About

Fanny Chapelin is an Assistant Professor in the Departments of Bioengineering and Radiology at the University of California, San Diego. She earned her Ph.D. in Bioengineering from UC San Diego in 2019. Following her doctorate, she became the first woman faculty member in the Department of Biomedical Engineering at the University of Kentucky, where she developed her research program for four years. Her research focuses on developing non-invasive imaging techniques to visualize cellular therapies and inflammation in cancer and other immune disorders. These efforts aim to provide scientists and clinicians with tools to visualize cell distribution, fate, and efficacy, ultimately improving clinical practice and patient care. Her impactful research has been recognized through several awards, including France’s Engineer of the Year Award for Science. Additionally, she serves as the Radiology T32 Clinician-Scientist Residency Program Co-Director.

Research topics

• Medicine
• Political Science
• Engineering ethics
• Biology
• Business
• Medical education
• Engineering
• Immunology
• Cancer research
• Molecular biology
• Internal medicine

Selected publications

• Bicomponent Mapping of Cortical Bone Using a New Interleaved <scp>UTE</scp> Imaging Sequence

  Magnetic Resonance in Medicine · 2026-01-04

  articleOpen access

  ABSTRACT Purpose Ultrashort echo time (UTE) MRI enables direct imaging of cortical bone and quantification of its water compartments via bicomponent T 2 * modeling. However, conventional approaches require multiple separate dual‐echo scans due to limitations in gradient power. This approach is prone to inter‐scan inconsistencies such as motion and signal drift, which degrade fitting accuracy. This study proposes an interleaved dual‐echo acquisition sequence that acquires multiple echo time (TE) images in a single scan to improve bicomponent T 2 * quantification in cortical bone. Methods The proposed UTE sequence utilizes interleaved dual‐echo acquisitions with flexible TE spacings. This sequence was tested on five healthy subjects' tibial midshafts and compared to conventional separate dual‐echo scans with and without image registration. Bicomponent T 2 * modeling was performed, and fitting accuracy was evaluated using normalized‐root‐mean‐squared error (NRMSE). Three subjects were scanned three times to evaluate the scan repeatability. Results The interleaved method significantly reduced NRMSE (3.2% ± 2.3% vs. 6.2% ± 3.1%, p = 0.0231) and yielded lower and more stable T 2 * (T 2s *; 0.50 ± 0.10 ms vs. 0.76 ± 0.13 ms, p &lt; 0.0001) and fraction (F s ; 78.2 ± 5.1 vs. 84.2% ± 7.1%, p = 0.0006) of short T 2 components compared to separate scans without registration. Image registration had a minimal improvement on mapping results for separate scans. Parameter maps from the interleaved scans confirmed more homogeneous distributions of T 2s * and F s with lower fitting errors. The much lower coefficients of variance of the interleaved scans demonstrated improved repeatability compared with separate scans. Conclusion The proposed interleaved UTE dual‐echo sequence improves the robustness of bicomponent T 2 * mapping of the cortical bone by reducing inter‐scan inconsistencies.

  PublisherOA PDFDOI

• Computer Navigated Spinal Surgery Using Magnetic Resonance Imaging and Augmented Reality

  Journal of Medical Devices · 2026-01-06

  article

  Abstract Current spinal pain management procedures, such as radio frequency ablation (RFA) and epidural steroid injection (ESI), rely on fluoroscopy for needle placement which exposes patients and physicians to ionizing radiation. In this paper, we investigate a radiation-free surgical navigation system for spinal pain management procedures that combines magnetic resonance imaging (MRI) with fiducial ArUco marker-based augmented reality (AR) to serve as a radiation-free alternative. High-resolution MRI scans of a lumbar spinal phantom were obtained and assembled as a surface mesh. Laplacian smoothing algorithms were then applied to smoothen the surface and improve the model fidelity. A commercially available stereo camera (ZED2) was used to track single or dual fiducial ArUco markers on the patient to determine the patient's real-time pose. Custom AR software was applied to overlay the MRI image onto the patient, allowing the physician to see not only the outer surface of the patient but also the complete anatomy of the patient below the surface. Needle-insertion trials on a 3D-printed three-vertebra phantom showed that dual ArUco marker tracking increased the accuracy of needle insertions and reduced the average needle misplacement distance compared to single ArUco marker procedures. The average needle misplacement is comparable to the average deviation of 2 mm for conventional epidural techniques using fluoroscopy. Our radiation-free system demonstrates promise to serve as an alternative to fluoroscopy by improving image-guided spinal navigation.

