256. https://doi.org/10.3389/fphar.2015.00256.

Borg, Jana Schaich, Mai-Anh Vu, Cristian Badea, Alexandra Badea, G Allan Johnson, and Kafui Dzirasa. “Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas.” ENeuro 2, no. 4 (2015). https://doi.org/10.1523/ENEURO.0017-15.2015.

Clark, Darin P., and Cristian T. Badea. “Spectral diffusion: an algorithm for robust material decomposition of spectral CT data.” Phys Med Biol 59, no. 21 (November 7, 2014): 6445–66. https://doi.org/10.1088/0031-9155/59/21/6445.

Clark, D. P., and C. T. Badea. “Micro-CT of rodents: state-of-the-art and future perspectives.” Phys Med 30, no. 6 (September 2014): 619–34. https://doi.org/10.1016/j.ejmp.2014.05.011.

Johnston, S. M., G. A. Johnson, and C. T. Badea. “Helical dual source cone-beam micro-CT.” In 2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014, 177–80, 2014. https://doi.org/10.1109/isbi.2014.6867838.

Badea, C. T., and D. Panetta. “High-Resolution CT for Small-Animal Imaging Research.” In Comprehensive Biomedical Physics, edited by A. Brahme, 2. X-Ray and Ultrasound Imaging:221–42. Oxford: Elsevier, 2014. https://doi.org/10.1016/B978-0-444-53632-7.00210-0.

Befera, Nicholas T., Cristian T. Badea, and G Allan Johnson. “Comparison of 4D-microSPECT and microCT for murine cardiac function.” Mol Imaging Biol 16, no. 2 (April 2014): 235–45. https://doi.org/10.1007/s11307-013-0686-z.

Lee, Chang-Lung, Hooney Min, Nicholas Befera, Darin Clark, Yi Qi, Shiva Das, G Allan Johnson, Cristian T. Badea, and David G. Kirsch. “Assessing cardiac injury in mice with dual energy-microCT, 4D-microCT, and microSPECT imaging after partial heart irradiation.” Int J Radiat Oncol Biol Phys 88, no. 3 (March 1, 2014): 686–93. https://doi.org/10.1016/j.ijrobp.2013.11.238.

Ashton, Jeffrey R., Darin P. Clark, Everett J. Moding, Ketan Ghaghada, David G. Kirsch, Jennifer L. West, and Cristian T. Badea. “Dual-energy micro-CT functional imaging of primary lung cancer in mice using gold and iodine nanoparticle contrast agents: a validation study.” PLoS One 9, no. 2 (2014): e88129. https://doi.org/10.1371/journal.pone.0088129.

Badea, C. T., N. Befera, D. Clark, Y. Qi, and G. A. Johnson. “Dual-energy micro-CT imaging of pulmonary airway obstruction: Correlation with micro-SPECT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9038, 2014. https://doi.org/10.1117/12.2043094.

Clark, D. P., G. A. Johnson, and C. T. Badea. “Robust material decomposition for spectral CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9038, 2014. https://doi.org/10.1117/12.2042546.

Ashton, Jeffrey R., Nicholas Befera, Darin Clark, Yi Qi, Lan Mao, Howard A. Rockman, G Allan Johnson, and Cristian T. Badea. “Anatomical and functional imaging of myocardial infarction in mice using micro-CT and eXIA 160 contrast agent.” Contrast Media Mol Imaging 9, no. 2 (2014): 161–68. https://doi.org/10.1002/cmmi.1557.

Clark, D. P., G. A. Johnson, and C. T. Badea. “A multi-resolution approach to retrospectively-gated cardiac micro-CT reconstruction.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9033, 2014. https://doi.org/10.1117/12.2043044.

Clark, D., S. M. Johnston, G. A. Johnson, and C. T. Badea. “The effect of scatter correction on dual energy micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 8668, 2013. https://doi.org/10.1117/12.2006904.

Clark, D., A. Badea, G. A. Johnson, and C. T. Badea. “Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications.” Progress in Biomedical Optics and Imaging - Proceedings of SPIE 8669 (June 3, 2013). https://doi.org/10.1117/12.2007043.

Mistry, N., C. Badea, R. Gullapalli, Z. Vujaskovic, and W. D’ Souza. “WE-G-134-08: Extracting Fractional Regional Ventilation in Mice.” Med Phys 40, no. 6Part31 (June 2013): 513. https://doi.org/10.1118/1.4815677.

