Background: The ever-growing need for cheap, simple, fast, and accurate healthcare solutions spurred a lot of research activities which are aimed at the reliable deployment of artificial intelligence in the medical fields. However, this has proved to be a daunting task especially when looking to make automated diagnoses using biomedical image data. Biomedical image data have complex patterns which human experts find very hard to comprehend. Against this backdrop, we applied a representation or feature learning algorithm: Invariant Scattering Convolution Network or Wavelet scattering Network to retinal fundus images and studied the the efficacy of the automatically extracted features therefrom for glaucoma diagnosis/detection. The influence of wavelet scattering network parameter settings as well as 2-D channel image type on the detection correctness is also examined. Our work is a distinct departure from the usual method where wavelet transform is applied to pre-processed retinal fundus images and handcrafted features are extracted from the decomposition results. Here, the RIM-ONE DL image dataset was fed into a wavelet scattering network developed in the Matlab environment to achieve a stage-wise decomposition process called wavelet scattering of the retinal fundus images thereby, automatically learning features from the images. These features were then used to build simple and computationally cheap classification algorithms.
Results: Maximum detection correctness of 98% was achieved on the held-out test set. Detection correctness is highly sensitive to scattering network parameter setting and 2-D channel image type.
Conclusion: A superficial comparison of the classification results obtained from our work and those obtained using a convolutional neural network underscores the potentiality of the proposed method for glaucoma detection.
{"title":"Wavelet image scattering based glaucoma detection.","authors":"Hafeez Alani Agboola, Jesuloluwa Emmanuel Zaccheus","doi":"10.1186/s42490-023-00067-5","DOIUrl":"https://doi.org/10.1186/s42490-023-00067-5","url":null,"abstract":"<p><strong>Background: </strong>The ever-growing need for cheap, simple, fast, and accurate healthcare solutions spurred a lot of research activities which are aimed at the reliable deployment of artificial intelligence in the medical fields. However, this has proved to be a daunting task especially when looking to make automated diagnoses using biomedical image data. Biomedical image data have complex patterns which human experts find very hard to comprehend. Against this backdrop, we applied a representation or feature learning algorithm: Invariant Scattering Convolution Network or Wavelet scattering Network to retinal fundus images and studied the the efficacy of the automatically extracted features therefrom for glaucoma diagnosis/detection. The influence of wavelet scattering network parameter settings as well as 2-D channel image type on the detection correctness is also examined. Our work is a distinct departure from the usual method where wavelet transform is applied to pre-processed retinal fundus images and handcrafted features are extracted from the decomposition results. Here, the RIM-ONE DL image dataset was fed into a wavelet scattering network developed in the Matlab environment to achieve a stage-wise decomposition process called wavelet scattering of the retinal fundus images thereby, automatically learning features from the images. These features were then used to build simple and computationally cheap classification algorithms.</p><p><strong>Results: </strong>Maximum detection correctness of 98% was achieved on the held-out test set. Detection correctness is highly sensitive to scattering network parameter setting and 2-D channel image type.</p><p><strong>Conclusion: </strong>A superficial comparison of the classification results obtained from our work and those obtained using a convolutional neural network underscores the potentiality of the proposed method for glaucoma detection.</p>","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":"5 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2023-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9979468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10826651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-17DOI: 10.1186/s42490-022-00066-y
Benjamin S Maxey, Luke A White, Giovanni F Solitro, Steven A Conrad, J Steven Alexander
Introduction: Short-term emergency ventilation is most typically accomplished through bag valve mask (BVM) techniques. BVMs like the AMBU® bag are cost-effective and highly portable but are also highly prone to user error, especially in high-stress emergent situations. Inaccurate and inappropriate ventilation has the potential to inflict great injury to patients through hyper- and hypoventilation. Here, we present the BVM Emergency Narration-Guided Instrument (BENGI) - a tidal volume feedback monitoring device that provides instantaneous visual and audio feedback on delivered tidal volumes, respiratory rates, and inspiratory/expiratory times. Providing feedback on the depth and regularity of respirations enables providers to deliver more consistent and accurate tidal volumes and rates. We describe the design, assembly, and validation of the BENGI as a practical tool to reduce manual ventilation-induced lung injury.