  PublisherDOI

• Nano-immunoimaging

  Elsevier eBooks · 2025-01-01

  book-chapterSenior author
  PublisherDOI

• Receptor-Mediated SPION Labeling of CD4+ T Cells for Longitudinal MRI Tracking of Distribution Following Systemic Injection in Mouse

  Nanomaterials · 2025-07-10 · 2 citations

  articleOpen accessSenior authorCorresponding

  Tracking T cells in vivo using MRI is a major challenge due to the difficulty of labeling these non-phagocytic cells with a sufficient contrast agent to generate a detectable signal change. In this study, we explored CD4-Superparamagnetic iron oxide nanoparticles (SPION), which is commonly used in magnetic cell sorting, as a potential receptor-mediated, specific CD4+ T cell MRI labeling agent. We optimized the labeling protocol for maximal CD4+ cell labeling and viability. Cell health was confirmed with trypan blue assay, and labeling efficacy was confirmed with Prussian blue staining, transmission electron microscopy, and MRI of labeled cell pellets. Key cell functionality was assessed by flow cytometry. Next, CD4-SPION-labeled T cells or unlabeled T cells were delivered via intravenous injection in naïve mice. Liver MRIs pre-, 24 h, and 72 h post-T cell injection were performed to determine in vivo tracking ability. Our results show that CD4-SPION induces significant attenuation of T2 signals in a concentration-dependent manner, confirming their potential as an effective MRI contrast agent. In vitro, analyses showed that CD4+ T cells were able to uptake CD4-SPION without affecting cellular activity and key functions, as evidenced by Prussian blue staining and flow cytometric analysis of IL-2 receptor and the IL-7 receptor α-chains, CD69 upregulation, and IFN-γ secretion. In vivo, systemically distributed CD4-SPION-labeled T cells could be tracked in the liver at 24 and 72 h after injection, contrary to controls. Histological staining of tissue sections validated the findings. Our results showed that SPION CD4+ T cell sorting coupled with longitudinal MR imaging is a valid method to track CD4+ T cells in vivo. This safe, specific, and sensitive approach will facilitate the use of SPION as an MRI contrast agent in clinical practice, allowing for non-invasive tracking of adoptive cell therapies in multiple disease conditions.

  PublisherOA PDFDOI

• Computer Navigated Spinal Surgery Using Magnetic Resonance Imaging and Augmented Reality

  ArXiv.org · 2025-10-18

  preprintOpen access

  Current spinal pain management procedures, such as radiofrequency ablation (RFA) and epidural steroid injection (ESI), rely on fluoroscopy for needle placement which exposes patients and physicians to ionizing radiation. In this paper, we investigate a radiation-free surgical navigation system for spinal pain management procedures that combines magnetic resonance imaging (MRI) with fiducial ArUco marker-based augmented reality (AR). High-resolution MRI scans of a lumbar spinal phantom were obtained and assembled as a surface mesh. Laplacian smoothing algorithms were then applied to smoothen the surface and improve the model fidelity. A commercially available stereo camera (ZED2) was used to track single or dual fiducial ArUco markers on the patient to determine the patient's real-time pose. Custom AR software was applied to overlay the MRI image onto the patient, allowing the physician to see not only the outer surface of the patient but also the complete anatomy of the patient below the surface. Needle-insertion trials on a 3D-printed 3-vertebra phantom showed that dual-ArUco marker tracking increased the accuracy of needle insertions and reduced the average needle misplacement distance compared to single-ArUco marker procedures. The average needle misplacement is comparable to the average deviation of 2 mm for conventional epidural techniques using fluoroscopy. Our radiation-free system demonstrates promise to serve as an alternative to fluoroscopy by improving image-guided spinal navigation.

  PublisherOA PDFDOI

• CRISPR-based Triple-Modality Imaging Ushers a New Era for Stem Cell Tracking in Stroke

  Radiology · 2025-09-01

  editorialOpen access1st authorCorresponding

  “Just Accepted” papers have undergone full peer review and have been accepted for publication in Radiology. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content.

  PublisherOA PDFDOI

• Receptor-Mediated Labeling of CD4 T cells for Longitudinal Tracking of Distribution Following Systemic Injection in Mouse

  Proceedings on CD-ROM - International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition/Proceedings of the International Society for Magnetic Resonance in Medicine, Scientific Meeting and Exhibition · 2025-09-16

  articleSenior author

  Motivation: This study aims to address the challenge of in vivo tracking of CD4+ T-cells by MRI, focusing on biodistribution monitoring in adoptive cell therapies. Goal(s): To develop and optimize a receptor-mediated labeling method of CD4+ T-cells with CD4-microbeads that enables in vivo MRI tracking. Approach: CD4+ T-cells were labeled with CD4-microbeads; internalization and signal attenuation were analyzed via Iron staining, electron microscopy, and MRI. Microbead-labeled cells were injected intravenously, followed by longitudinal MRI tracking and histological analyses. Results: Internalized CD4-microbeads in T-cells resulted in significant MRI signal reduction, and confirmed the feasibility of tracking labeled T-cells in liver tissue up to 72-hours post-injection. Impact: The CD4-targeted microbead approach to track CD4+ T cells in vivo with MRI is safe, specific and sensitive. This technique will allow rapid assessment of the efficacy of adoptive cell therapies in conditions such as transplantation and diabetes.

