Cristian Tudorel Badea | Scholars@Duke

Cristian Tudorel Badea
Professor in Radiology

Our lab's research focus lies primarily in developing novel quantitative imaging systems, reconstruction algorithms and analysis methods. My major expertise is in preclinical CT.
Currently, we are particularly interested in developing novel strategies for spectral CT imaging using nanoparticle-based contrast agents for theranostics (i.e. therapy and diagnostics).
We are also engaged in developing new approaches for multidimensional CT image reconstruction suitable to address difficult undersampling cases in cardiac and spectral CT (dual energy and photon counting) using compressed sensing and/or deep learning.

We are involved in co-clinical cancer trials and I serve as the Principal Investigator on the U24 Duke Preclinical Research Resources for Quantitative Imaging Biomarkers part of the NCI Co-Clinical Imaging Research Resources Program network (CIRP).

Current Research Interests

Spectral CT, Cardiac CT, Image Reconstruction, Deep Learning, Nanoparticles, Theranostics, Co-Clinical cancer trials, Small Animal Imaging

Current Appointments & Affiliations

Professor in Radiology, Radiology, Clinical Science Departments 2021
Professor in the Department of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2018
Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 2012

Contact Information

Bryan Research Building, Room 161F, Durham, NC 27710
cristian.badea@duke.edu (919) 684-7509
Google Scholar
Quantitative Imaging and Analysis Lab
The Duke Preclinical Research Resources for Quantitative Imaging Biomarkers
Webpage

Background
Education, Training, & Certifications
- Ph.D., University of Patras (Greece) 2001
Previous Appointments & Affiliations
- Professor in Radiology, Radiology, Clinical Science Departments 2018 - 2020
- Associate Professor in Radiology, Radiology, Clinical Science Departments 2009 - 2018
- Associate Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2013 - 2018
- Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2009 - 2013
- Assistant Professor in Radiology, Radiology, Clinical Science Departments 2006 - 2009
- Assistant Research Professor in Radiology, Radiology, Clinical Science Departments 2005 - 2006
Recognition
In the News
- JUL 14, 2021 https://www.auntminnie.com/
  
