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Abd-Alrazaq A, Alajlani M, Ahmad R, AlSaad R, Aziz S, Ahmed A, Alsahli M, Damseh R, Sheikh J. The Performance of Wearable AI in Detecting Stress Among Students: Systematic Review and Meta-Analysis. J Med Internet Res 2024; 26:e52622. [PMID: 38294846 PMCID: PMC10867751 DOI: 10.2196/52622] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/24/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Students usually encounter stress throughout their academic path. Ongoing stressors may lead to chronic stress, adversely affecting their physical and mental well-being. Thus, early detection and monitoring of stress among students are crucial. Wearable artificial intelligence (AI) has emerged as a valuable tool for this purpose. It offers an objective, noninvasive, nonobtrusive, automated approach to continuously monitor biomarkers in real time, thereby addressing the limitations of traditional approaches such as self-reported questionnaires. OBJECTIVE This systematic review and meta-analysis aim to assess the performance of wearable AI in detecting and predicting stress among students. METHODS Search sources in this review included 7 electronic databases (MEDLINE, Embase, PsycINFO, ACM Digital Library, Scopus, IEEE Xplore, and Google Scholar). We also checked the reference lists of the included studies and checked studies that cited the included studies. The search was conducted on June 12, 2023. This review included research articles centered on the creation or application of AI algorithms for the detection or prediction of stress among students using data from wearable devices. In total, 2 independent reviewers performed study selection, data extraction, and risk-of-bias assessment. The Quality Assessment of Diagnostic Accuracy Studies-Revised tool was adapted and used to examine the risk of bias in the included studies. Evidence synthesis was conducted using narrative and statistical techniques. RESULTS This review included 5.8% (19/327) of the studies retrieved from the search sources. A meta-analysis of 37 accuracy estimates derived from 32% (6/19) of the studies revealed a pooled mean accuracy of 0.856 (95% CI 0.70-0.93). Subgroup analyses demonstrated that the accuracy of wearable AI was moderated by the number of stress classes (P=.02), type of wearable device (P=.049), location of the wearable device (P=.02), data set size (P=.009), and ground truth (P=.001). The average estimates of sensitivity, specificity, and F1-score were 0.755 (SD 0.181), 0.744 (SD 0.147), and 0.759 (SD 0.139), respectively. CONCLUSIONS Wearable AI shows promise in detecting student stress but currently has suboptimal performance. The results of the subgroup analyses should be carefully interpreted given that many of these findings may be due to other confounding factors rather than the underlying grouping characteristics. Thus, wearable AI should be used alongside other assessments (eg, clinical questionnaires) until further evidence is available. Future research should explore the ability of wearable AI to differentiate types of stress, distinguish stress from other mental health issues, predict future occurrences of stress, consider factors such as the placement of the wearable device and the methods used to assess the ground truth, and report detailed results to facilitate the conduct of meta-analyses. TRIAL REGISTRATION PROSPERO CRD42023435051; http://tinyurl.com/3fzb5rnp.
