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Optimizing neuroscience data management by combining REDCap, BIDS and SQLite: a case study in Deep Brain Stimulation 结合 REDCap、BIDS 和 SQLite 优化神经科学数据管理:脑深部刺激案例研究
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-09-05 DOI: 10.3389/fninf.2024.1435971
Marc Stawiski, Vittoria Bucciarelli, Dorian Vogel, Simone Hemm
Neuroscience studies entail the generation of massive collections of heterogeneous data (e.g. demographics, clinical records, medical images). Integration and analysis of such data in research centers is pivotal for elucidating disease mechanisms and improving clinical outcomes. However, data collection in clinics often relies on non-standardized methods, such as paper-based documentation. Moreover, diverse data types are collected in different departments hindering efficient data organization, secure sharing and compliance to the FAIR (Findable, Accessible, Interoperable, Reusable) principles. Henceforth, in this manuscript we present a specialized data management system designed to enhance research workflows in Deep Brain Stimulation (DBS), a state-of-the-art neurosurgical procedure employed to treat symptoms of movement and psychiatric disorders. The system leverages REDCap to promote accurate data capture in hospital settings and secure sharing with research institutes, Brain Imaging Data Structure (BIDS) as image storing standard and a DBS-specific SQLite database as comprehensive data store and unified interface to all data types. A self-developed Python tool automates the data flow between these three components, ensuring their full interoperability. The proposed framework has already been successfully employed for capturing and analyzing data of 107 patients from 2 medical institutions. It effectively addresses the challenges of managing, sharing and retrieving diverse data types, fostering advancements in data quality, organization, analysis, and collaboration among medical and research institutions.
神经科学研究需要生成大量的异构数据(如人口统计学、临床记录、医学影像)。研究中心对这些数据进行整合和分析,对于阐明疾病机制和改善临床疗效至关重要。然而,诊所的数据收集通常依赖于非标准化的方法,如纸质文档。此外,不同部门收集的数据类型各异,妨碍了数据的高效组织、安全共享和符合 FAIR(可查找、可访问、可互操作、可重用)原则。因此,在本手稿中,我们介绍了一个专门的数据管理系统,旨在加强深部脑刺激(DBS)的研究工作流程,这是一种最先进的神经外科手术,用于治疗运动和精神障碍症状。该系统利用 REDCap 来促进医院环境中的准确数据采集以及与研究机构的安全共享,利用脑成像数据结构(BIDS)作为图像存储标准,利用 DBS 专用 SQLite 数据库作为综合数据存储和所有数据类型的统一接口。自主开发的 Python 工具可自动处理这三个组件之间的数据流,确保它们之间的全面互操作性。该框架已成功用于采集和分析两家医疗机构 107 名患者的数据。它有效地解决了管理、共享和检索不同数据类型的难题,促进了医疗和研究机构在数据质量、组织、分析和协作方面的进步。
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引用次数: 0
SEEG4D: a tool for 4D visualization of stereoelectroencephalography data SEEG4D:立体脑电图数据 4D 可视化工具
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-09-03 DOI: 10.3389/fninf.2024.1465231
James L. Evans, Matthew T. Bramlet, Connor Davey, Eliot Bethke, Aaron T. Anderson, Graham Huesmann, Yogatheesan Varatharajah, Andres Maldonado, Jennifer R. Amos, Bradley P. Sutton
Epilepsy is a prevalent and serious neurological condition which impacts millions of people worldwide. Stereoelectroencephalography (sEEG) is used in cases of drug resistant epilepsy to aid in surgical resection planning due to its high spatial resolution and ability to visualize seizure onset zones. For accurate localization of the seizure focus, sEEG studies combine pre-implantation magnetic resonance imaging, post-implant computed tomography to visualize electrodes, and temporally recorded sEEG electrophysiological data. Many tools exist to assist in merging multimodal spatial information; however, few allow for an integrated spatiotemporal view of the electrical activity. In the current work, we present SEEG4D, an automated tool to merge spatial and temporal data into a complete, four-dimensional virtual reality (VR) object with temporal electrophysiology that enables the simultaneous viewing of anatomy and seizure activity for seizure localization and presurgical planning. We developed an automated, containerized pipeline to segment tissues and electrode contacts. Contacts are aligned with electrical activity and then animated based on relative power. SEEG4D generates models which can be loaded into VR platforms for viewing and planning with the surgical team. Automated contact segmentation locations are within 1 mm of trained raters and models generated show signal propagation along electrodes. Critically, spatial–temporal information communicated through our models in a VR space have potential to enhance sEEG pre-surgical planning.
癫痫是一种普遍而严重的神经系统疾病,影响着全球数百万人。立体脑电图(sEEG)空间分辨率高,能直观显示癫痫发作区,因此被用于耐药性癫痫患者的手术切除规划。为了准确定位癫痫发作病灶,脑电图研究结合了植入前磁共振成像、植入后计算机断层扫描以观察电极,以及时间记录的脑电图电生理数据。目前有很多工具可以帮助合并多模态空间信息,但很少有工具可以对电活动进行综合时空分析。在当前的工作中,我们介绍了 SEEG4D,这是一种自动工具,可将空间和时间数据合并成一个完整的四维虚拟现实(VR)对象,该对象具有时间电生理学,可同时查看解剖和癫痫发作活动,以进行癫痫定位和手术前规划。我们开发了一种自动化、容器化的管道来分割组织和电极触点。触点与电活动对齐,然后根据相对功率进行动画处理。SEEG4D 生成的模型可载入 VR 平台,供手术团队查看和规划。自动触点分割位置与训练有素的评定者相差不超过 1 毫米,生成的模型可显示信号沿电极传播的情况。重要的是,在 VR 空间中通过我们的模型传递的时空信息有可能增强 sEEG 手术前规划。
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引用次数: 0
Interpretable machine learning comprehensive human gait deterioration analysis. 可解释的机器学习综合人体步态退化分析。
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-08-23 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1451529
Abdullah S Alharthi