  Spectral CT opens doors to new clinical applications
- JUL 11, 2014
  
  Dual Contrast Agent to Light Up Arterial Health Risks
Expertise
Subject Headings
Research
Selected Grants
- Simulation Tools for 3D and 4D CT and Dosimetry awarded by National Institutes of Health 2007 - 2024
- Cardiac photon counting CT and its application in studying interactions between Alzheimer's and heart disease awarded by National Institutes of Health 2021 - 2024
- The Duke Pre-Clinical Research Resources for Quantitative Imaging Biomarkers awarded by National Institutes of Health 2017 - 2023
- Image-Guided Radiation Therapy System for Small Animals awarded by National Institutes of Health 2021 - 2022
- Development of a New Generation Micro-CT imaging for Functional and Molecular Imaging of Cancer awarded by National Institutes of Health 2015 - 2022
- Training in Medical Imaging awarded by National Institutes of Health 2003 - 2020
- An Activatable Nanoparticle Probe for Molecular Imaging of Protease Activity by Dual Energy CT awarded by National Institutes of Health 2015 - 2018
- Defining the Cellular Target of Radiation Therapy awarded by National Institutes of Health 2014 - 2015
- Dual energy CT molecular imaging of vulnerable atherosclerotic plaques using a novel nanoparticle contrast agent awarded by American Heart Association 2014 - 2015
- Cross-disciplinary Training in Medical Physics awarded by National Institutes of Health 2007 - 2013
- Small Animal Imaging Resource Program awarded by National Institutes of Health 2001 - 2012
- Tumor perfusion in small animals with tomographic digital subtraction angiography awarded by National Institutes of Health 2007 - 2009
- The Duke University Molecular Imaging Center awarded by National Institutes of Health 2001 - 2006
Publications & Artistic Works
Selected Publications
- Academic Articles
  - 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.
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  - 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, April 21, 2023. https://doi.org/10.1007/s00330-023-09644-7.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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,” November 5, 2018. https://doi.org/10.1101/462861.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - “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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - Badea, C., Z. Kolitsi, N. Pallikarakis, and A. Papapanagiotou. “Medical device surveillance world-wide.” Stud Health Technol Inform 28 (1996): 157–74.
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  - 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.
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- Book Sections
  - 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.
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  - 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.
    Open Access Copy
  - 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.
  - 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.
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- Other Articles
  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
    Full Text
  - 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.
    Full Text
  - 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.
    Full Text
  - 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.
    Full Text
- Conference Papers
  - Allphin, Alex J., Rohan Nadkarni, Darin P. Clark, and Cristian T. Badea. “Ex vivo high-resolution hybrid micro-CT imaging using photon counting and energy integrating detectors.” In Medical Imaging 2023: Biomedical Applications in Molecular, Structural, and Functional Imaging, edited by Barjor S. Gimi and Andrzej Krol. SPIE, 2023. https://doi.org/10.1117/12.2654370.
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  - Allphin, Alex J., Darin P. Clark, Thomas Thuering, Prajwal Bhandari, Ketan B. Ghaghada, and Cristian T. Badea. “Spectral micro-CT imaging of multiple K-edge elements using GaAs and CdTe photon counting detectors.” In Medical Imaging 2023: Physics of Medical Imaging, edited by Rebecca Fahrig, John M. Sabol, and Lifeng Yu. SPIE, 2023. https://doi.org/10.1117/12.2654262.
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  - Clark, Darin P., Fides R. Schwartz, André Euler, Victor Mergen, Hatem Alkadhi, Daniele Marin, and Cristian T. Badea. “Unsupervised learning of robust models for cardiac and photon-counting x-ray CT denoising.” In Medical Imaging 2023: Physics of Medical Imaging, edited by Rebecca Fahrig, John M. Sabol, and Lifeng Yu. SPIE, 2023. https://doi.org/10.1117/12.2653640.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
  - 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.
  - 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., 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.
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  - 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.
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  - 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.
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  - 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.
  - 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.
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Teaching & Mentoring
Advising & Mentoring
- MENTORSHIP
  Rohan Nadkarni PhD student, Biomedical Engineering (BME) 2021–
  Alex Allphin PhD student, Biomedical Engineering (BME) 2020–
  Matthew Holbrook        PhD student, Biomedical Engineering (BME)          2017–2021
  Mengheng Touch MSc student, Medical Physics Graduate Program           2014–2017
  Jeffrey Ashton PhD / MSTP student co-mentorship with Dr. J. West (BME) 2013–2017
  Darin Clark PhD student, Biomedical Engineering (BME)                          2010–2015
                   Post-doctoral Associate                                                        2015-2021
  Xiaolian Guo BME PhD student visiting from China 2010-2011
  Samuel Johnston PhD student, Biomedical Engineering (BME) 2007-2012
  Xiaofeng Zhang Post-doctoral Associate 2008-2009
  Ivan Buliev,                   PhD Student, University of Patras                       2001-2003
  Delia Soimu                  PhD Student, University of Patras                        2001-2003
  Wojciech Chlewicki      Master Student, University of Patras                      2001-2003
- Samuel Johnston, PhD 2012
  Darin Clark,PhD, 2015
  Mengheng Touch, MSc, 2016
Teaching Activities
- TEACHING ACTIVITIES
  Medical Image Processing Course in the European Course in Biomedical Engineering
  Patras, Greece. Course available online: http://bme.med.upatras.gr/improc 2001-2003
  CT section, Medical Imaging BME Duke 2005-2006
  CT section, NCI Cancer Imaging Camp http://imaging.cancer.gov/newsevents/workshops/cric 2007-2012
  
  Medical Physics at Duke
  ADVANCED TOPICS OF IONIZING-BASED IMAGING MODALITIES MP 732 2007-
Scholarly, Clinical, & Service Activities
Service to the Profession
- Chair . NCI Co-Clinical Imaging Research Resources Program (CIRP). 2019 - 2020 2019 - 2020
- Member. Organizing Committee for the Fifth International Conference on Image Formation in X-Ray Computed Tomography. 2018 - 2022 2018 - 2022

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