  PublisherDOI

• 19F MRI To Monitor Cancer Progression Post-immunotherapy and Radiation Therapy

  Proceedings on CD-ROM - International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition/Proceedings of the International Society for Magnetic Resonance in Medicine, Scientific Meeting and Exhibition · 2025-09-16

  articleSenior author

  Motivation: Imaging is often combined with biopsies to diagnose and monitor cancer progression, but biopsies can be invasive and time-consuming. Goal(s): A promising alternative is 19F nanoemulsion as a contrast agent for MRI, which labels systemic macrophages, enabling noninvasive tracking of macrophages and tumor growth after treatment. Approach: This study used a fluorine nanoemulsion and 19F MRI to observe macrophage dynamics in murine cancer models post-radiation therapy or immunotherapy. Results: Our radiation therapy study showed significantly higher fluorine signals and reduced tumor growth in treated mice. Our immunotherapy study achieved a 75% response rate, distinguishing responders from non-responders through tumor size obtained via MRI. Impact: 19F MRI enables noninvasive monitoring of macrophage dynamics during radiation therapy and immunotherapy treatments, as well as anticipate tumor growth. This approach will be invaluable for future research on the role of inflammation in tumor response to therapy and recurrence.

  PublisherDOI

• Comparison of 3 Leukogram Determination Methods in Avian Species: Phloxine B Stain, Blood Smear, and an Automated Analyzer

  Journal of Avian Medicine and Surgery · 2025-05-22

  articleCorresponding

  Because avian blood cells are nucleated, most automated methods used in mammalian species for total white blood cell (WBC) counts and differentials are considered inaccurate. Therefore, manual methods are routinely used in birds, although this could result in variations in methods across laboratories. The objective of this study was to evaluate and compare 3 methods of avian leukogram determination: a commercial phloxine B stain method (PB), estimation from a blood smear (EBS), and an automated analyzer (Cell Dyn 3500, [CD]). Leukograms from 23 avian blood samples were compared using these methods. All samples were evaluated once by 4 observers to assess the repeatability and precision of the manual methods (PB and EBS). Analyses with the CD method were repeated 5 times on 3 samples to evaluate repeatability. The WBC counts and differentials obtained with CD were compared to the 2 other methods by calculating intraclass correlation coefficients (ICC). Agreement between WBC counts from EBS and PB and between CD and PB was assessed with Bland-Altman plots. Results based on the CD analyzer correlated poorly with the other methods. When compared with the EBS method, ICCs ranged from 0–4.3% for heterophils, 0–12% for lymphocytes, 0–23.4% for monocytes, and were equal to 0% for eosinophils. When comparing the CD with PB, ICCs for WBC counts ranged from 85.9–91.5% among observers. High interobserver agreement was seen for the leukograms obtained with EBS (ICC = 92.9%). A good agreement was noted between EBS and PB for WBC counts (ICC = 69.5–81.3%). Bland Altman plots indicated good agreement for WBC counts between EBS and PB (slope P value = 0.52) and CD and PB (slope P value = 0.13). Although less precise than PB, EBS proved to be clinically useful and was both time and cost-efficient. The CD method does not seem adapted for avian leukocyte differentials.

  PublisherDOI

• Magnetic resonance imaging of macrophage response to radiation therapy

  Proceedings on CD-ROM - International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition/Proceedings of the International Society for Magnetic Resonance in Medicine, Scientific Meeting and Exhibition · 2024-11-26

  articleSenior author

  Motivation: Cellular response to cancer treatment is difficult to track in real time. Standard practice involves immunostaining of a biopsied tumor, but this is severely limited by a number of factors. Goal(s): Non-invasive imaging methods such as MRI could obviate the need for biopsies and serve as a biomarker of radiation therapy efficacy. Approach: This study aimed to observe macrophage response in a mouse model by use of a fluorine nanoemulsion and 19F MRI. Results: It was shown that macrophage recruitment can be quantified through MRI. Moreover, the findings suggest that macrophage response to radiation therapy is dependent on several factors including tumor origin. Impact: Our results demonstrate the potential of 19F MRI to non-invasively track macrophages during radiation therapy and its prognostic value with regards to tumor growth. This technique will be extremely beneficial in future analysis of inflammation&amp;rsquo;s role in tumor recurrence.

  PublisherDOI

Frequent coauthors

• Aman Khurana

  29 shared

• Roberto Gedaly

  University of Kentucky

  25 shared

• Francesc Martí

  24 shared

• Eric T. Ahrens

  21 shared

• Hideho Okada

  UCSF Helen Diller Family Comprehensive Cancer Center

  20 shared

• Karen Messer

  Concordia University

  17 shared

• Deanne Lister

  Invicro (United States)

  16 shared

• Ruifeng Chen

  Human Longevity (United States)

  16 shared

Labs

• Chapelin LabPI

Awards & honors

• France’s Engineer of the Year Award for Science