We at UCSF take your care seriously. Click here for COVID-19 information

University of California San Francisco

Our Team

Jessica Scholey

Jessica E. Scholey, PhD

Assistant Professor
Physics Director of MR Simulation Program
Lead Physicist for Ocular Proton Program

Meet Dr. Scholey

I am motivated by my patients, their families, and my love of using physics to solve problems in medicine.

Dr. Jessica Scholey is an Assistant Professor, Physics Director of the MRI Simulation Program, and Physics Lead of the Proton Ocular Program in the Department of Radiation Oncology at the University of California, San Francisco. She received her BA in Physics from UC Berkeley and went on to receive her MSc and clinical residency training in medical physics from The University of Pennsylvania. Upon completion of her clinical training and ABR certification, she received her PhD from the Joint UC Berkeley-UCSF Bioengineering Program. She joined the faculty in 2017 and focuses on radiation oncology applications of MRI, proton therapy, and deep learning using medical imaging. Dr. Scholey leads the educational curriculum of MRI and proton therapy in the Department of Radiation Oncology and is an active member of the American Association of Physicists in Medicine, International Society for Magnetic Resonance in Medicine, Particle Therapy Co-Operative Group, and the UCSF Center for Intelligent Imaging.

MRI Simulation

Dr. Scholey’s clinical expertise and research focuses includes the application of MRI technology to Radiation Oncology, with particular focuses on MR-only treatment planning, motion-resolved MRI, and treatment planning integration.

  • MRI-only treatment planning of photon and proton radiotherapy
    • Applications of MRI in radiotherapy have increased significantly over the past decade due to the high level of soft tissue provided, often allowing for better visualization of tumors and organs at risk versus computed tomography (CT). Our group focuses on using advanced MR imaging methods to improve dose calculation accuracy through improved estimations of electron density (for photon radiotherapy) and stopping power ratio (for proton radiotherapy). Our approaches include both sequence- and deep learning-based techniques.
  • AI-targeted radiotherapy
    • Deep learning has been used for classifying tumors in a range of medical imaging modalities. Our group is developing deep learning models to predict prostate cancer maps from MRI and integrating these maps into radiotherapy treatment plans to deliver more targeted therapy to regions identified as high risk for aggressive cancer. We hope this strategy will allow for patient-individualized treatment using AI-driven technology that can provide uniformity of care accessible to both academic institutions and community hospitals.
  • Respiratory motion-resolved 4D MRI for tumors in the abdomen
    • Accurately accounting for tumor motion during radiotherapy delivery is critical when treating tumors that move with respiration, such as those in the abdomen and thorax. Respiratory-resolved MRI (4D MRI) has shown great promise for liver and pancreas tumors due to the superior soft tissue contrast relative to CT. Our group has developed and implemented 4D MRI protocols for patients treated with stereotactic body radiation to lesions within the abdomen.

Proton Therapy

Dr. Scholey’s clinical expertise includes treatment planning, quality assurance, and delivery of proton beam radiation to treat malignant and benign conditions of the eye. She is the Lead Physicist for the Ocular Proton Program, a collaborative program between clinicians, physicists, and engineers between the Department of Radiation Oncology at UCSF and Crocker National Laboratory at UC Davis. With an almost thirty-year history of treating patients on the cyclotron at the UC Davis Crocker National Lab. Research studies are focused on clinical outcomes and novel methods for reducing proton beam range uncertainty and improving quality assurance.



2021 University of California, San Francisco PhD Bioengineering
2017 University of Pennsylvania, Philadelphia, PA Resident Radiation Oncology – Medical Physics
2015 University of Pennsylvania, Philadelphia, PA MSc Medical Physics
2012 University of California, Berkeley BA Physics
Professional Experience

Professional Experience

2022-present UCSF Assistant Professor of Clinical Radiation Oncology Radiation Oncology
2017-2021 UCSF Clinical Instructor of Health Sciences Radiation Oncology

Awards & Honors

2023-2024 Associate of the AAPM Science Council Associates Mentorship Program
2015 1st Place – Grand Registration Challenge, Penn Biomedical Imaging Course
2012 UC Berkeley Physics Undergraduate Research Scholar
2011 UC Berkeley Dean’s Honors List
2010 UC Berkeley Leadership Award Finalist
2010 Faustman Perpetual Award for Excellent Academic Standing

