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Rodriguez-Obregon DE, Mejia-Rodriguez AR, Cendejas-Zaragoza L, Gutiérrez Mejía J, Arce-Santana ER, Charleston-Villalobos S, Aljama-Corrales T, Gabutti A, Santos-Díaz A. Semi-Supervised COVID-19 Volumetric Pulmonary Lesion Estimation on CT Images using Probabilistic Active Contour and CNN Segmentation. Biomed Signal Process Control 2023; 85:104905. [PMID: 36993838 PMCID: PMC10030333 DOI: 10.1016/j.bspc.2023.104905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 03/11/2023] [Accepted: 03/18/2023] [Indexed: 03/24/2023]
Abstract
Purpose A semi-supervised two-step methodology is proposed to obtain a volumetric estimation of COVID-19-related lesions on Computed Tomography (CT) images. Methods First, damaged tissue was segmented from CT images using a probabilistic active contours approach. Second, lung parenchyma was extracted using a previously trained U-Net. Finally, volumetric estimation of COVID-19 lesions was calculated considering the lung parenchyma masks. Our approach was validated using a publicly available dataset containing 20 CT COVID-19 images previously labeled and manually segmented. Then, it was applied to 295 COVID-19 patients CT scans admitted to an intensive care unit. We compared the lesion estimation between deceased and survived patients for high and low-resolution images. Results A comparable median Dice similarity coefficient of 0.66 for the 20 validation images was achieved. For the 295 images dataset, results show a significant difference in lesion percentages between deceased and survived patients, with a p-value of 9.1×10−4 in low-resolution and 5.1×10−5 for high-resolution images. Furthermore, the difference in lesion percentages between high and low-resolution images was 10% on average. Conclusion The proposed approach could help estimate the lesion size caused by COVID-19 in CT images and may be considered as an alternative to getting a volumetric segmentation for this novel disease without the requirement of large amounts of COVID-19 labeled data to train an artificial intelligence algorithm. The low variation between the estimated percentage of lesions in high and low-resolution CT images suggests that the proposed approach is robust and It may provide valuable information to differentiate between survived and deceased patients.
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Affiliation(s)
| | | | - Leopoldo Cendejas-Zaragoza
- Tecnologico de Monterrey, School of Engineering and Sciences, Mexico City, Mexico
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Juan Gutiérrez Mejía
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Mexico City, Mexico
| | | | | | | | - Alejandro Gabutti
- Department of Radiology and Imaging, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alejandro Santos-Díaz
- Tecnologico de Monterrey, School of Engineering and Sciences, Mexico City, Mexico
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Monterrey, Mexico
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Cendejas-Zaragoza L, Rodriguez-Obregon DE, Mejia-Rodriguez AR, Arce-Santana ER, Santos-Diaz A. COVID-19 Volumetric Pulmonary Lesion Estimation on CT Images using a U-NET and Probabilistic Active Contour Segmentation. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:3850-3853. [PMID: 34892074 DOI: 10.1109/embc46164.2021.9629532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A two-step method for obtaining a volumetric estimation of COVID-19 related lesion from CT images is proposed. The first step consists in applying a U-NET convolutional neural network to provide a segmentation of the lung-parenchyma. This architecture is trained and validated using the Thoracic Volume and Pleural Effusion Segmentations in Diseased Lungs for Benchmarking Chest CT Processing Pipelines (PleThora) dataset, which is publicly available. The second step consists in obtaining the volumetric lesion estimation using an automatic algorithm based on a probabilistic active contour (PACO) region delimitation approach. Our pipeline successfully segmented COVID-19 related lesions in CT images, with exception of some mislabeled regions including lung airways and vasculature. Our workflow was applied to images in a cohort of 50 patients.
