Dr. Richard M. Levenson Profile

Dr. Richard M. Levenson

Professor at UC Davis Health System

SPIE Involvement:

Conference Program Committee | Author | Editor | Instructor

Area of Expertise:

pathology , microscopy , image analysis , in vivo imaging

Publications (28)

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 | 3 April 2024 Presentation

Quantitative oblique back-illumination microscopy (qOBM) for stain-free tissue imaging with cycleGAN mode conversion can emulate H&E histology

Tanishq Abraham, Paloma Costa, Caroline Serafini, Francisco Robles, Richard Levenson

Proceedings Volume 12933, 1293311 (2024) https://doi.org/10.1117/12.3008530

KEYWORDS: Tissues, Microscopy, Tumors, Standards development, In vivo imaging, Education and training, Data modeling, 3D imaging standards, Spatial resolution, Phase imaging

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Proceedings Article | 13 March 2024 Presentation + Paper

Utilizing DUET imaging for quantification of collagen and elastin as biomarkers for studying disease

Willy Ju, Samuel Border, Anupam Mitra, Eniola Okon, Hyunjae Jeong, Richard Levenson, Avi Rosenberg, Kuang-Yu Jen, Pinaki Sarder, Farzad Fereidouni

Proceedings Volume 12862, 1286206 (2024) https://doi.org/10.1117/12.3009357

KEYWORDS: Collagen, Arteries, Fluorescence, Vascular diseases, Kidney, Tumors, Tissues, Diseases and disorders, Computer aided detection, Pathology

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Proceedings Article | 13 March 2024 Presentation

Towards in-vivo, non-invasive, label-free, real-time 3D H&E imaging for clinical applications via 3D phase contrast from quantitative oblique back illumination microcopy (qOBM)

Francisco Robles, Richard Levenson, Tanishq Abraham, Paloma Casteleiro Costa, Zhe Guang, Caroline Serafini

Proceedings Volume PC12852, PC128520Z (2024) https://doi.org/10.1117/12.3008577

KEYWORDS: 3D image processing, Biological imaging, Tissues, Stereoscopy, Real time imaging, Light sources and illumination, Biomedical applications, Phase contrast, In vivo imaging, 3D applications

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Proceedings Article | 7 April 2023 Presentation + Paper

Improving quantification of renal fibrosis using deep-DUET

Samuel Border, Avi Rosenberg, Jarcy Zee, Richard Levenson, Kuang-Yu Jen, Pinaki Sarder, Farzad Fereidouni

Proceedings Volume 12471, 124710G (2023) https://doi.org/10.1117/12.2654651

KEYWORDS: Collagen, Fluorescence, Image segmentation, Data modeling, Tissues, Pathology, Diseases and disorders, Biopsy, Reproducibility

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Proceedings Article | 16 March 2023 Presentation + Paper

Mode conversion of qOBM (quantitative oblique back-illumination microscopy) stain-free tissue images to emulate H&E histology via deep learning

Tanishq Mathew Abraham, Paloma Casteleiro Costa, Caroline Serafini, Francisco Robles, Richard Levenson

Proceedings Volume 12391, 1239109 (2023) https://doi.org/10.1117/12.2649484

KEYWORDS: Tissues, Education and training, Tumors, Microscopy, Deep learning, Brain tissue, Brain, Biological samples, Microscopes, Image classification

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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 | 20 May 2022 Presentation + Paper

Mode-mapping qOBM microscopy to virtual hematoxylin and eosin (H&E) histology via deep learning

Tanishq Mathew Abraham, Paloma Casteleiro Costa, Caroline Serafini, Francisco Robles, Richard Levenson

Proceedings Volume 12136, 121360Q (2022) https://doi.org/10.1117/12.2622160

KEYWORDS: Microscopy, Tumors, Tissues, Brain, Neuroimaging, Tissue optics, Imaging systems, Cancer, Phase contrast, Objectives

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Proceedings Article | 4 April 2022 Presentation

FIBI: a direct-to-digital microscopy approach for slide-free histology

Farzad Fereidouni, Taryn Morningstar, Alexander Borowsky, Richard Levenson

Proceedings Volume 12039, 1203903 (2022) https://doi.org/10.1117/12.2612748

KEYWORDS: Tissues, Microscopy, Pathology, Tissue optics, Telepathology, Surgery, Natural surfaces, Luminescence, Gold, Glasses

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Proceedings Article | 4 April 2022 Presentation

DUET dual-mode scanning of H&E slides reveals novel contrast

Farzad Fereidouni, Richard Levenson

Proceedings Volume 12039, 120390O (2022) https://doi.org/10.1117/12.2611917

KEYWORDS: Tissues, Scanners, Luminescence, Image processing, Image enhancement, Collagen

