Imaging AI Lab

medical imaging, deep learning, AI modeling, computer vision

magnetic resonance imaging, computed tomography, ultrasound, OCT, fundus photography

craig@imagingai.org

Selected Publications

Below is a selection of recent papers from my full list of approximately 100 peer reviewed journal articles.

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Recent Ophthalmology Publications

  1. Wang Y, Peng J, Dai Y, Jones C, Sair S, Shen J, Loizou N, Wu J, Hsu WC, Imami M, Yang L, Jiao Z, Zhang P, Bai H, "Enhancing vision-language models for medical imaging: bridging the 3D gap with innovative slice selection", NeurIPS D&B Track 2024.
  2. TYA Liu, Y Liu, MS Gastonguay, D Midgett, N Kuo, Y Zhao, K Ullah, G Alexander, T Hartman, ND Koseoglu, C Jones, "Predicting Imminent Conversion to Exudative Age-related Macular Degeneration Using Multimodal Data and Ensemble Machine Learning", Ophthalmology Science. 2025. In Press. doi: https://doi.org/10.1016/j.xops.2025.100785
  3. Cornelio A, Martinez AC, Lu H, Jones C, Kashani AH, "Rigid alignment method for secondary analyses of optical coherence tomography volumes", Biomed. Opt. Express 15, 938-952 (2024) https://doi.org/10.1364/BOE.508123.
  4. Liu TYA, Koseoglu ND, Jones CK, "Self-Supervised Deep Learning—The Next Frontier", JAMA Ophthalmol. Published online February 8, 2024. doi:10.1001/jamaophthalmol.2023.6650.
  5. Wu J, Koseoglu ND, Jones CK, Liu TYA. "Vision transformers: The next frontier for deep learning-based ophthalmic image analysis", Saudi Journal of Ophthalmology:, July 14, 2023. | DOI: 10.4103/sjopt.sjopt_91_23.
  6. Jones CK, Li B, Wu JH, Nakaguchi T, Xuan P, Liu TYA. "Comparative analysis of alignment algorithms for macular optical coherence tomography imaging", Int J Retin Vitr 2023;9(60) 2023, https://doi.org/10.1186/s40942-023-00497-2.
  7. Kashani AH, Liu TYA, Jones CK. "Optical Coherence Tomography Angiography, Artificial Intelligence, and the Missing Capillaries", JAMA Ophthalmol. Published online May 25, 2023. doi:10.1001/jamaophthalmol.2023.1829.
  8. Liu Y, Ota M, Han R, Siewerdsen J, Liu TYA, Jones CK, "Active Shape Model Registration of Ocular Structures in Computed Tomography Images." Physics in Medicine and Biology, 2022 (https://doi.org/10.1088/1361-6560/ac9a98).
  9. Liu TY, Ling C, Hahn L, Jones CK, Boon C, Singh M. "Prediction of Visual Impairment in Retinitis Pigmentosa Using Deep Learning and Multimodal Fundus Images". British Journal of Ophthalmology, 2022. (http://dx.doi.org/10.1136/bjo-2021-320897).

Recent Uncertainty, Active Learning, and Federated Learning Publications

  1. Kim DD, Chandra RS, Yang L, Wu J, Feng X, Atalay M, Bettegowda C, Jones C, Sair H, Liao WH, Zhu C, Zou B, Kazerooni AF, Nabavizadeh A, Jiao Z, Peng J, Bai HX, "Active Learning in Brain Tumor Segmentation with Uncertainty Sampling and Annotation Redundancy Restriction", J Imaging Inform Med. 2024 Oct;37(5):2099-2107. doi: 10.1007/s10278-024-01037-6.
  2. Liu SZ, Vagdargi P, Jones CK, Luciano M, Anderson WS, Helm PA, Uneri A, Siewerdsen JH, Zbijewski W, and Sisniega A, "One-shot estimation of epistemic uncertainty in deep learning image formation with application to high-quality cone-beam CT reconstruction", SPIE 2024.
  3. Duan R, Caffo B, Bai H, Sair HI, Jones CK. "Evidential Uncertainty Quantification: A Variance-Based Perspective." Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision, 2024.
  4. Yi M, Duan R, Li Z, Siewerdsen JH, Uneri A, Lee J, Jones CK. "Joint synthesis and registration of MRI and Cone-Beam CT Images using deep evidential uncertainty estimation of deformation fields." Proceedings Volume 12928, Medical Imaging 2024: Image-Guided Procedures, Robotic Interventions, and Modeling; 129280X (2024) https://doi.org/10.1117/12.3008899.
  5. Pati S, …. Jones CK, …., Bakas S., "Federated Learning Enables Big Data for Rare Cancer Boundary Detection", Nature Communications, 2022 Dec 5;13(1):7346. doi: 10.1038/s41467-022-33407-5.
  6. Jones CK, Wang G, Yedavalli V, Sair H. "Quantifying Epistemic and Aleatoric Uncertainty in 3D U-Net Segmentation". Journal of Medical Imaging 9(3), 034002, 2022. (http://dx.doi.org/10.1117/1.JMI.9.3.034002).
  7. Zhang X, Sisniega A, Zbijewski WB, Lee J, Jones CK, Wu P, Han R, Uneri A, Vagdargi P, Helm PA, Luciano M, Anderson WS, Siewerdsen JH. "Combining physics-based models with deep learning image synthesis and uncertainty in intraoperative cone-beam CT of the brain", Medical Physics 50(5) p. 2607-2624.