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Ramirez-Zamora A, Giordano J, Boyden ES, Gradinaru V, Gunduz A, Starr PA, Sheth SA, McIntyre CC, Fox MD, Vitek J, Vedam-Mai V, Akbar U, Almeida L, Bronte-Stewart HM, Mayberg HS, Pouratian N, Gittis AH, Singer AC, Creed MC, Lazaro-Munoz G, Richardson M, Rossi MA, Cendejas-Zaragoza L, D'Haese PF, Chiong W, Gilron R, Chizeck H, Ko A, Baker KB, Wagenaar J, Harel N, Deeb W, Foote KD, Okun MS. Proceedings of the Sixth Deep Brain Stimulation Think Tank Modulation of Brain Networks and Application of Advanced Neuroimaging, Neurophysiology, and Optogenetics. Front Neurosci 2019; 13:936. [PMID: 31572109 PMCID: PMC6751331 DOI: 10.3389/fnins.2019.00936] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/21/2019] [Indexed: 02/05/2023] Open
Abstract
The annual deep brain stimulation (DBS) Think Tank aims to create an opportunity for a multidisciplinary discussion in the field of neuromodulation to examine developments, opportunities and challenges in the field. The proceedings of the Sixth Annual Think Tank recapitulate progress in applications of neurotechnology, neurophysiology, and emerging techniques for the treatment of a range of psychiatric and neurological conditions including Parkinson’s disease, essential tremor, Tourette syndrome, epilepsy, cognitive disorders, and addiction. Each section of this overview provides insight about the understanding of neuromodulation for specific disease and discusses current challenges and future directions. This year’s report addresses key issues in implementing advanced neurophysiological techniques, evolving use of novel modulation techniques to deliver DBS, ans improved neuroimaging techniques. The proceedings also offer insights into the new era of brain network neuromodulation and connectomic DBS to define and target dysfunctional brain networks. The proceedings also focused on innovations in applications and understanding of adaptive DBS (closed-loop systems), the use and applications of optogenetics in the field of neurostimulation and the need to develop databases for DBS indications. Finally, updates on neuroethical, legal, social, and policy issues relevant to DBS research are discussed.
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Affiliation(s)
- Adolfo Ramirez-Zamora
- Department of Neurology, Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - James Giordano
- Neuroethics Studies Program, Department of Neurology and Department of Biochemistry, Georgetown University Medical Center, Washington, DC, United States
| | - Edward S Boyden
- Media Laboratory, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Aysegul Gunduz
- Department of Neuroscience and Department of Biomedical Engineering and Department of Neurology, Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Philip A Starr
- Graduate Program in Neuroscience, Department of Neurological Surgery, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, United States
| | - Sameer A Sheth
- Department of Neurological Surgery, Baylor College of Medicine, Houston, TX, United States
| | - Cameron C McIntyre
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Michael D Fox
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Jerrold Vitek
- Department of Neurology, University of Minnesota, Minneapolis, MN, United States
| | - Vinata Vedam-Mai
- Department of Neurosurgery, Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Umer Akbar
- Center for Neurorestoration and Neurotechnology, Rehabilitation R&D Service, Veterans Affairs Medical Center, Brown Institute for Brain Science, Brown University, Providence, RI, United States
| | - Leonardo Almeida
- Department of Neurology, Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Helen M Bronte-Stewart
- Department of Neurology and Department of Neurological Sciences and Department of Neurosurgery, Stanford University, Stanford, CA, United States
| | - Helen S Mayberg
- Department of Neurology and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nader Pouratian
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Aryn H Gittis
- Biological Sciences and Center for Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Annabelle C Singer
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University School of Medicine, Atlanta, GA, United States
| | - Meaghan C Creed
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Gabriel Lazaro-Munoz
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, United States
| | - Mark Richardson
- Center for the Neural Basis of Cognition, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Marvin A Rossi
- Department of Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, IL, United States
| | | | | | - Winston Chiong
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Ro'ee Gilron
- Graduate Program in Neuroscience, Department of Neurological Surgery, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, United States
| | - Howard Chizeck
- Graduate Program in Neuroscience, Department of Electrical Engineering, University of Washington, Seattle, WA, United States
| | - Andrew Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, United States
| | - Kenneth B Baker
- Movement Disorders Program, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Joost Wagenaar
- Department of Neurology, Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States
| | - Noam Harel
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, United States
| | - Wissam Deeb
- Department of Neurology, Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Kelly D Foote
- Department of Neurosurgery, Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Michael S Okun
- Department of Neurology, Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
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Rossi PJ, Gunduz A, Judy J, Wilson L, Machado A, Giordano JJ, Elias WJ, Rossi MA, Butson CL, Fox MD, McIntyre CC, Pouratian N, Swann NC, de Hemptinne C, Gross RE, Chizeck HJ, Tagliati M, Lozano AM, Goodman W, Langevin JP, Alterman RL, Akbar U, Gerhardt GA, Grill WM, Hallett M, Herrington T, Herron J, van Horne C, Kopell BH, Lang AE, Lungu C, Martinez-Ramirez D, Mogilner AY, Molina R, Opri E, Otto KJ, Oweiss KG, Pathak Y, Shukla A, Shute J, Sheth SA, Shih LC, Steinke GK, Tröster AI, Vanegas N, Zaghloul KA, Cendejas-Zaragoza L, Verhagen L, Foote KD, Okun MS. Proceedings of the Third Annual Deep Brain Stimulation Think Tank: A Review of Emerging Issues and Technologies. Front Neurosci 2016; 10:119. [PMID: 27092042 PMCID: PMC4821860 DOI: 10.3389/fnins.2016.00119] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/11/2016] [Indexed: 11/25/2022] Open
Abstract
The proceedings of the 3rd Annual Deep Brain Stimulation Think Tank summarize the most contemporary clinical, electrophysiological, imaging, and computational work on DBS for the treatment of neurological and neuropsychiatric disease. Significant innovations of the past year are emphasized. The Think Tank's contributors represent a unique multidisciplinary ensemble of expert neurologists, neurosurgeons, neuropsychologists, psychiatrists, scientists, engineers, and members of industry. Presentations and discussions covered a broad range of topics, including policy and advocacy considerations for the future of DBS, connectomic approaches to DBS targeting, developments in electrophysiology and related strides toward responsive DBS systems, and recent developments in sensor and device technologies.