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Affiliation(s)
- Alaa Abd-Alrazaq
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha, Qatar
| | - Mohannad Alajlani
- Institute of Digital Healthcare, WMG, University of Warwick, Warwick, United Kingdom
| | - Reham Ahmad
- Institute of Digital Healthcare, WMG, University of Warwick, Warwick, United Kingdom
| | - Rawan AlSaad
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha, Qatar
| | - Sarah Aziz
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha, Qatar
| | - Arfan Ahmed
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha, Qatar
| | - Mohammed Alsahli
- Health Informatics Department, College of Health Science, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Rafat Damseh
- Department of Computer Science and Software Engineering, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Javaid Sheikh
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha, Qatar
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Abd-Alrazaq A, AlSaad R, Harfouche M, Aziz S, Ahmed A, Damseh R, Sheikh J. Wearable Artificial Intelligence for Detecting Anxiety: Systematic Review and Meta-Analysis. J Med Internet Res 2023; 25:e48754. [PMID: 37938883 PMCID: PMC10666012 DOI: 10.2196/48754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/29/2023] [Accepted: 09/26/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Anxiety disorders rank among the most prevalent mental disorders worldwide. Anxiety symptoms are typically evaluated using self-assessment surveys or interview-based assessment methods conducted by clinicians, which can be subjective, time-consuming, and challenging to repeat. Therefore, there is an increasing demand for using technologies capable of providing objective and early detection of anxiety. Wearable artificial intelligence (AI), the combination of AI technology and wearable devices, has been widely used to detect and predict anxiety disorders automatically, objectively, and more efficiently. OBJECTIVE This systematic review and meta-analysis aims to assess the performance of wearable AI in detecting and predicting anxiety. METHODS Relevant studies were retrieved by searching 8 electronic databases and backward and forward reference list checking. In total, 2 reviewers independently carried out study selection, data extraction, and risk-of-bias assessment. The included studies were assessed for risk of bias using a modified version of the Quality Assessment of Diagnostic Accuracy Studies-Revised. Evidence was synthesized using a narrative (ie, text and tables) and statistical (ie, meta-analysis) approach as appropriate. RESULTS Of the 918 records identified, 21 (2.3%) were included in this review. A meta-analysis of results from 81% (17/21) of the studies revealed a pooled mean accuracy of 0.82 (95% CI 0.71-0.89). Meta-analyses of results from 48% (10/21) of the studies showed a pooled mean sensitivity of 0.79 (95% CI 0.57-0.91) and a pooled mean specificity of 0.92 (95% CI 0.68-0.98). Subgroup analyses demonstrated that the performance of wearable AI was not moderated by algorithms, aims of AI, wearable devices used, status of wearable devices, data types, data sources, reference standards, and validation methods. CONCLUSIONS Although wearable AI has the potential to detect anxiety, it is not yet advanced enough for clinical use. Until further evidence shows an ideal performance of wearable AI, it should be used along with other clinical assessments. Wearable device companies need to develop devices that can promptly detect anxiety and identify specific time points during the day when anxiety levels are high. Further research is needed to differentiate types of anxiety, compare the performance of different wearable devices, and investigate the impact of the combination of wearable device data and neuroimaging data on the performance of wearable AI. TRIAL REGISTRATION PROSPERO CRD42023387560; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=387560.
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Affiliation(s)
- Alaa Abd-Alrazaq
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Rawan AlSaad
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Manale Harfouche
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Sarah Aziz
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Arfan Ahmed
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Rafat Damseh
- Department of Computer Science and Software Engineering, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Javaid Sheikh
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
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Delafontaine-Martel P, Zhang C, Lu X, Damseh R, Lesage F, Marchand PJ. Targeted capillary photothrombosis via multiphoton excitation of Rose Bengal. J Cereb Blood Flow Metab 2023; 43:1713-1725. [PMID: 36647768 PMCID: PMC10581236 DOI: 10.1177/0271678x231151560] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/18/2023]
Abstract
Microvascular stalling, the process occurring when a capillary temporarily loses perfusion, has gained increasing interest in recent years through its demonstrated presence in various neuropathologies. Studying the impact of such stalls on the surrounding brain tissue is of paramount importance to understand their role in such diseases. Despite efforts trying to study the stalling events, investigations are hampered by their elusiveness and scarcity. In an attempt to alleviate these hurdles, we present here a novel methodology enabling transient occlusions of targeted microvascular segments through multiphoton excitation of Rose Bengal, an established photothrombotic agent. With n = 7 mice C57BL/6 J (5 males and 2 females) and 95 photothrombosis trials, we demonstrate the ability of triggering reversible blockages by illuminating a capillary segment during ∼300 s at 1000 nm, using a standard Ti:Sapphire femtosecond laser. Furthermore, we performed concurrent Optical Coherence Microscopy (OCM) angiography imaging of the microvascular network to highlight the specificity of the targeted occlusion and its duration. Through comparison with a control group, we conclude that blood flow cessation is indeed created by the photothrombotic agent via multiphoton excitation and is temporary, followed by a flow recovery in less than 24 h. Moreover, Immunohistology points toward a stalling mechanism driven by adherence of the neutrophil in the vascular lumen. This observation seems to be promoted by the inflammation locally created via multiphoton activation of Rose Bengal.