Methods: The prototype BENGI was assembled with custom 3D-printed housing and commercially available electronic components. A mass flow sensor in the central channel of the device measures air flow, which is used to calculate tidal volume. Tidal volumes are displayed via an LED ring affixed to the top of the BENGI. Additional feedback is provided through a speaker in the device. Central processing is accomplished through an Arduino microcontroller. Validation of the BENGI was accomplished using benchtop simulation with a clinical ventilator, BVM, and manikin test lung. Known respiratory quantities were delivered by the ventilator which were then compared to measurements from the BENGI to validate the accuracy of flow measurements, tidal volume calculations, and audio cue triggers.
Results: BENGI tidal volume measurements were found to lie within 4% of true delivered tidal volume values (95% CI of 0.53 to 3.7%) when breaths were delivered with 1-s inspiratory times, with similar performance for breaths delivered with 0.5-s inspiratory times (95% CI of 1.1 to 6.7%) and 2-s inspiratory times (95% CI of -1.1 to 2.3%). Audio cues "Bag faster" (1.84 to 2.03 s), "Bag slower" (0.35 to 0.41 s), and "Leak detected" (43 to 50%) were triggered close to target trigger values (2.00 s, 0.50 s, and 50%, respectively) across varying tidal volumes.
Conclusions: The BENGI achieved its proposed goals of accurately measuring and reporting tidal volumes delivered through BVM systems, providing immediate feedback on the quality of respiratory performance through audio and visual cues. The BENGI has the potential to reduce manual ventilation-induced lung injury and improve patient outcomes by providing accurate feedback on ventilatory parameters.
{"title":"Experimental validation of a portable tidal volume indicator for bag valve mask ventilation.","authors":"Benjamin S Maxey, Luke A White, Giovanni F Solitro, Steven A Conrad, J Steven Alexander","doi":"10.1186/s42490-022-00066-y","DOIUrl":"10.1186/s42490-022-00066-y","url":null,"abstract":"<p><strong>Introduction: </strong>Short-term emergency ventilation is most typically accomplished through bag valve mask (BVM) techniques. BVMs like the AMBU<sup>®</sup> bag are cost-effective and highly portable but are also highly prone to user error, especially in high-stress emergent situations. Inaccurate and inappropriate ventilation has the potential to inflict great injury to patients through hyper- and hypoventilation. Here, we present the BVM Emergency Narration-Guided Instrument (BENGI) - a tidal volume feedback monitoring device that provides instantaneous visual and audio feedback on delivered tidal volumes, respiratory rates, and inspiratory/expiratory times. Providing feedback on the depth and regularity of respirations enables providers to deliver more consistent and accurate tidal volumes and rates. We describe the design, assembly, and validation of the BENGI as a practical tool to reduce manual ventilation-induced lung injury.</p><p><strong>Methods: </strong>The prototype BENGI was assembled with custom 3D-printed housing and commercially available electronic components. A mass flow sensor in the central channel of the device measures air flow, which is used to calculate tidal volume. Tidal volumes are displayed via an LED ring affixed to the top of the BENGI. Additional feedback is provided through a speaker in the device. Central processing is accomplished through an Arduino microcontroller. Validation of the BENGI was accomplished using benchtop simulation with a clinical ventilator, BVM, and manikin test lung. Known respiratory quantities were delivered by the ventilator which were then compared to measurements from the BENGI to validate the accuracy of flow measurements, tidal volume calculations, and audio cue triggers.</p><p><strong>Results: </strong>BENGI tidal volume measurements were found to lie within 4% of true delivered tidal volume values (95% CI of 0.53 to 3.7%) when breaths were delivered with 1-s inspiratory times, with similar performance for breaths delivered with 0.5-s inspiratory times (95% CI of 1.1 to 6.7%) and 2-s inspiratory times (95% CI of -1.1 to 2.3%). Audio cues \"Bag faster\" (1.84 to 2.03 s), \"Bag slower\" (0.35 to 0.41 s), and \"Leak detected\" (43 to 50%) were triggered close to target trigger values (2.00 s, 0.50 s, and 50%, respectively) across varying tidal volumes.</p><p><strong>Conclusions: </strong>The BENGI achieved its proposed goals of accurately measuring and reporting tidal volumes delivered through BVM systems, providing immediate feedback on the quality of respiratory performance through audio and visual cues. The BENGI has the potential to reduce manual ventilation-induced lung injury and improve patient outcomes by providing accurate feedback on ventilatory parameters.</p>","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":" ","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2022-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9668705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40706274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-09-24DOI: 10.1186/s42490-022-00065-z
Gregory R Roytman, Matan Cutler, Kenneth Milligan, Steven M Tommasini, Daniel H Wiznia
Background: Finite element modelling the material behavior of bone in-silico is a powerful tool to predict the best suited surgical treatment for individual patients.
