Dr. Andrew Shoffstall Profile

Dr. Andrew Shoffstall

at Case Western Reserve Univ

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Publications (3)

SPIE Journal Paper | 18 June 2024 Open Access

NerveTracker: a Python-based software toolkit for visualizing and tracking groups of nerve fibers in serial block-face microscopy with ultraviolet surface excitation images

Chaitanya Kolluru, Naomi Joseph, James Seckler, Farzad Fereidouni, Richard Levenson, Andrew Shoffstall, Michael Jenkins, David Wilson

JBO, Vol. 29, Issue 07, 076501, (June 2024) https://doi.org/10.1117/12.10.1117/1.JBO.29.7.076501

KEYWORDS: Nerve, Visualization, Image segmentation, Microscopy, Video, 3D applications, Structured optical fibers, Ultraviolet radiation, Imaging systems, Image resolution

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SignificanceInformation about the spatial organization of fibers within a nerve is crucial to our understanding of nerve anatomy and its response to neuromodulation therapies. A serial block-face microscopy method [three-dimensional microscopy with ultraviolet surface excitation (3D-MUSE)] has been developed to image nerves over extended depths ex vivo. To routinely visualize and track nerve fibers in these datasets, a dedicated and customizable software tool is required.AimOur objective was to develop custom software that includes image processing and visualization methods to perform microscopic tractography along the length of a peripheral nerve sample.ApproachWe modified common computer vision algorithms (optic flow and structure tensor) to track groups of peripheral nerve fibers along the length of the nerve. Interactive streamline visualization and manual editing tools are provided. Optionally, deep learning segmentation of fascicles (fiber bundles) can be applied to constrain the tracts from inadvertently crossing into the epineurium. As an example, we performed tractography on vagus and tibial nerve datasets and assessed accuracy by comparing the resulting nerve tracts with segmentations of fascicles as they split and merge with each other in the nerve sample stack.ResultsWe found that a normalized Dice overlap (Dicenorm) metric had a mean value above 0.75 across several millimeters along the nerve. We also found that the tractograms were robust to changes in certain image properties (e.g., downsampling in-plane and out-of-plane), which resulted in only a 2% to 9% change to the mean Dicenorm values. In a vagus nerve sample, tractography allowed us to readily identify that subsets of fibers from four distinct fascicles merge into a single fascicle as we move ∼5 mm along the nerve’s length.ConclusionsOverall, we demonstrated the feasibility of performing automated microscopic tractography on 3D-MUSE datasets of peripheral nerves. The software should be applicable to other imaging approaches. The code is available at https://github.com/ckolluru/NerveTracker.

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Proceedings Article | 15 March 2023 Presentation

Imaging and tracking nerve fibers using block-face serial MUSE microscopy (Conference Presentation)

Chaitanya Kolluru, Aniruddha Upadhye, Andrew Shoffstall, Richard Levenson, Farzad Fereidouni, Michael Jenkins, David Wilson

Proceedings Volume PC12385, PC123850C (2023) https://doi.org/10.1117/12.2647020

KEYWORDS: Nerve, Microscopy, Image resolution, Visualization, Ultraviolet radiation, Stereoscopy, Modulation, Electron microscopy, Electrodes, Diffusion magnetic resonance imaging

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Proceedings Article | 5 March 2021 Presentation + Paper

3D imaging of the vagus nerve fascicular anatomy with cryo-imaging and UV excitation

Chaitanya Kolluru, Ananya Subramaniam, Yehe Liu, Aniruddha Upadhye, Monty Khela, Lindsey Druschel, Farzad Fereidouni, Richard Levenson, Andrew Shoffstall, Michael Jenkins, David Wilson

Proceedings Volume 11649, 1164910 (2021) https://doi.org/10.1117/12.2577037

KEYWORDS: Nerve, Ultraviolet radiation, Stereoscopy, Tissues, Tissue optics, Electrodes, Visualization, Tissue clearing, Image segmentation, Epilepsy

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