Recent Significant Publications

UCSF Profile: https://profiles.ucsf.edu/jessica.scholey
Google scholar: https://scholar.google.com/citations?user=gwSqxwEAAAAJ&hl=en


  • Massachi J, Singer L, Glastonbury C, Scholey J, Singhrao K, Calvin C, Yom SS, Chan JW. Incidental findings and safety events from magnetic resonance imaging simulation for head and neck radiation treatment planning: A single institution experience. Technical Innovations & Patient Support in Radiation Oncology. 2024 Mar 1;29:100228.
  • Singhrao K, Dugan CL, Calvin C, Pelayo L, Yom SS, Chan JW, Scholey JE*, Singer L*. Evaluating the Hounsfield unit assignment and dose differences between CT-based standard and deep learning-based synthetic CT images for MRI-only radiation therapy of the head and neck. J Appl Clin Med Phys. 2023 Dec 21; e14239. PMID: 38128040. PMCID: PMC10795453 *Shared senior authorship.
  • Valdes, G., Scholey, J.,Nano, T.F., Gennatas, E.D., Mohindra, P., Mohammed, N., Zeng, J., Kotecha, R., Rosen, L.R., Chang, J. and Tsai, H.K., 2023. Predicting the Effect of Proton Beam Therapy Technology on Pulmonary Toxicities for Patients With Locally Advanced Lung Cancer Enrolled in the Proton Collaborative Group Prospective Clinical Trial. International Journal of Radiation Oncology* Biology* Physics.
  • Marants R, Tattenberg S, Scholey JE, Kaza E, Miao X, Benkert T, Magneson O, Fischer J, Vinas L, Niepel KB, Bortfeld TR, Landry G, Parodi K, Verburg JM, Sudhyadhom A. Validation of an MR-based multimodal method for molecular composition and proton stopping power ratio determination usingex vivoanimal tissues and tissue-mimicking phantoms. Phys Med Biol. 2023 Jul 18. PMID: 37463589
  • Jiao C, Ling D, Bian S, Vassantachart A, Cheng K, Mehta S, Lock D, Zhu Z, Feng M, Thomas H, Scholey JE, Sheng K, Fan Z, Yang W. Contrast-Enhanced Liver Magnetic Resonance Image Synthesis Using Gradient Regularized Multi-Modal Multi-Discrimination Sparse Attention Fusion GAN. Cancers (Basel). 2023 Jul 08; 15(14). PMID: 37509207. PMCID: PMC10377331.
  • Chang, C.W., Marants, R., Gao, Y., Goette, M., Scholey, J.E., Bradley, J.D., Liu, T., Zhou, J., Sudhyadhom, A. and Yang, X., 2023, April. Physics-informed multi-modal imaging-based material characterization for proton therapy. In Medical Imaging 2023: Physics of Medical Imaging (Vol. 12463, pp. 545-550). SPIE.
  • Singhrao K, Zubair M, Nano T, Scholey JE, Descovich M. End-to-end validation of fiducial tracking accuracy in robotic radiosurgery using MRI-only simulation imaging. Med Phys. 2023 Dec 06. PMID: 38055419 (Editor’s Choice).
  • Chang CW, Marants R, Gao Y, Goette M, Scholey JE, Bradley JD, Liu T, Zhou J, Sudhyadhom A, Yang X. Multimodal imaging-based material mass density estimation for proton therapy using supervised deep learning. Br J Radiol. 2023 Dec; 96(1152):20220907. PMID: 37660372. PMCID: PMC10646631
  • Scholey J, Vinas L, Kearney V, Yom S, Larson PEZ, Descovich M, Sudhyadhom A. Improved accuracy of relative electron density and proton stopping power ratio through CycleGAN machine learning. Phys Med Biol. 2022 05 02; 67(10). PMID: 35417903. PMCID: PMC9121765
  • Scholey JE, Rajagopal A, Vasquez EG, Sudhyadhom A, Larson PEZ. Generation of synthetic megavoltage CT for MRI-only radiotherapy treatment planning using a 3D deep convolutional neural network. Med Phys. 2022 Oct; 49(10):6622-6634. PMID: 35870154. PMCID: PMC9588542