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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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Proceedings Article | 14 March 2018 Presentation

MUSE microscopy for thick tissue imaging with extended depth of field (Conference Presentation)

Farzad Fereidouni, John Tracy, Richard Levenson

Proceedings Volume 10489, 104890H (2018) https://doi.org/10.1117/12.2291087

KEYWORDS: Microscopy, Tissues, Ultraviolet radiation, Natural surfaces, Focus stacking, Luminescence, Nondestructive evaluation, Visible radiation

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Proceedings Article | 26 April 2016 Presentation

Slide-free histology via MUSE: UV surface excitation microscopy for imaging unsectioned tissue (Conference Presentation)

Richard Levenson, Zachary Harmany, Stavros Demos, Farzad Fereidouni

Proceedings Volume 9703, 97030J (2016) https://doi.org/10.1117/12.2219407

KEYWORDS: Tissues, Ultraviolet radiation, Natural surfaces, Microscopy, Tissue optics, Image resolution, Multiphoton microscopy, Nondestructive evaluation, Confocal microscopy, Optical coherence tomography

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Proceedings Article | 24 March 2016 Paper

The potential of pigeons as surrogate observers in medical image perception studies

Elizabeth Krupinski, Richard Levenson, Victor Navarro, Edward Wasserman

Proceedings Volume 9787, 97870J (2016) https://doi.org/10.1117/12.2207774

KEYWORDS: Medical imaging, Image quality, Visualization, Pathology, Image quality standards, Breast cancer, Breast, Tumor growth modeling, Image compression, Neodymium, Mammography, Visual compression, Radiology

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Proceedings Article | 11 March 2015 Paper

Microscopy with UV Surface Excitation (MUSE) for slide-free histology and pathology imaging

Farzad Fereidouni, Ananya Datta Mitra, Stavros Demos, Richard Levenson

Proceedings Volume 9318, 93180F (2015) https://doi.org/10.1117/12.2080408

KEYWORDS: Tissues, Ultraviolet radiation, Tissue optics, Microscopy, Light emitting diodes, Kidney, Natural surfaces, Luminescence, Pathology, Tunable lasers

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Proceedings Article | 9 March 2015 Paper

Translational cancer vaccine: from mouse to human to cat

Richard Levenson

Proceedings Volume 9324, 93240C (2015) https://doi.org/10.1117/12.2079538

KEYWORDS: Tumors, Cancer, Therapeutics, Biopsy, Teeth, Bone, Positron emission tomography, Diffusers, Computed tomography, Fiber lasers

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SPIE Journal Paper | 5 November 2013 Open Access

High-speed spectral nanocytology for early cancer screening

John Chandler, Hariharan Subramanian, Charles Maneval, Craig White, Richard Levenson, Vadim Backman

JBO, Vol. 18, Issue 11, 117002, (November 2013) https://doi.org/10.1117/12.10.1117/1.JBO.18.11.117002

KEYWORDS: Cancer, Diagnostics, Lung cancer, Spectroscopy, Algorithm development, Cervical cancer, Image segmentation, Cameras, Cell biology, Imaging systems

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SPIE Journal Paper | 6 September 2012 Open Access

Dynamic contrast-enhanced optical imaging of in vivo organ function

Cyrus Amoozegar, Tracy Wang, Matthew Bouchard, Addason McCaslin, Elizabeth Hillman, William Blaner, Richard Levenson

JBO, Vol. 17, Issue 9, 096003, (September 2012) https://doi.org/10.1117/12.10.1117/1.JBO.17.9.096003

KEYWORDS: Liver, Kidney, In vivo imaging, Optical imaging, Blood, Imaging systems, Tumors, Data acquisition, Tissue optics, Veins

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SPIE Journal Paper | 1 September 2007 Open Access

Validation of novel optical imaging technologies: the pathologists' view

Wendy Wells, Peter Barker, Calum MacAulay, Marco Novelli, Richard Levenson, James Crawford

JBO, Vol. 12, Issue 05, 051801, (September 2007) https://doi.org/10.1117/12.10.1117/1.2795569

KEYWORDS: Tissue optics, Optical imaging, Pathology, Tissues, Standards development, Diagnostics, Image analysis, Medicine, Imaging spectroscopy, Spectroscopy

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SPIE Journal Paper | 1 September 2007 Open Access

Recent advances in catheter-based optical coherence tomography (OCT) have provided the necessary resolution and acquisition speed for high-quality intravascular imaging. Complications associated with clearing blood from the vessel of a living patient have

Matthew Bouchard, Sarah MacLaurin, Peter Dwyer, James Mansfield, Richard Levenson, Thomas Krucker