Moding, Everett J., Darin P. Clark, Yi Qi, Yifan Li, Yan Ma, Ketan Ghaghada, G Allan Johnson, David G. Kirsch, and Cristian T. Badea. “Dual-energy micro-computed tomography imaging of radiation-induced vascular changes in primary mouse sarcomas.” Int J Radiat Oncol Biol Phys 85, no. 5 (April 1, 2013): 1353–59. https://doi.org/10.1016/j.ijrobp.2012.09.027.

Clark, Darin P., Ketan Ghaghada, Everett J. Moding, David G. Kirsch, and Cristian T. Badea. “In vivo characterization of tumor vasculature using iodine and gold nanoparticles and dual energy micro-CT.” Phys Med Biol 58, no. 6 (March 21, 2013): 1683–1704. https://doi.org/10.1088/0031-9155/58/6/1683.

Bhavane, Rohan, Cristian Badea, Ketan B. Ghaghada, Darin Clark, Deborah Vela, Anoosha Moturu, Akshaya Annapragada, G Allan Johnson, James T. Willerson, and Ananth Annapragada. “Dual-energy computed tomography imaging of atherosclerotic plaques in a mouse model using a liposomal-iodine nanoparticle contrast agent.” Circ Cardiovasc Imaging 6, no. 2 (March 1, 2013): 285–94. https://doi.org/10.1161/CIRCIMAGING.112.000119.

Badea, Cristian T., Laurence W. Hedlund, and G Allan Johnson. “A LabVIEW Platform for Preclinical Imaging Using Digital Subtraction Angiography and Micro-CT.” J Med Eng 2013 (2013): 581617. https://doi.org/10.1155/2013/581617.

Perez, Bradford A., A Paiman Ghafoori, Chang-Lung Lee, Samuel M. Johnston, Yifan Li, Jacob G. Moroshek, Yan Ma, et al. “Assessing the radiation response of lung cancer with different gene mutations using genetically engineered mice.” Front Oncol 3 (2013): 72. https://doi.org/10.3389/fonc.2013.00072.

Clark, Darin, Alexandra Badea, Yilin Liu, G Allan Johnson, and Cristian T. Badea. “Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization.” Phys Med Biol 57, no. 19 (October 7, 2012): 6125–45. https://doi.org/10.1088/0031-9155/57/19/6125.

Johnston, Samuel M., G Allan Johnson, and Cristian T. Badea. “Temporal and spectral imaging with micro-CT.” Med Phys 39, no. 8 (August 2012): 4943–58. https://doi.org/10.1118/1.4736809.

Badea, C. T., X. Guo, D. Clark, S. M. Johnston, C. D. Marshall, and C. A. Piantadosi. “Dual-energy micro-CT of the rodent lung.” Am J Physiol Lung Cell Mol Physiol 302, no. 10 (May 15, 2012): L1088–97. https://doi.org/10.1152/ajplung.00359.2011.

Johnston, S. M., and C. T. Badea. “A spectral calibration technique for x-ray CT.” Progress in Biomedical Optics and Imaging - Proceedings of SPIE 8313 (May 4, 2012). https://doi.org/10.1117/12.911532.

Guo, X., S. M. Johnston, G. A. Johnson, and C. T. Badea. “A comparison of sampling strategies for dual energy micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 8313, 2012. https://doi.org/10.1117/12.911548.

Badea, C. T., X. Guo, D. Clark, S. M. Johnston, C. Marshall, and C. Piantadosi. “Lung imaging in rodents using dual energy micro-CT.” Proc SPIE Int Soc Opt Eng 8317 (April 3, 2012). https://doi.org/10.1117/12.912155.

Clark, D., G. A. Johnson, and C. T. Badea. “Denoising of 4D Cardiac Micro-CT Data Using Median-Centric Bilateral Filtration.” In Proc SPIE Int Soc Opt Eng, Vol. 8314, 2012. https://doi.org/10.1117/12.911478.

Guo, Xiaolian, Samuel M. Johnston, Yi Qi, G Allan Johnson, and Cristian T. Badea. “4D micro-CT using fast prospective gating.” Phys Med Biol 57, no. 1 (January 7, 2012): 257–71. https://doi.org/10.1088/0031-9155/57/1/257.