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Affiliation(s)
- Patrick Delafontaine-Martel
- Department of Electrical Engineering, Polytechnique Montreal, Montreal, Canada
- Research Center, Montreal Heart Institute, Montreal, Canada
| | - Cong Zhang
- Department of Electrical Engineering, Polytechnique Montreal, Montreal, Canada
- Research Center, Montreal Heart Institute, Montreal, Canada
| | - Xuecong Lu
- Research Center, Montreal Heart Institute, Montreal, Canada
- DeGroote School of Business – McMaster University, Ontario, Canada
| | - Rafat Damseh
- Research Center, Montreal Heart Institute, Montreal, Canada
- College of Information Technology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Frédéric Lesage
- Department of Electrical Engineering, Polytechnique Montreal, Montreal, Canada
- Research Center, Montreal Heart Institute, Montreal, Canada
| | - Paul J Marchand
- Department of Electrical Engineering, Polytechnique Montreal, Montreal, Canada
- Research Center, Montreal Heart Institute, Montreal, Canada
- École polytechnique fédérale de Lausanne- EPFL, Lausanne, Switzerland
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Alomoush W, Khashan OA, Alrosan A, Damseh R, Attar HH, Alshinwan M, Abd-alrazaq AA. MRI brain segmentation based on improved global best-guided artificial bee colony.. [DOI: 10.21203/rs.3.rs-3097202/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Abstract
Brain Magnetic Resonance Imaging (MRI) plays a critical role in medical research and clinical applications, ranging from quantifying tissue volume, facilitating surgical simulations, assisting in treatment planning, enabling brain mapping, aiding in disease diagnosis, and evaluating therapeutic efficacy. This study introduces a novel method for MRI brain segmentation, which harnesses the power of a hybrid approach combining Artificial Bee Colony (ABC) algorithm with Fuzzy C-Means (FCM) clustering. Our approach leverages the exploration capability of the ABC algorithm, with an improved global best guidance (IABC), to optimally initialize the cluster centroid values of the FCM, thus enhancing the segmentation outputs. Comparative evaluation of the proposed method, denoted as IABC-FCM, conducted on a diverse set of MRI brain images, reveals its superior performance. The results indicate the potential of this hybrid approach as a robust tool for improved MRI brain segmentation tasks.
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Abd-Alrazaq A, AlSaad R, Alhuwail D, Ahmed A, Healy PM, Latifi S, Aziz S, Damseh R, Alabed Alrazak S, Sheikh J. Large Language Models in Medical Education: Opportunities, Challenges, and Future Directions. JMIR Med Educ 2023; 9:e48291. [PMID: 37261894 DOI: 10.2196/48291] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
The integration of large language models (LLMs), such as those in the Generative Pre-trained Transformers (GPT) series, into medical education has the potential to transform learning experiences for students and elevate their knowledge, skills, and competence. Drawing on a wealth of professional and academic experience, we propose that LLMs hold promise for revolutionizing medical curriculum development, teaching methodologies, personalized study plans and learning materials, student assessments, and more. However, we also critically examine the challenges that such integration might pose by addressing issues of algorithmic bias, overreliance, plagiarism, misinformation, inequity, privacy, and copyright concerns in medical education. As we navigate the shift from an information-driven educational paradigm to an artificial intelligence (AI)-driven educational paradigm, we argue that it is paramount to understand both the potential and the pitfalls of LLMs in medical education. This paper thus offers our perspective on the opportunities and challenges of using LLMs in this context. We believe that the insights gleaned from this analysis will serve as a foundation for future recommendations and best practices in the field, fostering the responsible and effective use of AI technologies in medical education.