Results: We demonstrate the development and use of a pre-processing plug-in program with a 3D modelling image processing software suite (Synopsys Simpleware, ScanIP) to assist with identifying, isolating, and defining cortical and trabecular bone material properties from patient specific computed tomography scans. The workflow starts by calibrating grayscale values of each constituent element with a phantom - a standardized object with defined densities. Using an established power law equation, we convert the apparent density value per voxel to a Young's Modulus. The resulting "calibrated" scan can be used for modeling and in-silico experimentation with Finite Element Analysis.
Conclusions: This process allows for the creation of realistic and personalized simulations to inform a surgeon's decision-making. We have made this plug-in program open and accessible as a supplemental file.
{"title":"An open-access plug-in program for 3D modelling distinct material properties of cortical and trabecular bone.","authors":"Gregory R Roytman, Matan Cutler, Kenneth Milligan, Steven M Tommasini, Daniel H Wiznia","doi":"10.1186/s42490-022-00065-z","DOIUrl":"https://doi.org/10.1186/s42490-022-00065-z","url":null,"abstract":"<p><strong>Background: </strong>Finite element modelling the material behavior of bone in-silico is a powerful tool to predict the best suited surgical treatment for individual patients.</p><p><strong>Results: </strong>We demonstrate the development and use of a pre-processing plug-in program with a 3D modelling image processing software suite (Synopsys Simpleware, ScanIP) to assist with identifying, isolating, and defining cortical and trabecular bone material properties from patient specific computed tomography scans. The workflow starts by calibrating grayscale values of each constituent element with a phantom - a standardized object with defined densities. Using an established power law equation, we convert the apparent density value per voxel to a Young's Modulus. The resulting \"calibrated\" scan can be used for modeling and in-silico experimentation with Finite Element Analysis.</p><p><strong>Conclusions: </strong>This process allows for the creation of realistic and personalized simulations to inform a surgeon's decision-making. We have made this plug-in program open and accessible as a supplemental file.</p>","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":"4 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2022-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9509591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10740442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-09-03DOI: 10.1186/s42490-022-00064-0
Christopher T Tsui, Preet Lal, Katelyn V R Fox, Matthew A Churchward, Kathryn G Todd
Neural interface devices interact with the central nervous system (CNS) to substitute for some sort of functional deficit and improve quality of life for persons with disabilities. Design of safe, biocompatible neural interface devices is a fast-emerging field of neuroscience research. Development of invasive implant materials designed to directly interface with brain or spinal cord tissue has focussed on mitigation of glial scar reactivity toward the implant itself, but little exists in the literature that directly documents the effects of electrical stimulation on glial cells. In this review, a survey of studies documenting such effects has been compiled and categorized based on the various types of stimulation paradigms used and their observed effects on glia. A hybrid neuroscience cell biology-engineering perspective is offered to highlight considerations that must be made in both disciplines in the development of a safe implant. To advance knowledge on how electrical stimulation affects glia, we also suggest experiments elucidating electrochemical reactions that may occur as a result of electrical stimulation and how such reactions may affect glia. Designing a biocompatible stimulation paradigm should be a forefront consideration in the development of a device with improved safety and longevity.
