Dr. Farzad Fereidouni Profile

Dr. Farzad Fereidouni

Assistant professor at Univ of California Davis

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Publications (14)

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 | 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 | 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 | 17 March 2023 Presentation

Anatomy-specific classification models using FLIm for head & neck cancer surgical guidance

Mohamed Hassan, Brent Weyers, Julien Bec, Farzad Fereidouni, Jinyi Qi, Dorina Gui, Andrew Birkeland, Arnaud Bewley, Marianne Abouyared, D. Gregory Farwell, Laura Marcu

Proceedings Volume 12354, 123540D (2023) https://doi.org/10.1117/12.2651235

KEYWORDS: Tumor growth modeling, Neck, Head, Cancer, Tongue, Tissues, Surgery, Physiology, Oncology, Lymphatic system

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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 | 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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SPIE Journal Paper | 2 February 2022 Open Access

First in patient assessment of brain tumor infiltrative margins using simultaneous time-resolved measurements of 5-ALA-induced PpIX fluorescence and tissue autofluorescence

Alba Alfonso García, Xiangnan Zhou, Julien Bec, Silvia Anbunesan, Farzad Fereidouni, Lee-Way Jin, Han Sung Lee, Orin Bloch, Laura Marcu

JBO, Vol. 27, Issue 02, 020501, (February 2022) https://doi.org/10.1117/12.10.1117/1.JBO.27.2.020501

KEYWORDS: Luminescence, Tumors, Tissues, Brain, Microscopes, In vivo imaging, Surgery, Video, Data acquisition, Visualization

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Significance: 5-aminolevulinic acid (5-ALA)-induced protoporphyrin IX (PpIX) fluorescence is currently used for image-guided glioma resection. Typically, this widefield imaging method highlights the bulk of high-grade gliomas, but it underperforms at the infiltrating edge where PpIX fluorescence is not visible to the eyes. Fluorescence lifetime imaging (FLIm) has the potential to detect PpIX fluorescence below the visible detection threshold. Moreover, simultaneous acquisition of time-resolved nicotinamide adenine (phosphate) dinucleotide [NAD(P)H] fluorescence may provide metabolic information from the tumor environment to further improve overall tumor detection. Aim: We investigate the ability of pulse sampling, fiber-based FLIm to simultaneously image PpIX and NAD(P)H fluorescence of glioma infiltrative margins in patients. Approach: A mesoscopic fiber-based point-scanning FLIm device (355 nm pulses) was used to simultaneously resolve the fluorescence decay of PpIX (629/53 nm) and NAD(P)H (470/28 nm). The FLIm device enabled data acquisition at room light and rapid (<33 ms) augmentation of FLIm parameters on the surgical field-of-view. FLIm measurements from superficial tumors and tissue areas around the resection margins were performed on three glioblastoma patients in vivo following inspection of PpIX visible fluorescence with a conventional neurosurgical microscope. Microbiopsies were collected from FLIm imaged areas for histopathological evaluation. Results: The average lifetime from PpIX and NAD(P)H fluorescence distinguished between tumor and surrounding tissue. FLIm measurements of resection margins presented a range of PpIX and NAD(P)H lifetime values (τPpIX   ∼ 3 to 14 ns, τNAD(P)H = 3 to 6 ns) associated with unaffected tissue and areas of low-density tumor infiltration. Conclusions: Intraoperative FLIm could simultaneously detect the emission of PpIX and NAD(P)H from patients in vivo during craniotomy procedures. This approach doubles as a clinical tool to identify tumor areas while performing tissue resection and as a research tool to study tumor microenvironmental changes in vivo. Intraoperative FLIm of 5-ALA-induced PpIX and tissue autofluorescence makes a promising surgical adjunct to guide tumor resection surgery.

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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 | 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 | 5 March 2015 Paper

Time-resolved spectral imaging: better photon economy, higher accuracy

Farzad Fereidouni, Keimpe Reitsma, Gerhard Blab, Hans Gerritsen

Proceedings Volume 9329, 93290H (2015) https://doi.org/10.1117/12.2080392

KEYWORDS: Fluorescence resonance energy transfer, Molecules, Imaging systems, Luminescence, Imaging spectroscopy, Field programmable gate arrays, Picosecond phenomena, Molecular interactions, Photodetectors, Quantum efficiency

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SPIE Journal Paper | 12 August 2013 Open Access

Blind unmixing of spectrally resolved lifetime images

Farzad Fereidouni, Gerhard Blab, Hans Gerritsen

JBO, Vol. 18, Issue 08, 086006, (August 2013) https://doi.org/10.1117/12.10.1117/1.JBO.18.8.086006

KEYWORDS: Image segmentation, Luminescence, Visualization, Clouds, Superposition, Binary data, RGB color model, Image analysis, Photons, Picosecond phenomena

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