Badea, Cristian T., Khannan K. Athreya, Gabriela Espinosa, Darin Clark, A Paiman Ghafoori, Yifan Li, David G. Kirsch, G Allan Johnson, Ananth Annapragada, and Ketan B. Ghaghada. “Computed tomography imaging of primary lung cancer in mice using a liposomal-iodinated contrast agent.” PLoS One 7, no. 4 (2012): e34496. https://doi.org/10.1371/journal.pone.0034496.

Badea, C. T., I. N. Stanton, S. M. Johnston, G. A. Johnson, and M. J. Therien. “Investigations on X-ray luminescence CT for small animal imaging.” In Proc SPIE Int Soc Opt Eng, 8313:83130T, 2012. https://doi.org/10.1117/12.911465.

Bell, Robert C., Deevakar Rogith, Craig W. Johnson, Cristian T. Badea, Khannan K. Athreya, Gabriela Espinosa, Darin Clark, et al. “Data analysis: evaluation of nanoscale contrast agent enhanced CT scan to differentiate between benign and malignant lung cancer in mouse model.” AMIA Annu Symp Proc 2012 (2012): 27–35.

Zhang, Xiaofeng, Cristian Badea, Greg Hood, Arthur Wetzel, Yi Qi, Joel Stiles, and G Allan Johnson. “High-resolution reconstruction of fluorescent inclusions in mouse thorax using anatomically guided sampling and parallel Monte Carlo computing.” Biomed Opt Express 2, no. 9 (September 1, 2011): 2449–60. https://doi.org/10.1364/BOE.2.002449.

Badea, Cristian T., Samuel M. Johnston, Yi Qi, and G Allan Johnson. “4D micro-CT for cardiac and perfusion applications with view under sampling.” Phys Med Biol 56, no. 11 (June 7, 2011): 3351–69. https://doi.org/10.1088/0031-9155/56/11/011.

Badea, C. T., K. Ghaghada, G. Espinosa, L. Strong, and A. Annapragada. “Multi-modality PET-CT imaging of breast cancer in an animal model using nanoparticle x-ray contrast agent and 18F-FDG.” Progress in Biomedical Optics and Imaging - Proceedings of SPIE 7965 (May 16, 2011). https://doi.org/10.1117/12.878024.

Johnston, S. M., and C. T. Badea. “Temporal and spectral reconstruction algorithms for x-ray CT.” Progress in Biomedical Optics and Imaging - Proceedings of SPIE 7961 (May 13, 2011). https://doi.org/10.1117/12.878107.

Badea, C. T., S. M. Johnston, Y. Qi, K. Ghaghada, and G. A. Johnson. “Dual-energy micro-CT imaging for differentiation of iodine- and gold-based nanoparticles.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 7961, 2011. https://doi.org/10.1117/12.878043.

Rajagopal, Sudarshan, Jeff Kovacs, Cristian Badea, G Allan Johnson, Howard A. Rockman, Claude A. Piantadosi, and Robert J. Lefkowitz. “BETA-ARRESTINS REGULATE SIGNALING BY BONE MORPHOGENETIC PROTEIN TYPE II RECEPTOR IN PULMONARY ARTERIAL HYPERTENSION.” Journal of the American College of Cardiology 57, no. 14 (April 2011): E2046–E2046. https://doi.org/10.1016/s0735-1097(11)62046-9.

Zhang, Xiaofeng, and Cristian T. Badea. “Highly efficient detection in fluorescence tomography of quantum dots using time-gated acquisition and ultrafast pulsed laser.” Proc SPIE Int Soc Opt Eng 7896 (January 23, 2011). https://doi.org/10.1117/12.875502.

Ghaghada, Ketan B., Cristian T. Badea, Lohitash Karumbaiah, Nicole Fettig, Ravi V. Bellamkonda, G. A. Johnson, and Ananth Annapragada. “Evaluation of tumor microenvironment in an animal model using a nanoparticle contrast agent in computed tomography imaging.” Acad Radiol 18, no. 1 (January 2011): 20–30. https://doi.org/10.1016/j.acra.2010.09.003.

Badea, Cristian T., Laurence W. Hedlund, James Cook, Brian R. Berridge, and G Allan Johnson. “Micro-CT imaging assessment of dobutamine-induced cardiac stress in rats.” J Pharmacol Toxicol Methods 63, no. 1 (2011): 24–29. https://doi.org/10.1016/j.vascn.2010.04.002.