Recent Deep Learning Publications

  1. P Vagdargi, A Uneri, SZ Liu, CK Jones, A Sisniega, J Lee, PA Helm, RP Lee, MG Luciano, GD Hager, JH Siewerdsen "Self-Supervised Feature Detection and 3D Reconstruction for Real-Time Neuroendoscopic Guidance", IEEE Transactions in Biomedical Engineering (in press).
  2. Latheef AAP, Santamaria-Pang A, Jones CK, Sair HI, "Emergent Language Symbolic Autoencoder (ELSA) with Weak Supervision to Model Hierarchical Brain Networks", arXiv:2404.10031, MICCAI 2024.
  3. Hu Y, Huang Y, Song A, Jones CK, Siewerdsen JH, Basar B, Helm PA, Uneri A, "Probe positioning for robot-assisted intraoperative ultrasound imaging using deep reinforcement learning", Proceedings Volume 12928, Medical Imaging 2024: Image-Guided Procedures, Robotic Interventions, and Modeling; 1292803 (2024) https://doi.org/10.1117/12.3006918.
  4. Vagdargi P, Uneri A, Liu S, Jones CK, Sisniega A, Lee J, Helm PA, Anderson WS, Luciano M, Hager GD, Siewerdsen JH, "End-to-end 3D neuroendoscopic video reconstruction for robot-assisted ventriculostomy", Proceedings Volume 12928, Medical Imaging 2024: Image-Guided Procedures, Robotic Interventions, and Modeling; 129280M (2024) https://doi.org/10.1117/12.3008758.
  5. Kambli H, Santamaria-Pang A, Tarapov I, Beheshtian E, Luna L, Sair HI, Jones C, "Atlas-Based Labeling of Resting-State fMRI", Brain Connectivity, Published Online: 30 May 2024, https://doi.org/10.1089/brain.2023.0080.
  6. Wang Y, Peng J, Dai Y, Jones C, Sair S, Shen J, Loizou N, Wu J, Hsu WC, Imami M, Yang L, Jiao Z, Zhang P, Bai H, "Enhancing vision-language models for medical imaging: bridging the 3D gap with innovative slice selection", NeurIPS D&B Track 2024.
  7. Ghate S, Santamaria-Pang A, Tarapov I, Sair HI, Jones CK. "Deep Labeling of fMRI Brain Networks Using Cloud Based Processing".17th International Symposium on Visual Computing (ISVC 2022).
  8. Han R, Jones CK, Lee J, Wu P, Vagdargi P, Uneri A, Helm PA, Luciano M, Anderson WS, Siewerdsen JH. "Deformable MR-CT Image Registration Using an Unsupervised, Dual-Channel Network for Neurosurgical Guidance." Medical Image Analysis, 2021 Med Image Anal. 2022 Jan;75:102292. DOI: https://doi.org/10.1016/j.media.2021.102292
  9. Han R, Jones C.K, Ketch M, Wu P, Vagdargi P, Uneri A, Lee J, Luciano M, Anderson WS, Siewerdsen JH, "Deformable MR-CT image registration using an unsupervised end-to-end synthesis and registration network for endoscopic neurosurgery." Proc. SPIE 11598, Medical Imaging 2021: Image-Guided Procedures, Robotic Interventions, and Modeling, 1159819
  10. Han R, Jones CK, Wu P, Vagdargi P, Zhang X, Uneri A, Lee J, Luciano M, Anderson WS, Siewerdsen JH, "Deformable Registration of MRI to Intraoperative Cone-Beam CT of the Brain Using a Joint Synthesis and Registration Network." SPIE Medical Imaging 2022.
  11. Han R, Jones CK, Lee J, Zhang X, Wu P, Vagdargi P, Uneri A, Helm PA, Luciano M, Anderson WS, Siewerdsen JH. "Joint Synthesis and Registration Network for Deformable MR-CBCT Image Registration for Neurosurgical Guidance", Physics in Medicine and Biology v67, 2022.
  12. Huang Y, Jones CK, Zhang X, Johnston A, Waktola S, Aygun N, Witham TF, Bydon A, Theodore N, Helm PA, Siewerdsen JH, Uneri A. "Multi-perspective region-based CNNs for vertebrae labeling in intraoperative long-length images." Computer Methods and Programs in Biomedicine, Volume 227, December 2022. https://doi.org/10.1016/j.cmpb.2022.107222
  13. Huang Y, Jones CK, Zhang X, Johnston A, Waktola S, Aygun N, Witham TF, Bydon A, Theodore N, Helm PA, Siewerdsen JH, Uneri A. "Multi-Perspective Region-Based CNNs for Vertebrae Labeling in Intraoperative Long-Length Images." Proceedings Volume 12034, Medical Imaging 2022: Image-Guided Procedures, Robotic Interventions, and Modeling; 120340U (2022) https://doi.org/10.1117/12.2611912

Craig Jones, PhD (craig@imagingai.org)