{"title":"The effects of electrical stimulation on glial cell behaviour.","authors":"Christopher T Tsui, Preet Lal, Katelyn V R Fox, Matthew A Churchward, Kathryn G Todd","doi":"10.1186/s42490-022-00064-0","DOIUrl":"https://doi.org/10.1186/s42490-022-00064-0","url":null,"abstract":"<p><p>Neural interface devices interact with the central nervous system (CNS) to substitute for some sort of functional deficit and improve quality of life for persons with disabilities. Design of safe, biocompatible neural interface devices is a fast-emerging field of neuroscience research. Development of invasive implant materials designed to directly interface with brain or spinal cord tissue has focussed on mitigation of glial scar reactivity toward the implant itself, but little exists in the literature that directly documents the effects of electrical stimulation on glial cells. In this review, a survey of studies documenting such effects has been compiled and categorized based on the various types of stimulation paradigms used and their observed effects on glia. A hybrid neuroscience cell biology-engineering perspective is offered to highlight considerations that must be made in both disciplines in the development of a safe implant. To advance knowledge on how electrical stimulation affects glia, we also suggest experiments elucidating electrochemical reactions that may occur as a result of electrical stimulation and how such reactions may affect glia. Designing a biocompatible stimulation paradigm should be a forefront consideration in the development of a device with improved safety and longevity.</p>","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":" ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2022-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9441051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40345852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-04DOI: 10.1186/s42490-022-00063-1
F Metzner, C Neupetsch, A Carabello, M Pietsch, T Wendler, W-G Drossel
Replicating the mechanical behavior of human bones, especially cancellous bone tissue, is challenging. Typically, conventional bone models primarily consist of polyurethane foam surrounded by a solid shell. Although nearly isotropic foam components have mechanical properties similar to cancellous bone, they do not represent the anisotropy and inhomogeneity of bone architecture. To consider the architecture of bone, models were developed whose core was additively manufactured based on CT data. This core was subsequently coated with glass fiber composite. Specimens consisting of a gyroid-structure were fabricated using fused filament fabrication (FFF) techniques from different materials and various filler levels. Subsequent compression tests showed good accordance between the mechanical behavior of the printed specimens and human bone. The unidirectional fiberglass composite showed higher strength and stiffness than human cortical bone in 3-point bending tests, with comparable material behaviors being observed. During biomechanical investigation of the entire assembly, femoral prosthetic stems were inserted into both artificial and human bones under controlled conditions, while recording occurring forces and strains. All of the artificial prototypes, made of different materials, showed analogous behavior to human bone. In conclusion, it was shown that low-cost FFF technique can be used to generate valid bone models and selectively modify their properties by changing the infill.
{"title":"Biomechanical validation of additively manufactured artificial femoral bones.","authors":"F Metzner, C Neupetsch, A Carabello, M Pietsch, T Wendler, W-G Drossel","doi":"10.1186/s42490-022-00063-1","DOIUrl":"https://doi.org/10.1186/s42490-022-00063-1","url":null,"abstract":"<p><p>Replicating the mechanical behavior of human bones, especially cancellous bone tissue, is challenging. Typically, conventional bone models primarily consist of polyurethane foam surrounded by a solid shell. Although nearly isotropic foam components have mechanical properties similar to cancellous bone, they do not represent the anisotropy and inhomogeneity of bone architecture. To consider the architecture of bone, models were developed whose core was additively manufactured based on CT data. This core was subsequently coated with glass fiber composite. Specimens consisting of a gyroid-structure were fabricated using fused filament fabrication (FFF) techniques from different materials and various