Badea, Cristian T., Laurence W. Hedlund, Yi Qi, Brian Berridge, and G Allan Johnson. “In vivo imaging of rat coronary arteries using bi-plane digital subtraction angiography.” J Pharmacol Toxicol Methods 64, no. 2 (2011): 151–57. https://doi.org/10.1016/j.vascn.2011.05.008.

Lin, MingDe, Yi Qi, Antonia F. Chen, Cristian T. Badea, and G Allan Johnson. “Phenylephrine-modulated cardiopulmonary blood flow measured with use of X-ray digital subtraction angiography.” J Pharmacol Toxicol Methods 64, no. 2 (2011): 180–86. https://doi.org/10.1016/j.vascn.2011.08.001.

Ladstätter, F., E. Garrosa, C. Badea, and B. Moreno. “Application of artificial neural networks to a study of nursing burnout.” Ergonomics 53, no. 9 (September 2010): 1085–96. https://doi.org/10.1080/00140139.2010.502251.

Mos, R. B., M. S. Gabor, M. Nasui, T. Petrisor, C. Badea, A. Rufoloni, and L. Ciontea. “Synthesis of epitaxial BaZrO3 thin films by chemical solution deposition.” In Thin Solid Films, 518:4714–17. Elsevier BV, 2010. https://doi.org/10.1016/j.tsf.2009.12.066.

Johnston, S. M., B. A. Perez, D. G. Kirsch, and C. T. Badea. “Phase-selective image reconstruction of the lungs in small animals using Micro-CT.” Proc SPIE Int Soc Opt Eng 7622 (February 15, 2010): 76223G.1-76223G.9. https://doi.org/10.1117/12.844359.

Dumbrava, A., C. Badea, G. Prodan, and V. Ciupina. “SYNTHESIS AND CHARACTERIZATION OF CADMIUM SULFIDE OBTAINED AT ROOM TEMPERATURE.” CHALCOGENIDE LETTERS 7, no. 2 (February 1, 2010): 111–18.

Zhang, Xiaofeng, Cristian T. Badea, Greg Hood, Arthur W. Wetzel, Joel R. Stiles, and G Allan Johnson. “Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT.” In Proc SPIE Int Soc Opt Eng, Vol. 7757, 2010. https://doi.org/10.1117/12.841891.

Badea, Cristian T., Samuel M. Johnston, Ergys Subashi, Yi Qi, Laurence W. Hedlund, and G Allan Johnson. “Lung perfusion imaging in small animals using 4D micro-CT at heartbeat temporal resolution.” Med Phys 37, no. 1 (January 2010): 54–62. https://doi.org/10.1118/1.3264619.

Johnston, S. M., G. A. Johnson, and C. T. Badea. “GPU-based iterative reconstruction with total variation minimization for micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 7622, 2010. https://doi.org/10.1117/12.844368.

Lin, MingDe, Craig T. Marshall, Yi Qi, Samuel M. Johnston, Cristian T. Badea, Claude A. Piantadosi, and G Allan Johnson. “Quantitative blood flow measurements in the small animal cardiopulmonary system using digital subtraction angiography.” Med Phys 36, no. 11 (November 2009): 5347–58. https://doi.org/10.1118/1.3231823.

Samei. “Micro-CT imaging of breast tumors in rodents using a liposomal, nanoparticle contrast agent.” International Journal of Nanomedicine, November 2009, 277–277. https://doi.org/10.2147/ijn.s7881.

Perez, B. A., A. P. Ghafoori, S. M. Johnston, L. B. Jeffords, Y. Kim, C. T. Badea, G. A. Johnson, and D. G. Kirsch. “Dissecting the Mechanism of Tumor Response to Radiation Therapy with Primary Lung Cancers in Mice.” In International Journal of Radiation Oncology*Biology*Physics, 75:S537–S537. Elsevier BV, 2009. https://doi.org/10.1016/j.ijrobp.2009.07.1227.

Ghafoori, A., C. Lee, B. Perez, S. Johnston, R. Rodrigues, C. Badea, Y. Kim, S. Lowe, and D. G. Kirsch. “In Vivo shRNA to Study the Molecular Mechanisms of Radiation Response of Primary Cancers in Mice.” In International Journal of Radiation Oncology*Biology*Physics, 75:S171–72. Elsevier BV, 2009. https://doi.org/10.1016/j.ijrobp.2009.07.401.