Introduction: Gait analysis, an expanding research area, employs non-invasive sensors and machine learning techniques for a range of applications. In this study, we investigate the impact of cognitive decline conditions on gait performance, drawing connections between gait deterioration in Parkinson's Disease (PD) and healthy individuals dual tasking.

Methods: We employ Explainable Artificial Intelligence (XAI) specifically Layer-Wise Relevance Propagation (LRP), in conjunction with Convolutional Neural Networks (CNN) to interpret the intricate patterns in gait dynamics influenced by cognitive loads.

Results: We achieved classification accuracies of 98% F1 scores for PD dataset and 95.5% F1 scores for the combined PD dataset. Furthermore, we explore the significance of cognitive load in healthy gait analysis, resulting in robust classification accuracies of 90% ± 10% F1 scores for subject cognitive load verification. Our findings reveal significant alterations in gait parameters under cognitive decline conditions, highlighting the distinctive patterns associated with PD-related gait impairment and those induced by multitasking in healthy subjects. Through advanced XAI techniques (LRP), we decipher the underlying features contributing to gait changes, providing insights into specific aspects affected by cognitive decline.

Discussion: Our study establishes a novel perspective on gait analysis, demonstrating the applicability of XAI in elucidating the shared characteristics of gait disturbances in PD and dual-task scenarios in healthy individuals. The interpretability offered by XAI enhances our ability to discern subtle variations in gait patterns, contributing to a more nuanced comprehension of the factors influencing gait dynamics in PD and dual-task conditions, emphasizing the role of XAI in unraveling the intricacies of gait control.

导言:步态分析是一个不断扩展的研究领域,它采用非侵入式传感器和机器学习技术,应用范围广泛。在这项研究中,我们调查了认知能力下降情况对步态表现的影响,得出了帕金森病(PD)和健康人双重任务步态退化之间的联系:我们采用了可解释人工智能(XAI),特别是层相关性传播(LRP),结合卷积神经网络(CNN)来解释受认知负荷影响的步态动态的复杂模式:我们在PD数据集上取得了98%的F1分类准确率,在综合PD数据集上取得了95.5%的F1分类准确率。此外,我们还探索了认知负荷在健康步态分析中的意义,结果显示,在主体认知负荷验证中,分类准确率达到 90% ± 10% F1 分数。我们的研究结果揭示了认知能力下降条件下步态参数的重大变化,突出了与帕金森病相关的步态损伤和健康受试者多任务诱发的步态损伤的独特模式。通过先进的 XAI 技术(LRP),我们破译了导致步态变化的基本特征,提供了对受认知衰退影响的特定方面的见解:我们的研究为步态分析确立了一个新的视角,证明了 XAI 在阐明帕金森病步态障碍和健康人双任务情景的共同特征方面的适用性。XAI 提供的可解释性提高了我们辨别步态模式微妙变化的能力,有助于更细致地理解影响帕金森病和双任务情况下步态动态的因素,强调了 XAI 在揭示步态控制复杂性方面的作用。
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引用次数: 0
Predicting the clinical prognosis of acute ischemic stroke using machine learning: an application of radiomic biomarkers on non-contrast CT after intravascular interventional treatment. 利用机器学习预测急性缺血性脑卒中的临床预后:血管内介入治疗后非对比CT上放射生物标志物的应用。
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-08-22 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1400702
Hongxian Gu, Yuting Yan, Xiaodong He, Yuyun Xu, Yuguo Wei, Yuan Shao

Purpose: This study aimed to develop a radiomic model based on non-contrast computed tomography (NCCT) after interventional treatment to predict the clinical prognosis of acute ischemic stroke (AIS) with large vessel occlusion.

Methods: We retrospectively collected 141 cases of AIS from 2016 to 2020 and analyzed the patients' clinical data as well as NCCT data after interventional treatment. Then, the total dataset was divided into training and testing sets according to the subject serial number. The cerebral hemispheres on the infarct side were segmented for radiomics signature extraction. After radiomics signatures were standardized and dimensionality reduced, the training set was used to construct a radiomics model using machine learning. The testing set was then used to validate the prediction model, which was evaluated based on discrimination, calibration, and clinical utility. Finally, a joint model was constructed by incorporating the radiomics signatures and clinical data.