  • Thomas, H.R., Miao, X., Ferguson, D., Calvin, C., Krishnamurthy, U.B., Anwar, M., Feng, M. and Scholey, J., 2022. Contrast-enhanced 4D-MRI for internal target volume generation in treatment planning for liver tumors. Radiotherapy and Oncology.
  • Singer, L. and Scholey, J., 2022. Finding Resonance: Using MRI to Improve the Care of Oligometastatic Disease. International Journal of Radiation Oncology, Biology, Physics, 114(5), pp.936-940.
  • Claessens M, Oria CS, Brouwer CL, Ziemer BP, Scholey JE, Lin H, Witztum A, Morin O, Naqa IE, Van Elmpt W, Verellen D. Quality Assurance for AI-Based Applications in Radiation Therapy. Semin Radiat Oncol. 2022 10; 32(4):421-431. PMID: 36202444
  • Scholey, J. E., Chandramohan, D., Naren, T., Liu, W., Larson, P. E. Z., & Sudhyadhom, A. (2021). A methodology for improved accuracy in stopping power estimation using MRI and CT. Medical physics, 48(1), 342-353.
  • Vinas, L., Scholey, J., Descovich, M., Kearney, V., & Sudhyadhom, A. (2021). Improved contrast and noise of megavoltage computed tomography (MVCT) through cycle‐consistent generative machine learning. Medical physics, 48(2), 676-690.
  • Zako, C., Scholey, J., Daftari, I. K., Weinberg, V. K., Swason, C., Quivey, J. M., … & Mishra, K. K. (2021). Long Term Clinical Outcomes With Dedicated Proton Ocular Beam and Helium Ion Radiation for Uveal Melanoma Patients Aged 45 and Younger. International Journal of Radiation Oncology, Biology, Physics, 111(3), e395-e396.
  • Mishra, K. K., Scholey, J. E., Daftari, I. K., Afshar, A., Tsai, T., Park, S., … & Char, D. H. (2020). Oral isotretinoin and topical retinoid use in a series of young patients with ocular melanoma. American Journal of Ophthalmology Case Reports, 19, 100787.
  • Mishra, K. K., Kacperek, A., Daftari, I. K., Afshar, A. R.,Scholey, J., Damato, B., … & Quivey, J. M. (2020). Key Clinical Concepts from Multi-Institutional Experience with Dedicated Fixed Low-Energy Proton Ocular Beamlines. International Journal of Radiation Oncology, Biology, Physics, 108(3), e827.
  • Anwar, M., Lee, K., Faddegon, B., Scholey, J., Mishra, K., & Maharbiz, M. (2021, October). A Diode-based 64X64 X-ray Detector for Cancer Radiotherapy. In AMERICAN JOURNAL OF CLINICAL ONCOLOGY-CANCER CLINICAL TRIALS(Vol. 44, No. 10, pp. S139-S139). TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA, PA 19103 USA: LIPPINCOTT WILLIAMS & WILKINS.
  • Lin, L. L., Kirk, M., Scholey, , Taku, N., Kiely, J. B., White, B., & Both, S. (2016). Initial report of pencil beam scanning proton therapy for posthysterectomy patients with gynecologic cancer. International Journal of Radiation Oncology* Biology* Physics, 95(1), 181-189.
  • Hasse, K., Scholey, J., Ziemer, B. P., Natsuaki, Y., Morin, O., Solberg, T. D., … & Witztum, A. (2021). Use of Receiver Operating Curve Analysis and Machine Learning With an Independent Dose Calculation System Reduces the Number of Physical Dose Measurements Required for Patient-Specific Quality Assurance. International Journal of Radiation Oncology* Biology* Physics, 109(4), 1086-1095.
  • Scholey, J. E., Nithianantham, S., Scholey, J. M., & Al-Bassam, J. (2014). Structural basis for the assembly of the mitotic motor Kinesin-5 into bipolar tetramers. Elife, 3, e02217.
  • Scholey, J. E. (2021). Multimodal imaging and deep learning-based methods for improved dose calculation accuracy in photon and proton radiotherapy(Doctoral dissertation, UCSF).


Redefining Possible