Dumbrava, A., C. Badea, G. Prodan, I. Popovici, and V. Ciupina. “ZINC SULFIDE FINE PARTICLES OBTAINED AT LOW TEMPERATURE.” CHALCOGENIDE LETTERS 6, no. 9 (September 1, 2009): 437–43.

Badea, C. T., S. M. Johnston, M. Lin, L. W. Hedlund, and G. A. Johnson. “4D micro-CT-based perfusion imaging in small animals.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 7258, 2009. https://doi.org/10.1117/12.811213.

Johnston, S. M., G. A. Johnson, and C. T. Badea. “A material decomposition method for dual energy micro-CT.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 7258, 2009. https://doi.org/10.1117/12.811673.

Zhang, Xiaofeng, and Cristian Badea. “Effects of sampling strategy on image quality in noncontact panoramic fluorescence diffuse optical tomography for small animal imaging.” Opt Express 17, no. 7 (March 30, 2009): 5125–38. https://doi.org/10.1364/oe.17.005125.

Zhang, Xiaofeng, Cristian Badea, Mathews Jacob, and G Allan Johnson. “Development of a noncontact 3-D fluorescence tomography system for small animal in vivo imaging.” In Proc SPIE Int Soc Opt Eng, 7191:nihpa106691, 2009. https://doi.org/10.1117/12.808199.

Samei, Ehsan, Robert S. Saunders, Cristian T. Badea, Ketan B. Ghaghada, Laurence W. Hedlund, Yi Qi, Hong Yuan, Rex C. Bentley, and Srinivasan Mukundan. “Micro-CT imaging of breast tumors in rodents using a liposomal, nanoparticle contrast agent.” Int J Nanomedicine 4 (2009): 277–82.

Zhang, Xiaofeng, Cristian T. Badea, and G Allan Johnson. “Three-dimensional reconstruction in free-space whole-body fluorescence tomography of mice using optically reconstructed surface and atlas anatomy.” J Biomed Opt 14, no. 6 (2009): 064010. https://doi.org/10.1117/1.3258836.

Dumbrava, A., A. Georgescu, G. Damache, C. Badea, I. Enache, C. Oprea, and M. A. Girtu. “Dye-sensitized solar cells based on nanocrystalline TiO2 and natural pigments.” In JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS, 10:2996–3002. NATL INST OPTOELECTRONICS, 2008.

Badea, C. T., M. Drangova, D. W. Holdsworth, and G. A. Johnson. “In vivo small-animal imaging using micro-CT and digital subtraction angiography.” Phys Med Biol 53, no. 19 (October 7, 2008): R319–50. https://doi.org/10.1088/0031-9155/53/19/R01.

Johnson, K., C. Badea, L. Hedlund, and G. A. Johnson. “Imaging techniques for small animal imaging models of pulmonary disease: Micro-CT (Toxicologic Pathology (2007) 35, 5 (9-64)).” Toxicologic Pathology 36, no. 6 (October 1, 2008): 895. https://doi.org/10.1177/0192623308323921.

Shofer, Scott, Cristian Badea, Yi Qi, Erin Potts, W Michael Foster, and G Allan Johnson. “A micro-CT analysis of murine lung recruitment in bleomycin-induced lung injury.” J Appl Physiol (1985) 105, no. 2 (August 2008): 669–77. https://doi.org/10.1152/japplphysiol.00980.2007.

Bogdan, M., A. Parnau, C. Badea, and I. Ardelean. “Time-Dependent Diffusion Studies on Miglyol Molecules Confined in Permeable Polymeric Capsules.” In Applied Magnetic Resonance, 34:63–69. Springer Science and Business Media LLC, 2008. https://doi.org/10.1007/s00723-008-0089-5.

Saunders, R., E. Samei, C. Badea, H. Yuan, K. Ghaghada, Y. Qi, L. W. Hedlund, and S. Mukundan. “Optimization of dual energy contrast enhanced breast tomosynthesis for improved mammographic lesion detection and diagnosis.” Progress in Biomedical Optics and Imaging - Proceedings of SPIE 6913 (May 14, 2008). https://doi.org/10.1117/12.772042.

Badea, C. T., E. Samei, K. Ghaghada, R. Saunders, H. Yuan, Y. Qi, L. W. Hedlund, and S. Mukundan. “Utility of a prototype liposomal contrast agent for x-ray imaging of breast cancer: A proof of concept using micro-CT in small animals.” Progress in Biomedical Optics and Imaging - Proceedings of SPIE 6913 (May 14, 2008). https://doi.org/10.1117/12.772307.

