Software engineer specializing in medical imaging, computer vision, and 3D reconstruction.
eimenrachel@gmail.com
About Me
I am a software engineer specializing in computer vision and image processing for
medical applications. I hold a Ph.D. in Biomedical Engineering from Vanderbilt University
and a B.S. in Computer Engineering from Clemson University.
Currently, I serve as the lead software engineer at Yaya Scientific, LLC,
developing tools for nerve detection in surgical settings.
Research Interests: Computer vision, image processing, 3D reconstruction, artificial intelligence (AI), real-time image analysis.
Experience: My expertise spans software development and algorithm design, computer vision, image processing, and 3D reconstruction for clinical use. I have worked extensively on projects involving virtual simulation, frame reacquisition, artificial intelligence (AI), and real-time image analysis, with applications in urology, gastroenterology, and neurosurgery.
Projects
AlinaTM for Intraoperative Nerve Imaging
Working as the lead software engineer for a translational medical imaging device at Yaya Scientific, LLC. I pilot software design and development efforts, research implementation strategy, and manage co-workers on the software development team.
Architecting and implementing real-time software to control a custom hardware setup to collect and process polarized and non-polarized imaging data for nerve detection in surgical settings using Python, artificial intelligence (AI), image processing, and computer vision, enabling actionable intraoperative feedback and improving accuracy for intraoperative nerve detection.
Helped plan, execute, and deliver the first clinical evaluation prototype — currently deployed at two surgical research sites to generate validation data for nerve-detection algorithms.
Designing image-processing and 3D vision pipelines for high-dynamic range (HDR), multi-camera view registration, and intensity-based nerve segmentation using porcine and human data.
Designing a custom UI/UX for real-time data acquisition, processing, and clinical feedback using Python, DearPyGUI, and OpenCV, enabling efficient surgeon-in-the-loop testing.
3D Virtual Bladder Reconstruction
Dissertation research developing software to improve virtual 3D reconstruction of the bladder from clinical white light cystoscopy videos and to facilitate technical development of clinical tools.
Fiberscope Data Reconstruction: Developed a novel algorithm to produce accurate 3D bladder reconstructions from flexible cystoscopy videos captured with a fiberscope.
Frame Reacquisition: Created a real-time pipeline to detect low-quality frames that inhibit reconstruction and provide immediate clinician feedback for recollection.
Virtual Cystoscopy Simulator: Built a realistic, customizable simulator in Blender to mimic clinical imaging conditions (motion blur, debris) for development and testing of reconstruction technology.
Virtual Endoscopy Simulator
Collaborated on creating a virtual endoscopy simulator to assess the effect of varying imaging conditions on 3D reconstructions, enabling controlled evaluation of algorithm robustness.
Specular Reflection Removal
Mentored undergraduate development of an algorithm to remove specular reflections from endoscopy videos by replacing affected regions with organ views from other frames.
fNIRS Alignment and Optimization
Helped a Ph.D. candidate to develop a method of ensuring proper alignment of a wearable functional Near Infrared Spectroscopy (fNIRS) system.
Worked on a team to optimize real-time code for an fNIRS application.
Aided in fNIRS data collection through an IRB-approved study.
Publications, Software & Presentations
Show Full Publications
S. B. Crawford, D. Liu, C. Caveness, R. Eimen, A. K. Bowden, "Distinguishing Fowler’s and Semi-Fowler’s Patient Postures Within Continuous-Wave Functional Near-Infrared Spectroscopy During Auditory Stimulus and Resting," Brain Sciences 15(11), 1172 (2025). DOI
R. Eimen, K. R. Scarpato, and A. K. Bowden, "Virtual simulator for cystoscopy containing motion blur and bladder debris to aid the development of clinical tools," Biomed Opt Express, 15(11), 6228 (2024). DOI | Code
R. Eimen, M. Pillai, K. R. Scarpato, and A. K. Bowden, "Towards improved 3D reconstruction of cystoscopies through real-time feedback for frame reacquisition," Biomedical Optics Express, 15(5), 3394–3411 (2024). DOI | Code
R. L. Eimen, H. Krzyzanowska, K. R. Scarpato, and A. K. Bowden, "Fiberscopic pattern removal for optimal coverage in 3D bladder reconstructions of fiberscope cystoscopy videos," Journal of Medical Imaging, 11(3), 034002 (2024). DOI | Code
H. Yin, R. Eimen, D. Moyer, and A. K. Bowden, "SpecReFlow: an algorithm for specular reflection restoration using flow-guided video completion," Journal of Medical Imaging, 11(02), (2024). DOI | Code
Y. Zhou, R. Eimen, E. J. Seibel, and A. K. Bowden, "Cost-Efficient Video Synthesis and Evaluation for Development of Virtual 3D Endoscopy," IEEE J Transl Eng Health Med, 9, (2021). DOI | Code
Show Software Releases
R. Eimen, K. R. Scarpato, and A. K. Bowden, EVS3D-Cysto (2024).
H. Yin, R. L. Eimen, D. Moyer, and A. K. Bowden, SpecReFlow (2024).
Y. Zhou, R. Eimen, E. Seibel, and A. K. Bowden, EVS-3D (2021).
Show Presentations
"Towards improved 3D reconstruction of cystoscopies through real-time feedback for frame reacquisition," Vanderbilt Institute for Surgery and Engineering Presentation Bootcamp (2024).
"An improved virtual simulator for clinical cystoscopy," Gordon Research Conference / Gordon Research Seminar (2024).
"SpecFlow: an end-to-end framework for specular reflection restoration in endoscopy videos," SPIE Photonics West (2023).
"A real-time classifier to predict the contribution of cystoscopy frames to 3D reconstructions," SPIE Photonics West (2023).
"Software tools to enable 3D bladder reconstruction from clinical white light cystoscopy videos," 3-Minute Thesis Competition, Vanderbilt University (2023).
"Removing a fiberscope-induced pattern from flexible cystoscopy frames to enable 3D bladder reconstructions," Engineering & Urology Society Annual Meeting (2022).
"A metric to predict the utility of cystoscopy frames in 3D bladder reconstructions," Engineering & Urology Society Annual Meeting (2022).
"Point-of-Care Clinician Guidance to Improve 3D Bladder Reconstructions," VISE Symposium (2021).
"Real-Time Clinician Guidance to Improve 3D Bladder Reconstructions," VISE Research in Progress Seminar (2021).