filler levels. Subsequent compression tests showed good accordance between the mechanical behavior of the printed specimens and human bone. The unidirectional fiberglass composite showed higher strength and stiffness than human cortical bone in 3-point bending tests, with comparable material behaviors being observed. During biomechanical investigation of the entire assembly, femoral prosthetic stems were inserted into both artificial and human bones under controlled conditions, while recording occurring forces and strains. All of the artificial prototypes, made of different materials, showed analogous behavior to human bone. In conclusion, it was shown that low-cost FFF technique can be used to generate valid bone models and selectively modify their properties by changing the infill.</p>","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":"4 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2022-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10579198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-20DOI: 10.1186/s42490-022-00062-2
Arefe Momeni, M. Rostami-Nejad, R. Salarian, M. Rabiee, Elham Aghamohammadi, M. Zali, N. Rabiee, F. Tay, Pooyan Makvandi
{"title":"Gold-based nanoplatform for a rapid lateral flow immunochromatographic test assay for gluten detection","authors":"Arefe Momeni, M. Rostami-Nejad, R. Salarian, M. Rabiee, Elham Aghamohammadi, M. Zali, N. Rabiee, F. Tay, Pooyan Makvandi","doi":"10.1186/s42490-022-00062-2","DOIUrl":"https://doi.org/10.1186/s42490-022-00062-2","url":null,"abstract":"","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65794516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-19DOI: 10.1186/s42490-022-00061-3
Ali, Muhaddisa Barat, Gu, Irene Yu-Hua, Lidemar, Alice, Berger, Mitchel S., Widhalm, Georg, Jakola, Asgeir Store
For brain tumors, identifying the molecular subtypes from magnetic resonance imaging (MRI) is desirable, but remains a challenging task. Recent machine learning and deep learning (DL) approaches may help the classification/prediction of tumor subtypes through MRIs. However, most of these methods require annotated data with ground truth (GT) tumor areas manually drawn by medical experts. The manual annotation is a time consuming process with high demand on medical personnel. As an alternative automatic segmentation is often used. However, it does not guarantee the quality and could lead to improper or failed segmented boundaries due to differences in MRI acquisition parameters across imaging centers, as segmentation is an ill-defined problem. Analogous to visual object tracking and classification, this paper shifts the paradigm by training a classifier using tumor bounding box areas in MR images. The aim of our study is to see whether it is possible to replace GT tumor areas by tumor bounding box areas (e.g. ellipse shaped boxes) for classification without a significant drop in performance. In patients with diffuse gliomas, training a deep learning classifier for subtype prediction by employing tumor regions of interest (ROIs) using ellipse bounding box versus manual annotated data. Experiments were conducted on two datasets (US and TCGA) consisting of multi-modality MRI scans where the US dataset contained patients with diffuse low-grade gliomas (dLGG) exclusively. Prediction rates were obtained on 2 test datasets: 69.86% for 1p/19q codeletion status on US dataset and 79.50% for IDH mutation/wild-type on TCGA dataset. Comparisons with that of using annotated GT tumor data for training showed an average of 3.0% degradation (2.92% for 1p/19q codeletion status and 3.23% for IDH genotype). Using tumor ROIs, i.e., ellipse bounding box tumor areas to replace annotated GT tumor areas for training a deep learning scheme, cause only a modest decline in performance in terms of subtype prediction. With more data that can be made available, this may be a reasonable trade-off where decline in performance may be counteracted with more data.
对于脑肿瘤,通过磁共振成像(MRI)识别分子亚型是可取的,但仍然是一项具有挑战性的任务。最近的机器学习和深度学习(DL)方法可能有助于通过mri对肿瘤亚型进行分类/预测。然而,这些方法中的大多数都需要医学专家手动绘制的带有ground truth (GT)肿瘤区域的注释数据。手工标注耗时长,对医护人员要求高。作为一种替代方法,经常使用自动分割。然而,由于分割是一个定义不明确的问题,它并不能保证质量,并且由于不同成像中心的MRI采集参数不同,可能导致分割边界不正确或失败。与视觉目标跟踪和分类类似,本文通过使用MR图像中的肿瘤边界框区域训练分类器来改变范式。我们研究的目的是看看是否有可能用肿瘤边界框区域(如椭圆形框)代替GT肿瘤区域进行分类,而不会显著降低性能。在弥漫性胶质瘤患者中,通过使用椭圆边界框与手动注释数据对比,使用感兴趣的肿瘤区域(roi)来训练深度学习分类器进行亚型预测。实验在由多模态MRI扫描组成的两个数据集(US和TCGA)上进行,其中US数据集仅包含弥漫性低级别胶质瘤(dLGG)患者。在2个测试数据集上获得了预测率:美国数据集对1p/19q编码状态的预测率为69.86%,TCGA数据集对IDH突变/野生型的预测率为79.50%。与使用带注释的GT肿瘤数据进行训练的结果相比,平均降解率为3.0% (1p/19q编码状态为2.92%,IDH基因型为3.23%)。使用肿瘤roi(即椭圆边界框肿瘤区域)代替带注释的GT肿瘤区域来训练深度学习方案,在亚型预测方面只会导致性能的适度下降。由于可以提供更多的数据,这可能是一种合理的权衡,性能下降可以用更多的数据来抵消。