Johnston, Samuel M., G Allan Johnson, and Cristian T. Badea. “Geometric calibration for a dual tube/detector micro-CT system.” Med Phys 35, no. 5 (May 2008): 1820–29. https://doi.org/10.1118/1.2900000.

Badea, C. T., S. Johnston, B. Johnson, M. Lin, L. W. Hedlund, and G Allan Johnson. “A dual micro-CT system for small animal imaging.” In Proc SPIE Int Soc Opt Eng, 6913:691342, 2008. https://doi.org/10.1117/12.772303.

Badea, Cristian T., Arthur W. Wetzel, Nilesh Mistry, Stuart Pomerantz, Demian Nave, and G Allan Johnson. “Left ventricle volume measurements in cardiac micro-CT: the impact of radiation dose and contrast agent.” Comput Med Imaging Graph 32, no. 3 (April 2008): 239–50. https://doi.org/10.1016/j.compmedimag.2007.12.004.

Badea, Cristian T., Eduard Schreibmann, and Tim Fox. “A registration based approach for 4D cardiac micro-CT using combined prospective and retrospective gating.” Med Phys 35, no. 4 (April 2008): 1170–79. https://doi.org/10.1118/1.2868778.

Lin, Ming de, Lutao Ning, Cristian T. Badea, Nilesh N. Mistry, Yi Qi, and G Allan Johnson. “A high-precision contrast injector for small animal x-ray digital subtraction angiography.” IEEE Trans Biomed Eng 55, no. 3 (March 2008): 1082–91. https://doi.org/10.1109/TBME.2007.909541.

Schreibmann, E., C. Badea, and T. Fox. “TH‐C‐351‐02: Registration Based Automatic Segmentation and Wall Motion Analysis for 4D Cardiac Micro‐CT in Mice.” In Medical Physics, 35:2974, 2008. https://doi.org/10.1118/1.2962858.

Song, Jiayu, Qing H. Liu, G Allan Johnson, and Cristian T. Badea. “Sparseness prior based iterative image reconstruction for retrospectively gated cardiac micro-CT.” Med Phys 34, no. 11 (November 2007): 4476–83. https://doi.org/10.1118/1.2795830.

Nahrendorf, Matthias, Cristian Badea, Laurence W. Hedlund, Jose-Luiz Figueiredo, David E. Sosnovik, G Allan Johnson, and Ralph Weissleder. “High-resolution imaging of murine myocardial infarction with delayed-enhancement cine micro-CT.” Am J Physiol Heart Circ Physiol 292, no. 6 (June 2007): H3172–78. https://doi.org/10.1152/ajpheart.01307.2006.

Badea, Cristian T., Laurence W. Hedlund, Ming De Lin, Julie S Boslego Mackel, Ehsan Samei, and G Allan Johnson. “Tomographic digital subtraction angiography for lung perfusion estimation in rodents.” Med Phys 34, no. 5 (May 2007): 1546–55. https://doi.org/10.1118/1.2717384.

Badea, Cristian T., Laurence W. Hedlund, Julie F Boslego Mackel, Lan Mao, Howard A. Rockman, and G Allan Johnson. “Cardiac micro-computed tomography for morphological and functional phenotyping of muscle LIM protein null mice.” Mol Imaging 6, no. 4 (2007): 261–68.

Wetzel, A. W., C. T. Badea, S. M. Pomerantz, N. Mistry, D. Nave, and G. A. Johnson. “Measurement and modeling of 4D live mouse heart volumes from CT time series.” In Proceedings of SPIE - The International Society for Optical Engineering, Vol. 6491, 2007. https://doi.org/10.1117/12.704792.

Shofer, Scott, Cristian Badea, Scott Auerbach, David A. Schwartz, and G Allan Johnson. “A micro-computed tomography-based method for the measurement of pulmonary compliance in healthy and bleomycin-exposed mice.” Exp Lung Res 33, no. 3–4 (2007): 169–83. https://doi.org/10.1080/01902140701364458.

Badea, C. T., L. W. Hedlund, M. D. Lin, J. F. Boslego, and G. A. Johnson. “Functional imaging in small animals using tomographic digital subtraction angiography.” In 2006 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro - Proceedings, 2006:1208–11, 2006.

