About

Jennifer K. Barton is a Professor of Optical Sciences and the Director of the BIO5 Institute at The University of Arizona. She is also a faculty member in the Department of Electrical and Computer Engineering. Her research interests include optical imaging, specifically optical coherence tomography, laser-tissue interaction, and bioinstrumentation. Dr. Barton holds degrees from the University of Texas at Austin and the University of California at Irvine, including a Ph.D. from the University of Texas at Austin earned in 1998. She is affiliated with multiple departments and institutes, including Biomedical Engineering, Agricultural and Biosystems Engineering, and the BIO5 Institute, reflecting her interdisciplinary approach to research in optical sciences and biomedical applications.

Research topics

• Optics
• Biomedical engineering
• Artificial Intelligence
• Computer Science
• Medicine
• Biology
• Pathology
• Radiology
• Machine Learning
• Physics
• Chemistry
• Materials science
• Biochemistry
• Anatomy
• Biotechnology

Selected publications

• OCT UTJ Fiber Analysis Algorithms

  ReDATA · 2026-01-01

  otherOpen accessSenior author

  These algorithms are intended to be used with an existing fiber mapping code (10.7916/d8-9tj0-d475) to analyze collagen fiber bundle orientation over depth and by region (ostia, proximal, middle, distal UTJ) from optical coherence tomography (OCT) images of the uterotubal junction (UTJ). Codes which were modified from the original are provided herein.<br><i>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</i>

  PublisherDOI

• Improved endoscope for imaging and cell collection in the fallopian tubes

  Biophotonics discovery. · 2026-03-17

  articleOpen accessSenior authorCorresponding

  SignificanceEarly detection of ovarian cancer requires the observation of subtle changes within the fallopian tubes, where serous tubal intraepithelial carcinoma lesions, the putative precursor of high-grade ovarian serous carcinoma, may be present and detectable.AimThe cell-acquiring fallopian endoscope was designed to detect and interrogate potentially pathological sites in the fallopian tubes via alterations in fluorescence signal and the collection of epithelial cells.ApproachWe performed a comprehensive redesign of a first-generation endoscope prototype and demonstrated its performance in whole, human ex vivo fallopian tubes. Through the iterative improvements to the design, the endoscope features improved imaging, cell collection, and general ease of use. Specifically, improvements included a larger core count fiber imaging bundle, a redesigned close-focus lens, more flexible materials, an altered cell collection method, and a lighter-weight handle.ResultsWith benign fallopian tube samples from three patients, we demonstrate cell collection on the order of 104 cells per collection and imaging capabilities that result in average image intensity ratios.ConclusionsThis second-generation endoscope is suitable for the study of intact fallopian tubes.

  PublisherDOI

• OCT UTJ Fiber Analysis Algorithms

  Open MIND · 2026-01-01

  otherSenior author

  These algorithms are intended to be used with an existing fiber mapping code (10.7916/d8-9tj0-d475) to analyze collagen fiber bundle orientation over depth and by region (ostia, proximal, middle, distal UTJ) from optical coherence tomography (OCT) images of the uterotubal junction (UTJ). Codes which were modified from the original are provided herein.<br><i>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</i>

  DOI

• 3D OCT UTJ Datasets

  Open MIND · 2026-03-10

  datasetSenior author

  OCT image volumes and data used to support the conclusions of the paper "Quantitative analysis of collagen architecture in the human uterotubal junction (UTJ) using optical coherence tomography imaging (OCT)". Hu# refers to deidentified patient#, 000 scan# to a distinct region of each UTJ imaged (from uterus to isthmus, see utj_scan_segment), and x, y, z pixel size provided in image title (in air). Image volumes were obtained using Thorlabs Tel221 SD-OCT system, and were manually cropped and intensity adjusted.<br><br><br><i>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</i>

  DOI

• Optical coherence tomography and elastography for ex vivo visualization of early gastric cancer.