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Affiliation(s)
- Alaa Abd-Alrazaq
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Rawan AlSaad
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Doha, Qatar
- College of Computing and Information Technology, University of Doha for Science and Technology, Doha, Qatar
| | - Dari Alhuwail
- Information Science Department, College of Life Sciences, Kuwait University, Kuwait, Kuwait
| | - Arfan Ahmed
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Padraig Mark Healy
- Office of Educational Development, Division of Medical Education, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Syed Latifi
- Office of Educational Development, Division of Medical Education, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Sarah Aziz
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Rafat Damseh
- Department of Computer Science and Software Engineering, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - Sadam Alabed Alrazak
- Department of Mechanical & Industrial Engineering, Faculty of Applied Science and Engineering, University of Toronto, Toronto, ON, Canada
| | - Javaid Sheikh
- AI Center for Precision Health, Weill Cornell Medicine-Qatar, Doha, Qatar
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Abd-alrazaq A, Alsaad R, Alhuwail D, Ahmed A, Healy PM, Latifi S, Aziz S, Damseh R, Alabed Alrazak S, Sheikh J. Large Language Models in Medical Education: Opportunities, Challenges, and Future Directions (Preprint).. [DOI: 10.2196/preprints.48291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
UNSTRUCTURED
The integration of large language models (LLMs), such as those in the Generative Pre-trained Transformers (GPT) series, into medical education has the potential to transform learning experiences for students and elevate their knowledge, skills, and competence. Drawing on a wealth of professional and academic experience, we propose that LLMs hold promise for revolutionizing medical curriculum development, teaching methodologies, personalized study plans and learning materials, student assessments, and more. However, we also critically examine the challenges that such integration might pose by addressing issues of algorithmic bias, overreliance, plagiarism, misinformation, inequity, privacy, and copyright concerns in medical education. As we navigate the shift from an information-driven educational paradigm to an artificial intelligence (AI)–driven educational paradigm, we argue that it is paramount to understand both the potential and the pitfalls of LLMs in medical education. This paper thus offers our perspective on the opportunities and challenges of using LLMs in this context. We believe that the insights gleaned from this analysis will serve as a foundation for future recommendations and best practices in the field, fostering the responsible and effective use of AI technologies in medical education.
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7
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Milecki L, Poree J, Belgharbi H, Bourquin C, Damseh R, Delafontaine-Martel P, Lesage F, Gasse M, Provost J. A Deep Learning Framework for Spatiotemporal Ultrasound Localization Microscopy. IEEE Trans Med Imaging 2021; 40:1428-1437. [PMID: 33534705 DOI: 10.1109/tmi.2021.3056951] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ultrasound Localization Microscopy (ULM) can resolve the microvascular bed down to a few micrometers. To achieve such performance, microbubble contrast agents must perfuse the entire microvascular network. Microbubbles are then located individually and tracked over time to sample individual vessels, typically over hundreds of thousands of images. To overcome the fundamental limit of diffraction and achieve a dense reconstruction of the network, low microbubble concentrations must be used, which leads to acquisitions lasting several minutes. Conventional processing pipelines are currently unable to deal with interference from multiple nearby microbubbles, further reducing achievable concentrations. This work overcomes this problem by proposing a Deep Learning approach to recover dense vascular networks from ultrasound acquisitions with high microbubble concentrations. A realistic mouse brain microvascular network, segmented from 2-photon microscopy, was used to train a three-dimensional convolutional neural network (CNN) based on a V-net architecture. Ultrasound data sets from multiple microbubbles flowing through the microvascular network were simulated and used as ground truth to train the 3D CNN to track microbubbles. The 3D-CNN approach was validated in silico using a subset of the data and in vivo in a rat brain. In silico, the CNN reconstructed vascular networks with higher precision (81%) than a conventional ULM framework (70%). In vivo, the CNN could resolve micro vessels as small as 10 μ m with an improvement in resolution when compared against a conventional approach.