De Lin, Ming, Ehsan Samei, Cristian T. Badea, Terry T. Yoshizumi, and G. Allan Johnson. “Optimized radiographic spectra for small animal digital subtraction angiography.” Med Phys 33, no. 11 (November 2006): 4249–57. https://doi.org/10.1118/1.2356646.

Oldham, Mark, Harshad Sakhalkar, Tim Oliver, Ying Min Wang, John Kirpatrick, Yiting Cao, Cristian Badea, G Allan Johnson, and Mark Dewhirst. “Three-dimensional imaging of xenograft tumors using optical computed and emission tomography.” Med Phys 33, no. 9 (September 2006): 3193–3202. https://doi.org/10.1118/1.2217109.

Mukundan, Srinivasan, Ketan B. Ghaghada, Cristian T. Badea, Chen-Yu Kao, Laurence W. Hedlund, James M. Provenzale, G Allan Johnson, Emmanuel Chen, Ravi V. Bellamkonda, and Ananth Annapragada. “A liposomal nanoscale contrast agent for preclinical CT in mice.” AJR Am J Roentgenol 186, no. 2 (February 2006): 300–307. https://doi.org/10.2214/AJR.05.0523.

Badea, Cristian T., Laurence W. Hedlund, Ming De Lin, Julie F. Boslego Mackel, and G Allan Johnson. “Tumor imaging in small animals with a combined micro-CT/micro-DSA system using iodinated conventional and blood pool contrast agents.” Contrast Media Mol Imaging 1, no. 4 (2006): 153–64. https://doi.org/10.1002/cmmi.103.

Badea, Cristian T., Elizabeth Bucholz, Laurence W. Hedlund, Howard A. Rockman, and G Allan Johnson. “Imaging methods for morphological and functional phenotyping of the rodent heart.” Toxicol Pathol 34, no. 1 (2006): 111–17. https://doi.org/10.1080/01926230500404126.

Pallikarakis, N. “Development and evaluation of an ODL course on Medical Image Processing.” Med Eng Phys 27, no. 7 (September 2005): 549–54. https://doi.org/10.1016/j.medengphy.2004.12.018.

Maï, Wilfried, Cristian T. Badea, Charles T. Wheeler, Laurence W. Hedlund, and G Allan Johnson. “Effects of breathing and cardiac motion on spatial resolution in the microscopic imaging of rodents.” Magn Reson Med 53, no. 4 (April 2005): 858–65. https://doi.org/10.1002/mrm.20400.

Badea, Cristian T., Boma Fubara, Laurence W. Hedlund, and G Allan Johnson. “4-D micro-CT of the mouse heart.” Mol Imaging 4, no. 2 (2005): 110–16. https://doi.org/10.1162/15353500200504187.

Mai, W., C. T. Badea, C. T. Wheeler, L. W. Hedlund, and G. A. Johnson. “Effects of breathing motion on the spatial resolution in microscopic imaging techniques of rodents.” In 2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano, 1:472–75, 2004.

Badea, C., L. W. Hedlund, and G. A. Johnson. “Micro-CT with respiratory and cardiac gating.” Med Phys 31, no. 12 (December 2004): 3324–29. https://doi.org/10.1118/1.1812604.

Badea, C. T., L. W. Hedlund, C. T. Wheeler, W. Mai, and G. A. Johnson. “Volumetric micro-CT system for in vivo microscopy.” In 2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano, 2:1377–80, 2004.

De Lin, M., C. T. Badea, and G. A. Johnson. “Optimized radiographic spectra for digital subtraction angiography in the mouse.” In 2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano, 2:1412–15, 2004.

Badea, Cristian, and Richard Gordon. “Experiments with the nonlinear and chaotic behaviour of the multiplicative algebraic reconstruction technique (MART) algorithm for computed tomography.” Phys Med Biol 49, no. 8 (April 21, 2004): 1455–74. https://doi.org/10.1088/0031-9155/49/8/006.

Badea, C., and N. Pallikarakis. “Development and evaluation of an ODL course on medical image processing.” In Proceedings of the IASTED International Conference on Web-Based Education, 470–73, 2004.

Buliev, Ivan G., Cristian T. Badea, Zoi Kolitsi, and Nicolas Pallikarakis. “Estimation of the heart respiratory motion with applications for cone beam computed tomography imaging: a simulation study.” IEEE Trans Inf Technol Biomed 7, no. 4 (December 2003): 404–11. https://doi.org/10.1109/titb.2003.821336.