  Apollo (University of Cambridge) · 2026-02-01

  articleOpen accessSenior author

  SIGNIFICANCE: Stomach (gastric) cancer survival depends significantly on the stage in which it is detected, and surveillance with white light endoscopy exhibits poor contrast between gastric cancer and healthy tissue, especially at early stages. Early gastric cancer can exhibit changes in epithelial microstructure, including loss of regular gastric pit structure and collagen alterations which increase tissue stiffness. AIM: To improve contrast between early cancer and normal tissue, we investigate the use of optical coherence tomography (OCT) and elastography (OCE) to visualize changes in tissue structure and stiffness consistent with gastric cancer. APPROACH: Images of eight samples of ex vivo human stomach tissue from three patients were collected with a benchtop OCT system. OCT was performed for qualitative visualization of tissue structure. OCE was then performed on 17 regions of interest using a simplified optical palpation method to extract relative stiffness measurements. A transparent silicone reference layer was placed on the tissue, and axial compression was applied. The resulting deformation (strain) of the reference layer was measured, and the corresponding stress applied to the sample surface was extracted from the characteristic stress-strain curve of the reference material. Spatially resolved stress measurements were mapped and overlaid on en face OCT images. Tissue classification was confirmed by pathology. RESULTS: OCT image volumes showed more distinct gastric pit and tissue layer structure, as well as less optical attenuation, in normal tissue compared to gastric metaplasia and focal signet ring cell carcinoma (SRCC). Exemplary OCE-derived stress maps showed a trend of increasing measured stress with progression of precancer (metaplasia and dysplasia) and SRCC, suggesting increased tissue stiffness. CONCLUSIONS: This proof-of-concept study provides evidence that OCT and OCE may be capable of visualizing differences in tissue structure and stiffness between normal, metaplastic, dysplastic, and early cancerous gastric tissue, potentially providing the basis for improved screening tools with higher sensitivity.

  Publisher

• Optical coherence tomography and elastography for ex vivo visualization of early gastric cancer

  Journal of Biomedical Optics · 2026-02-13

  articleOpen accessSenior author

  Significance: Stomach (gastric) cancer survival depends significantly on the stage in which it is detected, and surveillance with white light endoscopy exhibits poor contrast between gastric cancer and healthy tissue, especially at early stages. Early gastric cancer can exhibit changes in epithelial microstructure, including loss of regular gastric pit structure and collagen alterations which increase tissue stiffness. Aim: To improve contrast between early cancer and normal tissue, we investigate the use of optical coherence tomography (OCT) and elastography (OCE) to visualize changes in tissue structure and stiffness consistent with gastric cancer. Approach: human stomach tissue from three patients were collected with a benchtop OCT system. OCT was performed for qualitative visualization of tissue structure. OCE was then performed on 17 regions of interest using a simplified optical palpation method to extract relative stiffness measurements. A transparent silicone reference layer was placed on the tissue, and axial compression was applied. The resulting deformation (strain) of the reference layer was measured, and the corresponding stress applied to the sample surface was extracted from the characteristic stress-strain curve of the reference material. Spatially resolved stress measurements were mapped and overlaid on en face OCT images. Tissue classification was confirmed by pathology. Results: OCT image volumes showed more distinct gastric pit and tissue layer structure, as well as less optical attenuation, in normal tissue compared to gastric metaplasia and focal signet ring cell carcinoma (SRCC). Exemplary OCE-derived stress maps showed a trend of increasing measured stress with progression of precancer (metaplasia and dysplasia) and SRCC, suggesting increased tissue stiffness. Conclusions: This proof-of-concept study provides evidence that OCT and OCE may be capable of visualizing differences in tissue structure and stiffness between normal, metaplastic, dysplastic, and early cancerous gastric tissue, potentially providing the basis for improved screening tools with higher sensitivity.

  PublisherOA PDFDOI

• 3D OCT UTJ Datasets

  ReDATA · 2026-03-10

  datasetOpen accessSenior author

  OCT image volumes and data used to support the conclusions of the paper "Quantitative analysis of collagen architecture in the human uterotubal junction (UTJ) using optical coherence tomography imaging (OCT)". Hu# refers to deidentified patient#, 000 scan# to a distinct region of each UTJ imaged (from uterus to isthmus, see utj_scan_segment), and x, y, z pixel size provided in image title (in air). Image volumes were obtained using Thorlabs Tel221 SD-OCT system, and were manually cropped and intensity adjusted.<br><br><br><i>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</i>

  PublisherDOI

• Lens design strategies for miniature scanning fiber endoscopes

  Optical Engineering · 2025-09-22 · 1 citations

  articleSenior authorCorresponding

  This paper provides guidance for the illumination configuration optical design of scanning fiber endoscopes (SFEs), offering insights into salient optical principles and relevant optical system properties, as well as trade-offs and considerations necessary for achieving the desired image performance in miniature endoscopic systems. The specific design examined is a piezoelectric scanner tube-based cantilevered SFE with a concentrically mounted, cantilevered single mode fiber. The assumption of monochromaticity is made for simplicity. Example designs are provided, simulated in Ansys Zemax OpticStudio. The purpose of this guide is to assist designers who may have limited optical design experience by addressing each phase of the SFE design process, from fiber oscillation modeling to optical element selection. Beginning with the motivation for utilizing SFE and introduction of design principles, the guide then describes appropriate approximations for the object, in this case the light emitted from the tip of the scanning fiber over its scanning range (including deflection, sag, and normal angle). Important optical system properties are described, including optical system length, working distance, field of view, throughput, magnification, common aberrations, resolution, and depth of focus, as well as cost. Example optical designs are then modeled in Ansys Zemax OpticStudio, to illustrate common trade-offs in optical performance. The examples are separated into two main categories, variable magnification systems, and fixed magnification systems. Both variable and fixed magnification designs start from a paraxial pre-design followed by a one utilizing real commercial off the shelf (COTS) lenses, both conventional and gradient index (GRIN) lenses. A final design provides an example of optimizing performance priorities utilizing a hybrid of COTS and custom elements. This guide provides the design steps and starting points needed to create an intuitive and well-performing SFE optical design.