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Tahir W, Kura S, Zhu J, Cheng X, Damseh R, Tadesse F, Seibel A, Lee BS, Lesage F, Sakadžic S, Boas DA, Tian L. Anatomical Modeling of Brain Vasculature in Two-Photon Microscopy by Generalizable Deep Learning. BME Frontiers 2021. [DOI: 10.34133/2021/8620932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Objective and Impact Statement. Segmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here, we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis. Introduction. Vascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems and is able to segment large-scale angiograms. Methods. We employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and total variation regularization on the network’s output. Its effectiveness is demonstrated on experimentally acquired in vivo angiograms from mouse brains of dimensions up to 808×808×702 μm. Results. To demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art. Conclusion. Our work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning-based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.
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Affiliation(s)
- Waleed Tahir
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Sreekanth Kura
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Jiabei Zhu
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Xiaojun Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rafat Damseh
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada
| | - Fetsum Tadesse
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Alex Seibel
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Blaire S. Lee
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara, Turkey
| | - Frédéric Lesage
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada
| | - Sava Sakadžic
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA
| | - David A. Boas
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
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Damseh R, Delafontaine-Martel P, Pouliot P, Cheriet F, Lesage F. Laplacian Flow Dynamics on Geometric Graphs for Anatomical Modeling of Cerebrovascular Networks. IEEE Trans Med Imaging 2021; 40:381-394. [PMID: 32986549 DOI: 10.1109/tmi.2020.3027500] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Generating computational anatomical models of cerebrovascular networks is vital for improving clinical practice and understanding brain oxygen transport. This is achieved by extracting graph-based representations based on pre-mapping of vascular structures. Recent graphing methods can provide smooth vessels trajectories and well-connected vascular topology. However, they require water-tight surface meshes as inputs. Furthermore, adding vessels radii information on their graph compartments restricts their alignment along vascular centerlines. Here, we propose a novel graphing scheme that works with relaxed input requirements and intrinsically captures vessel radii information. The proposed approach is based on deforming geometric graphs constructed within vascular boundaries. Under a laplacian optimization framework, we assign affinity weights on the initial geometry that drives its iterative contraction toward vessels centerlines. We present a mechanism to decimate graph structure at each run and a convergence criterion to stop the process. A refinement technique is then introduced to obtain final vascular models. Our implementation is available on https://github.com/Damseh/VascularGraph. We benchmarked our results with that obtained using other efficient and state-of-the-art graphing schemes, validating on both synthetic and real angiograms acquired with different imaging modalities. The experiments indicate that the proposed scheme produces the lowest geometric and topological error rates on various angiograms. Furthermore, it surpasses other techniques in providing representative models that capture all anatomical aspects of vascular structures.
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Tahir W, Kura S, Zhu J, Cheng X, Damseh R, Tadesse F, Seibel A, Lee BS, Lesage F, Sakadžic S, Boas DA, Tian L. Anatomical Modeling of Brain Vasculature in Two-Photon Microscopy by Generalizable Deep Learning. BME Front 2020; 2020:8620932. [PMID: 37849965 PMCID: PMC10521669 DOI: 10.34133/2020/8620932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/12/2020] [Indexed: 10/19/2023] Open
Abstract
Objective and Impact Statement. Segmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here, we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis. Introduction. Vascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems and is able to segment large-scale angiograms. Methods. We employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and total variation regularization on the network's output. Its effectiveness is demonstrated on experimentally acquired in vivo angiograms from mouse brains of dimensions up to 808 × 808 × 702 μ m . Results. To demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art. Conclusion. Our work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning-based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.