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Affiliation(s)
- P Justin Rossi
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Aysegul Gunduz
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Jack Judy
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Linda Wilson
- Formerly affiliated with the International Technology Roadmap for Semiconductors (ITRS) Washington, USA
| | - Andre Machado
- Neurological Institute Cleveland Clinic Cleveland, OH, USA
| | - James J Giordano
- Neuroethics Studies Program, Department of Neurology, Georgetown University Medical Center Washington, DC, USA
| | - W Jeff Elias
- Neurological Surgery and Neurology, Stereotactic and Functional Neurosurgery, Department of Neurosurgery, University of Virginia Health Science Center Charlottesville, VA, USA
| | - Marvin A Rossi
- Department of Neurology, Rush University Medical Center Chicago, IL, USA
| | - Christopher L Butson
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Michael D Fox
- Beth Israel Deaconess Medical Center, Harvard Medical School Boston, MA, USA
| | - Cameron C McIntyre
- Department of Biomedical Engineering, School of Medicine, Case Western Reserve University Cleveland, OH, USA
| | - Nader Pouratian
- Department of Neurosurgery, University of California, Los Angeles Los Angeles, CA, USA
| | - Nicole C Swann
- University of California, San Francisco San Francisco, CA, USA
| | | | | | - Howard J Chizeck
- Department of Electrical Engineering, University of Washington Seattle, WA, USA
| | - Michele Tagliati
- Movement Disorders Program, Department of Neurology, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Andres M Lozano
- Department of Neurosurgery, University of Toronto Toronto, ON, Canada
| | - Wayne Goodman
- The Icahn School of Medicine at Mount Sinai New York, NY, USA
| | | | - Ron L Alterman
- Beth Israel Deaconess Medical Center, Harvard Medical School Boston, MA, USA
| | - Umer Akbar
- Department of Neurology, Alpert Medical School, Brown University Providence, RI, USA
| | | | - Warren M Grill
- Department of Biomedical Engineering, Duke University Durham, NC, USA
| | - Mark Hallett
- National Institute of Neurological Disorders and Stroke, National Institutes of Health Bethesda, MD, USA
| | - Todd Herrington
- Massachusetts General Hospital, Harvard Medical School Boston, MA, USA
| | - Jeffrey Herron
- Department of Electrical Engineering, University of Washington Seattle, WA, USA
| | | | - Brian H Kopell
- The Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Anthony E Lang
- Department of Neurosurgery, University of Toronto Toronto, ON, Canada
| | - Codrin Lungu
- National Institute of Neurological Disorders and Stroke, National Institutes of Health Bethesda, MD, USA
| | - Daniel Martinez-Ramirez
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Alon Y Mogilner
- Department of Neurosurgery-Center for Neuromodulation, NYU Langone Medical Center New York, NY, USA
| | - Rene Molina
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Enrico Opri
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Kevin J Otto
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Karim G Oweiss
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Yagna Pathak
- Neurological Institute, Columbia University Medical Center New York, NY, USA
| | - Aparna Shukla
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Jonathan Shute
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Sameer A Sheth
- Neurological Institute, Columbia University Medical Center New York, NY, USA
| | - Ludy C Shih
- Beth Israel Deaconess Medical Center, Harvard Medical School Boston, MA, USA
| | | | - Alexander I Tröster
- Department of Clinical Neuropsychology, Barrow Neurological Institute Phoenix, AZ, USA
| | - Nora Vanegas
- Neurological Institute, Columbia University Medical Center New York, NY, USA
| | - Kareem A Zaghloul
- National Institute of Neurological Disorders and Stroke, National Institutes of Health Bethesda, MD, USA
| | | | - Leonard Verhagen
- Department of Neurology, Rush University Medical Center Chicago, IL, USA
| | - Kelly D Foote
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
| | - Michael S Okun
- Department of Neuroscience, Center for Movement Disorders and Neurorestoration, University of Florida Gainesville, FL, USA
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