  PublisherDOI

• Resolution cascade: simulated MTF of a coherent fiber bundle-based microendoscopic system

  Applied Optics · 2025-12-11 · 1 citations

  articleSenior author

  Despite advances in miniaturization of CMOS sensors, current submillimeter diameter microendoscopic systems rely on coherent fiber bundles to transfer the image from its collection point to the detector. Determining the resolution of an endoscopic optical system that employs a fiber bundle is nontrivial, and there is limited published information about how to calculate the theoretical modulation transfer function (MTF) of a system that may include a distal lens, fiber bundle, relay optics, and a camera sensor. While the fiber bundle is frequently considered the resolution-limiting element, greater information may be gained from computing the full system MTF. In this paper, we describe a resolution cascade method that calculates theoretical MTFs for common components, as well as for the entire microendoscopic system. These theoretical calculations compare favorably to experimentally gathered data for four different optical configurations. The software developed for these calculations is freely available to predict the MTF of other coherent fiber bundle-based systems. Brief instructions and necessary assumptions/conditions are described.

  PublisherDOI

• Optical Coherence Tomography Enables the Depth‐Resolved Measurement of Cilia Beat Frequency in Ex Vivo Human Fallopian Tubes

  Lasers in Surgery and Medicine · 2025-07-18

  articleSenior authorCorresponding

  OBJECTIVES: The movement of cilia in the fallopian tubes (FTs) facilitates important processes involved in fertility, and abnormalities in cilia function are linked with diseases including endometriosis and pelvic inflammatory disease. For the first time, we demonstrate the use of optical coherence tomography (OCT) to create depth-resolved mapping of motile cilia locations and quantify cilia beat frequency (CBF) in human FT samples ex vivo. METHODS: Segments of the FT ampulla were acquired from five patients following salpingectomy under an IRB approved protocol. The samples were longitudinally opened to expose the luminal surface for imaging. A sequence of at least 500 OCT images were acquired at 5-10 locations on each sample. To define the location of the motile cilia in the images, pixel-wise Fast Fourier Transform (FFT) analysis of intensity fluctuations with a sliding temporal window was performed on each image sequence. The frequencies corresponding to the physiological range of CBF (2-10 Hz) were selected for mapping, while the part of the FFT spectrum at higher frequencies (> 23 Hz) was used to define the noise threshold. The frequency with the highest FFT amplitude for each supra-threshold pixel was considered the CBF for this pixel and used to create a color-coded CBF map. The CBF map was overlaid with the OCT intensity image sequences to reveal cilia locations. Frequency histograms from the sliding window were examined to assess temporal consistency of the mapping and evaluate movement artifacts. RESULTS: OCT image sequences clearly showed the structure of FT plicae. The ciliated epithelium was obvious as a "shimmering" (rapidly changing intensity) layer atop plicae. Colored pixels on CBF maps visually aligned to these shimmering regions. Frequency histograms revealed that the image sequence peak CBF could be robustly determined, even in the presence of outliers attributable to table vibrations or bulk sample movement. CONCLUSIONS: OCT can provide depth-resolved maps of CBF in human ex vivo FT tissue. Potentially, this technique can aid in understanding cilia dynamics in the normal human FT over the menstrual cycle and across age, as well as in diseases that affect the FTs. Future work will be directed toward in vivo implementation including miniaturization and robust motion compensation.

  PublisherDOI

Recent grants

• Cardiovascular Biomedical Engineering Training Grant

  NIH · $5.4M · 2000–2022

• NIH Grant R21CA229707

  NIH · $385k · 2022

• NIH Grant R01CA195723

  NIH · $1.1M · 2019

• NIH Grant R01CA119200

  NIH · $1.7M · 2012

• NIH Grant R25EB012973

  NIH · $214k · 2017

Frequent coauthors

• Photini F. S. Rice

  University of Arizona

  58 shared

• Raymond K. Kostuk

  47 shared

• Urs Utzinger

  43 shared

• Ashley J. Welch

  Universitair Ziekenhuis Brussel

  40 shared

• George Barbastathis

  Massachusetts Institute of Technology

  35 shared

• Yuan Luo

  National Taiwan University

  31 shared

• Alexandre R. Tumlinson

  26 shared

• Mark Zealand

  Centre Hospitalier de Beauvais

  25 shared

Labs

• Tissue Optics LabPI