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Affiliation(s)
- Waleed Tahir
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Sreekanth Kura
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Jiabei Zhu
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Xiaojun Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rafat Damseh
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada
| | - Fetsum Tadesse
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Alex Seibel
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Blaire S. Lee
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Ankara, Turkey
| | - Frédéric Lesage
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada
| | - Sava Sakadžic
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA
| | - David A. Boas
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
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Damseh R, Delafontaine-Martel P, James-Marchand P, Sirpal P, Cheriet F, Lesage F. Automated Analysis of Brain Microvasculature: From Segmentation to Anatomical Modeling. Annu Int Conf IEEE Eng Med Biol Soc 2020; 2020:1907-1910. [PMID: 33018374 DOI: 10.1109/embc44109.2020.9176322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Two-photon microscopy (TPM) can provide a detailed microscopic information of cerebrovascular structures. Extracting anatomical vascular models from TPM angiograms remains a tedious task due to image degeneration associated with TPM acquisitions and the complexity of microvascular networks. Here, we propose a fully automated pipeline capable of providing useful anatomical models of vascular structures captured with TPM. In the proposed method, we segment blood vessels using a fully convolutional neural network and employ the resulting binary labels to create an initial geometric graph enclosed within vessels boundaries. The initial geometry is then decimated and refined to form graphed curve skeletons that can retain both the vascular shape and its topology. We validate the proposed method on 3D realistic TPM angiographies and compare our results with that obtained through manual annotations.
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Lu X, Moeini M, Li B, Lu Y, Damseh R, Pouliot P, Thorin É, Lesage F. A Pilot Study Investigating Changes in Capillary Hemodynamics and Its Modulation by Exercise in the APP-PS1 Alzheimer Mouse Model. Front Neurosci 2019; 13:1261. [PMID: 31920472 PMCID: PMC6915102 DOI: 10.3389/fnins.2019.01261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 03/28/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022] Open
Abstract
Dysfunction in neurovascular coupling that results in a mismatch between cerebral blood flow and neuronal activity has been suggested to play a key role in the pathogenesis of Alzheimer's disease (AD). Meanwhile, physical exercise is a powerful approach for maintaining cognitive health and could play a preventive role against the progression of AD. Given the fundamental role of capillaries in oxygen transport to tissue, our pilot study aimed to characterize changes in capillary hemodynamics with AD and AD supplemented by exercise. Exploiting two-photon microscopy, intrinsic signal optical imaging, and magnetic resonance imaging, we found hemodynamic alterations and lower vascular density with AD that were reversed by exercise. We further observed that capillary properties were branch order-dependent and that stimulation-evoked changes were attenuated with AD but increased by exercise. Our study provides novel indications into cerebral microcirculatory disturbances with AD and the modulating role of voluntary exercise on these alterations.
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Affiliation(s)
- Xuecong Lu
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Mohammad Moeini
- Department of Biomedical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Baoqiang Li
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States
| | - Yuankang Lu
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Rafat Damseh
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Philippe Pouliot
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Éric Thorin
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
- Department of Surgery, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Frédéric Lesage
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
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Damseh R, Pouliot P, Gagnon L, Sakadzic S, Boas D, Cheriet F, Lesage F. Automatic Graph-Based Modeling of Brain Microvessels Captured With Two-Photon Microscopy. IEEE J Biomed Health Inform 2019; 23:2551-2562. [PMID: 30507542 PMCID: PMC6546554 DOI: 10.1109/jbhi.2018.2884678] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Graph models of cerebral vasculature derived from two-photon microscopy have shown to be relevant to study brain microphysiology. Automatic graphing of these microvessels remain problematic due to the vascular network complexity and two-photon sensitivity limitations with depth. In this paper, we propose a fully automatic processing pipeline to address this issue. The modeling scheme consists of a fully-convolution neural network to segment microvessels, a three-dimensional surface model generator, and a geometry contraction algorithm to produce graphical models with a single connected component. Based on a quantitative assessment using NetMets metrics, at a tolerance of 60 μm, false negative and false positive geometric error 19 rates are 3.8% and 4.2%, respectively, whereas false nega- 20 tive and false positive topological error rates are 6.1% and 4.5%, respectively. Our qualitative evaluation confirms the efficiency of our scheme in generating useful and accurate graphical models.