{"title":"Prediction of glioma-subtypes: comparison of performance on a DL classifier using bounding box areas versus annotated tumors","authors":"Ali, Muhaddisa Barat, Gu, Irene Yu-Hua, Lidemar, Alice, Berger, Mitchel S., Widhalm, Georg, Jakola, Asgeir Store","doi":"10.1186/s42490-022-00061-3","DOIUrl":"https://doi.org/10.1186/s42490-022-00061-3","url":null,"abstract":"For brain tumors, identifying the molecular subtypes from magnetic resonance imaging (MRI) is desirable, but remains a challenging task. Recent machine learning and deep learning (DL) approaches may help the classification/prediction of tumor subtypes through MRIs. However, most of these methods require annotated data with ground truth (GT) tumor areas manually drawn by medical experts. The manual annotation is a time consuming process with high demand on medical personnel. As an alternative automatic segmentation is often used. However, it does not guarantee the quality and could lead to improper or failed segmented boundaries due to differences in MRI acquisition parameters across imaging centers, as segmentation is an ill-defined problem. Analogous to visual object tracking and classification, this paper shifts the paradigm by training a classifier using tumor bounding box areas in MR images. The aim of our study is to see whether it is possible to replace GT tumor areas by tumor bounding box areas (e.g. ellipse shaped boxes) for classification without a significant drop in performance. In patients with diffuse gliomas, training a deep learning classifier for subtype prediction by employing tumor regions of interest (ROIs) using ellipse bounding box versus manual annotated data. Experiments were conducted on two datasets (US and TCGA) consisting of multi-modality MRI scans where the US dataset contained patients with diffuse low-grade gliomas (dLGG) exclusively. Prediction rates were obtained on 2 test datasets: 69.86% for 1p/19q codeletion status on US dataset and 79.50% for IDH mutation/wild-type on TCGA dataset. Comparisons with that of using annotated GT tumor data for training showed an average of 3.0% degradation (2.92% for 1p/19q codeletion status and 3.23% for IDH genotype). Using tumor ROIs, i.e., ellipse bounding box tumor areas to replace annotated GT tumor areas for training a deep learning scheme, cause only a modest decline in performance in terms of subtype prediction. With more data that can be made available, this may be a reasonable trade-off where decline in performance may be counteracted with more data.","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138516386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-21DOI: 10.1186/s42490-022-00060-4
Manan Sethia, Mesut Sahin
Background: Electrocorticography (ECoG) arrays are commonly used to record the brain activity both in animal and human subjects. There is a lack of guidelines in the literature as to how the array geometry, particularly the via holes in the substrate, affects the recorded signals. A finite element (FE) model was developed to simulate the electric field generated by neurons located at different depths in the rat brain cortex and a micro ECoG array (μECoG) was placed on the pia surface for recording the neural signal. The array design chosen was a typical array of 8 × 8 circular (100 μm in diam.) contacts with 500 μm pitch. The size of the via holes between the recording contacts was varied to see the effect.
Results: The results showed that recorded signal amplitudes were reduced if the substrate was smaller than about four times the depth of the neuron in the gray matter. The signal amplitude profiles had dips around the via holes and the amplitudes were also lower at the contact sites as compared to the design without the holes; an effect that increased with the hole size. Another noteworthy result is that the spatial selectivity of the multi-contact recordings could be improved or reduced by the selection of the via hole sizes, and the effect depended on the distance between the neuron pair targeted for selective recording and its depth.
Conclusions: The results suggest that the via-hole size clearly affects the recorded neural signal amplitudes and it can be leveraged as a parameter to reduce the inter-channel correlation and thus maximize the information content of neural signals with μECoG arrays.