JBO, Vol. 12, Issue 05, 051601, (September 2007) https://doi.org/10.1117/12.10.1117/1.2799188

KEYWORDS: Luminescence, Skin, In vivo imaging, Multispectral imaging, Imaging systems, Molecular imaging, Signal detection, Data acquisition, Visible radiation, Drug discovery

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SPIE Journal Paper | 1 July 2005 Open Access

Autofluorescence removal, multiplexing, and automated analysis methods for in-vivo fluorescence imaging

James Mansfield, Kirk Gossage, Clifford Hoyt, Richard Levenson

JBO, Vol. 10, Issue 04, 041207, (July 2005) https://doi.org/10.1117/12.10.1117/1.2032458

KEYWORDS: Quantum dots, Luminescence, Multiplexing, Multispectral imaging, RGB color model, In vivo imaging, Skin, Imaging systems, Imaging spectroscopy, Tissues

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Proceedings Article | 2 July 2003 Paper

Spectral imaging for brightfield microscopy

Richard Levenson, Paul Cronin, Kirill Pankratov

Proceedings Volume 4959, (2003) https://doi.org/10.1117/12.485550

KEYWORDS: Imaging spectroscopy, RGB color model, Liquid crystals, Tunable filters, Microscopy, Pathology, Light sources, Optical filters, Luminescence, Multiplexing

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Proceedings Article | 15 May 2003 Paper

Investigation of automated feature extraction techniques for applications in cancer detection from multispectral histopathology images

Neal Harvey, Richard Levenson, David Rimm

Proceedings Volume 5032, (2003) https://doi.org/10.1117/12.480831

KEYWORDS: Cancer, Tissues, Image classification, Feature extraction, Multispectral imaging, Breast, Pathology, Image processing, Satellite imaging, Earth observing sensors

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Proceedings Article | 2 July 2001 Paper

Beyond image cubes: an agile lamp for practical 100% photon-efficient spectral imaging

Peter Miller, Richard Levenson

Proceedings Volume 4259, (2001) https://doi.org/10.1117/12.432485

KEYWORDS: Fiber optic illuminators, Sensors, Image filtering, Lamps, Imaging spectroscopy, Optical filters, Imaging systems, Image processing, Interferometers, Tunable filters

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Proceedings Article | 22 May 2001 Paper

Novel high-sensitivity fluorescence polarization reader

Clifford Hoyt, Richard Levenson, Peter Banks

Proceedings Volume 4255, (2001) https://doi.org/10.1117/12.426755

KEYWORDS: Polarization, Luminescence, Liquid crystals, CCD cameras, Molecules, Receptors, Drug discovery, Charge-coupled devices, Signal detection, Prototyping

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Proceedings Article | 21 April 1999 Paper

Biomedical applications of the information-efficient spectral imaging sensor (ISIS)

Stephen Gentry, Richard Levenson

Proceedings Volume 3603, (1999) https://doi.org/10.1117/12.346734

KEYWORDS: RGB color model, Sensors, Colorectal cancer, Biomedical optics, Imaging spectroscopy, Image sensors, Image classification, Optical filters, Imaging systems, Signal to noise ratio

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Proceedings Article | 16 October 1998 Paper

Spectral imaging in biomedicine: a selective overview

Richard Levenson, Elliot Wachman, Wenhua Niu, Daniel Farkas

Proceedings Volume 3438, (1998) https://doi.org/10.1117/12.328111

KEYWORDS: Imaging spectroscopy, Tissues, Spectroscopy, Optical filters, Pathology, Image filtering, Luminescence, Infrared imaging, Infrared radiation, Tunable filters

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Proceedings Article | 23 May 1997 Paper

Digital spectral imaging for histopathology and cytopathology

Richard Levenson, Daniel Farkas

Proceedings Volume 2983, (1997) https://doi.org/10.1117/12.274331

KEYWORDS: Imaging spectroscopy, Diagnostics, Image segmentation, Tumors, Pathology, Cancer, Tissues, Statistical analysis, Breast cancer, Biopsy

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Showing 5 of 28 publications

Proceedings Volume Editor (8)

SPIE Conference Volume | 2 May 2022

Medical Imaging 2022: Digital and Computational Pathology

SPIE Conference Volume | 1 April 2005

Advanced Biomedical and Clinical Diagnostic Systems III

SPIE Conference Volume | 23 March 2005

Spectral Imaging: Instrumentation, Applications, and Analysis III

SPIE Conference Volume | 1 July 2004

Advanced Biomedical and Clinical Diagnostic Systems II

SPIE Conference Volume | 22 July 2003

Advanced Biomedical and Clinical Diagnostic Systems

Showing 5 of 8 publications

Conference Committee Involvement (29)