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Affiliation(s)
- Rafat Damseh
- Institute of Biomedical Engineering, École Polytechnique de Montréal, Montreal, QC, Canada
| | - Philippe Pouliot
- Department of Electrical Engineering, École Polytechnique de Montréal, Montreal, QC, Canada
- Research Centre, Montreal Hearth Institute, Montreal, QC, Canada
| | - Louis Gagnon
- Physics Department, Université Laval, Quebec, QC, Canada
| | - Sava Sakadzic
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - David Boas
- Neurophotonics Center, Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Farida Cheriet
- Department of Computer and Software Engineering, École Polytechnique de Montréal, Montreal, QC, Canada
| | - Frederic Lesage
- Institute of Biomedical Engineering, École Polytechnique de Montréal, Montreal, QC, Canada
- Department of Electrical Engineering, École Polytechnique de Montréal, Montreal, QC, Canada
- Research Centre, Montreal Hearth Institute, Montreal, QC, Canada
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Damseh R, Cheriet F, Lesage F. Fully Convolutional DenseNets for Segmentation of Microvessels in Two-photon Microscopy. Annu Int Conf IEEE Eng Med Biol Soc 2019; 2018:661-665. [PMID: 30440483 DOI: 10.1109/embc.2018.8512285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Segmentation of microvessels measured using two-photon microscopy has been studied in the literature with limited success due to uneven intensities associated with optical imaging and shadowing effects. In this work, we address this problem using a customized version of a recently developed fully convolutional neural network, namely, FC-DensNets. To train and validate the network, manual annotations of 8 angiograms from two-photon microscopy was used. Segmentation results are then compared with that of a state-of-the-art scheme that was developed for the same purpose and also based on deep learning. Experimental results show improved performance of used FC-DenseNet in providing accurate and yet end-to-end segmentation of microvessels in two-photon microscopy.
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Moeini M, Lu X, Avti PK, Damseh R, Bélanger S, Picard F, Boas D, Kakkar A, Lesage F. Compromised microvascular oxygen delivery increases brain tissue vulnerability with age. Sci Rep 2018; 8:8219. [PMID: 29844478 PMCID: PMC5974237 DOI: 10.1038/s41598-018-26543-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/16/2018] [Indexed: 11/22/2022] Open
Abstract
Despite the possible role of impaired cerebral tissue oxygenation in age-related cognition decline, much is still unknown about the changes in brain tissue pO2 with age. Using a detailed investigation of the age-related changes in cerebral tissue oxygenation in the barrel cortex of healthy, awake aged mice, we demonstrate decreased arteriolar and tissue pO2 with age. These changes are exacerbated after middle-age. We further uncovered evidence of the presence of hypoxic micro-pockets in the cortex of awake old mice. Our data suggests that from young to middle-age, a well-regulated capillary oxygen supply maintains the oxygen availability in cerebral tissue, despite decreased tissue pO2 next to arterioles. After middle-age, due to decreased hematocrit, reduced capillary density and higher capillary transit time heterogeneity, the capillary network fails to compensate for larger decreases in arterial pO2. The substantial decrease in brain tissue pO2, and the presence of hypoxic micro-pockets after middle-age are of significant importance, as these factors may be related to cognitive decline in elderly people.
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Affiliation(s)
- Mohammad Moeini
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada.,Research Center of Montreal Heart Institute, Montréal, QC, Canada.,Department of Chemistry, McGill University, Montréal, QC, Canada
| | - Xuecong Lu
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada.,Research Center of Montreal Heart Institute, Montréal, QC, Canada
| | - Pramod K Avti
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada.,Research Center of Montreal Heart Institute, Montréal, QC, Canada.,Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rafat Damseh
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada
| | - Samuel Bélanger
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada.,Research Center of Montreal Heart Institute, Montréal, QC, Canada
| | - Frédéric Picard
- Centre de Recherche de l'Institut Universitaire de Cardiologie et Pneumologie de Québec (IUCPQ), Québec, QC, Canada
| | - David Boas
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.,Biomedical Engineering Department, College of Engineering, Boston University, Boston, MA, USA
| | - Ashok Kakkar
- Department of Chemistry, McGill University, Montréal, QC, Canada
| | - Frédéric Lesage
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montréal, QC, Canada. .,Research Center of Montreal Heart Institute, Montréal, QC, Canada.
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