Buliev, I. G., C. T. Badea, and N. Pallikarakis. “Respiratory displacement modelling in cone beam computed tomography.” Computers in Cardiology 30 (January 1, 2003): 617–20. https://doi.org/10.1109/cic.2003.1291231.

Soimu, Delia, Cristian Badea, and Nicolas Pallikarakis. “A novel approach for distortion correction for X-ray image intensifiers.” Comput Med Imaging Graph 27, no. 1 (2003): 79–85. https://doi.org/10.1016/s0895-6111(02)00055-1.

Buliev, I., C. Badea, and N. Pallikarakis. “Logarithmic amplifier for computed tomography tasks using fluoroscopic projections.” J Med Eng Technol 26, no. 6 (2002): 247–52. https://doi.org/10.1080/03091900210156832.

Badea, C., Z. Kolitsi, and N. Pallikarakis. “Image quality in extended arc filtered digital tomosynthesis.” Acta Radiol 42, no. 2 (March 2001): 244–48. https://doi.org/10.1080/028418501127346585.

Chlewicki, W., C. Badea, and N. Pallikarakis. “Cone based 3D reconstruction: A FDK-SART comparison for limited number of projections.” In MEDICON 2001: PROCEEDINGS OF THE INTERNATIONAL FEDERATION FOR MEDICAL & BIOLOGICAL ENGINEERING, PTS 1 AND 2, edited by R. Magjarevic, S. Tonkovic, V. Bilas, and I. Lackovic, 495–97. UNIV ZAGREB, 2001.

Badea, C., Z. Kolitsi, and N. Pallikarakis. “A 3-D imaging system for in-theatre orthopedic applications based on Digital Tomosynthesis.” In CARS 2001: COMPUTER ASSISTED RADIOLOGY AND SURGERY, edited by H. U. Lemke, M. W. Vannier, K. Inamura, A. G. Farman, and K. Doi, 1230:1138–1138. ELSEVIER SCIENCE BV, 2001.

Badea, Cristian T., Zoi Kolitsi, and Nicolas Pallikarakis. “A 3D imaging system for in-theatre orthopedic applications based on Digital Tomosynthesis.” In CARS, edited by Heinz U. Lemke, Michael W. Vannier, Kiyonari Inamura, Allan G. Farman, and Kunio Doi, 1230:1209–10. Elsevier, 2001.

Badea, C., Z. Kolitsi, and N. Pallikarakis. “A 3D imaging system for dental imaging based on digital tomosynthesis and cone beam CT.” In MEDICON 2001: PROCEEDINGS OF THE INTERNATIONAL FEDERATION FOR MEDICAL & BIOLOGICAL ENGINEERING, PTS 1 AND 2, edited by R. Magjarevic, S. Tonkovic, V. Bilas, and I. Lackovic, 739–41. UNIV ZAGREB, 2001.

Messaris, G., Z. Kolitsi, C. Badea, and N. Pallikarakis. “Three-dimensional localisation based on projectional and tomographic image correlation: an application for digital tomosynthesis.” Med Eng Phys 21, no. 2 (March 1999): 101–9. https://doi.org/10.1016/s1350-4533(99)00015-6.

Bocioaca, A., C. Badea, C. Papatheodoropoulos, and G. Kostopoulos. “A software tool to assist the planning of electrophysiological experiments on rat brain slices.” Studies in Health Technology and Informatics 68 (January 1, 1999): 976–79. https://doi.org/10.3233/978-1-60750-912-7-976.

Badea, C., Z. Kolitsi, and N. Pallikarakis. “A wavelet-based method for removal of out-of-plane structures in digital tomosynthesis.” Comput Med Imaging Graph 22, no. 4 (1998): 309–15. https://doi.org/10.1016/s0895-6111(98)00037-8.

Badea, C., Z. Kolitsi, N. Pallikarakis, and A. Papapanagiotou. “Medical device surveillance world-wide.” Stud Health Technol Inform 28 (1996): 157–74.

Kosta, M., G. Messaris, C. Badea, and Z. Kolitsi. “427A localization tool on the basis of digital tomosynthesis.” Radiotherapy and Oncology 40 (January 1996): S110–S110. https://doi.org/10.1016/s0167-8140(96)80436-1.