{"title":"The size of via holes influence the amplitude and selectivity of neural signals in Micro-ECoG arrays.","authors":"Manan Sethia, Mesut Sahin","doi":"10.1186/s42490-022-00060-4","DOIUrl":"https://doi.org/10.1186/s42490-022-00060-4","url":null,"abstract":"<p><strong>Background: </strong>Electrocorticography (ECoG) arrays are commonly used to record the brain activity both in animal and human subjects. There is a lack of guidelines in the literature as to how the array geometry, particularly the via holes in the substrate, affects the recorded signals. A finite element (FE) model was developed to simulate the electric field generated by neurons located at different depths in the rat brain cortex and a micro ECoG array (μECoG) was placed on the pia surface for recording the neural signal. The array design chosen was a typical array of 8 × 8 circular (100 μm in diam.) contacts with 500 μm pitch. The size of the via holes between the recording contacts was varied to see the effect.</p><p><strong>Results: </strong>The results showed that recorded signal amplitudes were reduced if the substrate was smaller than about four times the depth of the neuron in the gray matter. The signal amplitude profiles had dips around the via holes and the amplitudes were also lower at the contact sites as compared to the design without the holes; an effect that increased with the hole size. Another noteworthy result is that the spatial selectivity of the multi-contact recordings could be improved or reduced by the selection of the via hole sizes, and the effect depended on the distance between the neuron pair targeted for selective recording and its depth.</p><p><strong>Conclusions: </strong>The results suggest that the via-hole size clearly affects the recorded neural signal amplitudes and it can be leveraged as a parameter to reduce the inter-channel correlation and thus maximize the information content of neural signals with μECoG arrays.</p>","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":" ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2022-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8935835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40310714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-14DOI: 10.1186/s42490-022-00059-x
White, Luke A., Maxey, Benjamin S., Solitro, Giovanni F., Takei, Hidehiro, Conrad, Steven A., Alexander, J. Steven
The COVID-19 pandemic revealed a substantial and unmet need for low-cost, easily accessible mechanical ventilation strategies for use in medical resource-challenged areas. Internationally, several groups developed non-conventional COVID-19 era emergency ventilator strategies as a stopgap measure when conventional ventilators were unavailable. Here, we compared our FALCON emergency ventilator in a rabbit model and compared its safety and functionality to conventional mechanical ventilation. New Zealand white rabbits (n = 5) received mechanical ventilation from both the FALCON and a conventional mechanical ventilator (Engström Carestation™) for 1 h each. Airflow and pressure, blood O2 saturation, end tidal CO2, and arterial blood gas measurements were measured. Additionally, gross and histological lung samples were compared to spontaneously breathing rabbits (n = 3) to assess signs of ventilator induced lung injury. All rabbits were successfully ventilated with the FALCON. At identical ventilator settings, tidal volumes, pressures, and respiratory rates were similar between both ventilators, but the inspiratory to expiratory ratio was lower using the FALCON. End tidal CO2 was significantly higher on the FALCON, and arterial blood gas measurements demonstrated lower arterial partial pressure of O2 at 30 min and higher arterial partial pressure of CO2 at 30 and 60 min using the FALCON. However, when ventilated at higher respiratory rates, we observed a stepwise decrease in end tidal CO2. Poincaré plot analysis demonstrated small but significant increases in short-term and long-term variation of peak inspiratory pressure generation from the FALCON. Wet to dry lung weight and lung injury scoring between the mechanically ventilated and spontaneously breathing rabbits were similar. Although conventional ventilators are always preferable outside of emergency use, the FALCON ventilator safely and effectively ventilated healthy rabbits without lung injury. Emergency ventilation using accessible and inexpensive strategies like the FALCON may be useful for communities with low access to medical resources and as a backup form of emergency ventilation.
