Darin Clark | Scholars@Duke

Darin Clark
Assistant Professor in Radiology

Current Appointments & Affiliations

Assistant Professor in Radiology, Radiology, Clinical Science Departments 2022

Contact Information

311 Research Drive, Bryan Research Building Room 156, Durham, NC 27710
DUMC Box 3302, Durham, NC 27710
darin.clark@duke.edu (919) 684-0947

Background
Education, Training, & Certifications
- Ph.D., Duke University 2015
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
- Development of a New Generation Micro-CT imaging for Functional and Molecular Imaging of Cancer awarded by National Institutes of Health 2015 - 2022
Publications & Artistic Works
Selected Publications
- Academic Articles
  - 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.” European Journal of Radiology 139 (June 2021): 109734. https://doi.org/10.1016/j.ejrad.2021.109734.
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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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  - Ding, Yifu, Daniel J. Vanselow, Maksim A. Yakovlev, Spencer R. Katz, Alex Y. Lin, Darin P. Clark, Phillip Vargas, et al. “Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography.” Elife 8 (May 7, 2019). https://doi.org/10.7554/eLife.44898.
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  - Donaldson, Keri, Jeanine M. Buchanich, Patricia Sue Grigson, Erin Deneke, Kent E. Vrana, David B. Sacks, Gregory J. Kuehn, et al. “Abstracts of Presentations at the Association of Clinical Scientists 139th Meeting Hershey, PA, May 15-18, 2019.” Ann Clin Lab Sci 49, no. 3 (May 2019): 403–16.
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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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  - 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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  - Lin, Alex Y., Yifu Ding, Daniel J. Vanselow, Spencer R. Katz, Maksim A. Yakovlev, Darin P. Clark, David Mandrell, Jean E. Copper, Damian B. van Rossum, and Keith C. Cheng. “Rigid Embedding of Fixed and Stained, Whole, Millimeter-Scale Specimens for Section-free 3D Histology by Micro-Computed Tomography.” J Vis Exp, no. 140 (October 17, 2018). https://doi.org/10.3791/58293.
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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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  - 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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  - 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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  - 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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  - 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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  - 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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  - 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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  - 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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  - 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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- Conference Papers
  - 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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  - 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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  - 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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  - Xin, X., D. Clark, K. C. Ang, D. B. Van Rossum, J. Copper, X. Xiao, P. J. La Riviere, and K. C. Cheng. “Synchrotron microCT imaging of soft tissue in juvenile zebrafish reveals retinotectal projections.” In Progress in Biomedical Optics and Imaging Proceedings of Spie, Vol. 10060, 2017. https://doi.org/10.1117/12.2267477.
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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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  - 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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  - 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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Education, Training, & Certifications

Selected Grants

Selected Publications

Academic Articles

Conference Papers