{"title":"Efficacy and safety testing of a COVID-19 era emergency ventilator in a healthy rabbit lung model","authors":"White, Luke A., Maxey, Benjamin S., Solitro, Giovanni F., Takei, Hidehiro, Conrad, Steven A., Alexander, J. Steven","doi":"10.1186/s42490-022-00059-x","DOIUrl":"https://doi.org/10.1186/s42490-022-00059-x","url":null,"abstract":"The COVID-19 pandemic revealed a substantial and unmet need for low-cost, easily accessible mechanical ventilation strategies for use in medical resource-challenged areas. Internationally, several groups developed non-conventional COVID-19 era emergency ventilator strategies as a stopgap measure when conventional ventilators were unavailable. Here, we compared our FALCON emergency ventilator in a rabbit model and compared its safety and functionality to conventional mechanical ventilation. New Zealand white rabbits (n = 5) received mechanical ventilation from both the FALCON and a conventional mechanical ventilator (Engström Carestation™) for 1 h each. Airflow and pressure, blood O2 saturation, end tidal CO2, and arterial blood gas measurements were measured. Additionally, gross and histological lung samples were compared to spontaneously breathing rabbits (n = 3) to assess signs of ventilator induced lung injury. All rabbits were successfully ventilated with the FALCON. At identical ventilator settings, tidal volumes, pressures, and respiratory rates were similar between both ventilators, but the inspiratory to expiratory ratio was lower using the FALCON. End tidal CO2 was significantly higher on the FALCON, and arterial blood gas measurements demonstrated lower arterial partial pressure of O2 at 30 min and higher arterial partial pressure of CO2 at 30 and 60 min using the FALCON. However, when ventilated at higher respiratory rates, we observed a stepwise decrease in end tidal CO2. Poincaré plot analysis demonstrated small but significant increases in short-term and long-term variation of peak inspiratory pressure generation from the FALCON. Wet to dry lung weight and lung injury scoring between the mechanically ventilated and spontaneously breathing rabbits were similar. Although conventional ventilators are always preferable outside of emergency use, the FALCON ventilator safely and effectively ventilated healthy rabbits without lung injury. Emergency ventilation using accessible and inexpensive strategies like the FALCON may be useful for communities with low access to medical resources and as a backup form of emergency ventilation.","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138542599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-24DOI: 10.1186/s42490-022-00058-y
Shane Shahrestani, Gabriel Zada, Yu-Chong Tai
Background: Detection of locally increased blood concentration and perfusion is critical for assessment of functional cortical activity as well as diagnosis of conditions such as intracerebral hemorrhage (ICH). Current paradigms for assessment of regional blood concentration in the brain rely on computed tomography (CT), magnetic resonance imaging (MRI), and perfusion blood oxygen level dependent functional magnetic resonance imaging (BOLD-fMRI).
Results: In this study, we developed computational models to test the feasibility of novel magnetic sensors capable of detecting hemodynamic changes within the brain on a microtesla-level. We show that low-field magnetic sensors can accurately detect changes in magnetic flux density and eddy current damping signals resulting from increases in local blood concentration. These models predicted that blood volume changes as small as 1.26 mL may be resolved by the sensors, implying potential use for diagnosis of ICH and assessment of regional blood flow as a proxy for cerebral metabolism and neuronal activity. We then translated findings from our computational model to demonstrate feasibility of accurate detection of modeled ICH in a simulated human cadaver setting.
Conclusions: Overall, microtesla-level magnetic scanning is feasible, safe, and has distinct advantages compared to current standards of care. Computational modeling may facilitate rapid prototype development and testing of novel medical devices with minimal risk to human participants prior to device construction and clinical trials.
{"title":"Development of computational models for microtesla-level magnetic brain scanning: a novel avenue for device development.","authors":"Shane Shahrestani, Gabriel Zada, Yu-Chong Tai","doi":"10.1186/s42490-022-00058-y","DOIUrl":"https://doi.org/10.1186/s42490-022-00058-y","url":null,"abstract":"<p><strong>Background: </strong>Detection of locally increased blood concentration and perfusion is critical for assessment of functional cortical activity as well as diagnosis of conditions such as intracerebral hemorrhage (ICH). Current paradigms for assessment of regional blood concentration in the brain rely on computed tomography (CT), magnetic resonance imaging (MRI), and perfusion blood oxygen level dependent functional magnetic resonance imaging (BOLD-fMRI).</p><p><strong>Results: </strong>In this study, we developed computational models to test the feasibility of novel magnetic sensors capable of detecting hemodynamic changes within the brain on a microtesla-level. We show that low-field magnetic sensors can accurately detect changes in magnetic flux density and eddy current damping signals resulting from increases in local blood concentration. These models predicted that blood volume changes as small as 1.26 mL may be resolved by the sensors, implying potential use for diagnosis of ICH and assessment of regional blood flow as a proxy for cerebral metabolism and neuronal activity. We then translated findings from our computational model to demonstrate feasibility of accurate detection of modeled ICH in a simulated human cadaver setting.</p><p><strong>Conclusions: </strong>Overall, microtesla-level magnetic scanning is feasible, safe, and has distinct advantages compared to current standards of care. Computational modeling may facilitate rapid prototype development and testing of novel medical devices with minimal risk to human participants prior to device construction and clinical trials.</p>","PeriodicalId":72425,"journal":{"name":"BMC biomedical engineering","volume":"4 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2022-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8785482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10672863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}