Results: The AUCs of the joint model, radiomics signature, NIHSS score, and hypertension were 0.900, 0.863, 0.727, and 0.591, respectively, in the training set. In the testing set, the AUCs of the joint model, radiomics signature, NIHSS score, and hypertension were 0.885, 0.840, 0.721, and 0.590, respectively.

Conclusion: Our results provided evidence that using post-interventional NCCT for a radiomic model could be a valuable tool in predicting the clinical prognosis of AIS with large vessel occlusion.

目的:本研究旨在建立一个基于介入治疗后非对比计算机断层扫描(NCCT)的放射学模型,以预测大血管闭塞性急性缺血性卒中(AIS)的临床预后:我们回顾性收集了2016年至2020年的141例AIS病例,分析了患者的临床数据以及介入治疗后的NCCT数据。然后,根据受试者序列号将总数据集分为训练集和测试集。对梗死侧的大脑半球进行分割,提取放射组学特征。在对放射组学特征进行标准化和降维处理后,训练集被用于利用机器学习构建放射组学模型。然后使用测试集验证预测模型,并根据辨别、校准和临床实用性对预测模型进行评估。最后,结合放射组学特征和临床数据构建了联合模型:在训练集中,联合模型、放射组学特征、NIHSS 评分和高血压的 AUC 分别为 0.900、0.863、0.727 和 0.591。在测试集中,联合模型、放射组学特征、NIHSS 评分和高血压的 AUC 分别为 0.885、0.840、0.721 和 0.590:我们的研究结果证明,使用介入后 NCCT 建立放射组学模型是预测大血管闭塞 AIS 临床预后的重要工具。
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引用次数: 0
Investigating cortical complexity and connectivity in rats with schizophrenia. 研究精神分裂症大鼠大脑皮层的复杂性和连通性。
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-08-15 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1392271
Zongya Zhao, Yifan Feng, Menghan Wang, Jiarong Wei, Tao Tan, Ruijiao Li, Heshun Hu, Mengke Wang, Peiqi Chen, Xudong Gao, Yinping Wei, Chang Wang, Zhixian Gao, Wenshuai Jiang, Xuezhi Zhou, Mingcai Li, Chong Wang, Ting Pang, Yi Yu

Background: The above studies indicate that the SCZ animal model has abnormal gamma oscillations and abnormal functional coupling ability of brain regions at the cortical level. However, few researchers have focused on the correlation between brain complexity and connectivity at the cortical level. In order to provide a more accurate representation of brain activity, we studied the complexity of electrocorticogram (ECoG) signals and the information interaction between brain regions in schizophrenic rats, and explored the correlation between brain complexity and connectivity.

Methods: We collected ECoG signal from SCZ rats. The frequency domain and time domain functional connectivity of SCZ rats were evaluated by magnitude square coherence and mutual information (MI). Permutation entropy (PE) and permutation Lempel-Ziv complexity (PLZC) were used to analyze the complexity of ECoG, and the relationship between them was evaluated. In addition, in order to further understand the causal structure of directional information flow among brain regions, we used phase transfer entropy (PTE) to analyze the effective connectivity of the brain.

Results: Firstly, in the high gamma band, the complexity of brain regions in SCZ rats is higher than that in normal rats, and the neuronal activity is irregularity. Secondly, the information integration ability of SCZ rats decreased and the communication of brain network information was hindered at the cortical level. Finally, compared with normal rats, the causal relationship between brain regions of SCZ rats was closer, but the information interaction center was not clear.

Conclusion: The above findings suggest that at the cortical level, complexity and connectivity are valid biomarkers for identifying SCZ. This bridges the gap between peak potentials and EEG. This may help to understand the pathophysiological mechanisms at the cortical level in schizophrenics.

研究背景上述研究表明,SCZ 动物模型的伽马振荡异常,大脑皮层水平的脑区功能耦合能力异常。然而,很少有研究人员关注大脑皮层的复杂性与连通性之间的相关性。为了更准确地表征大脑活动,我们研究了精神分裂症大鼠脑皮质图(ECoG)信号的复杂性和脑区之间的信息交互,并探讨了大脑复杂性与连通性之间的相关性:方法:我们采集了精神分裂症大鼠的心电图信号。方法:我们采集了精神分裂症大鼠的心电信号,通过幅度平方相干性和互信息(MI)评估了精神分裂症大鼠的频域和时域功能连通性。采用置换熵(PE)和置换 Lempel-Ziv 复杂性(PLZC)分析心电图的复杂性,并评估它们之间的关系。此外,为了进一步了解脑区之间定向信息流的因果结构,我们使用相位传递熵(PTE)来分析大脑的有效连通性:结果:首先,在高γ波段,SCZ大鼠脑区的复杂性高于正常大鼠,且神经元活动不规则。其次,SCZ 大鼠的信息整合能力下降,大脑皮层的网络信息交流受阻。最后,与正常大鼠相比,SCZ 大鼠脑区之间的因果关系更密切,但信息交互中心不明确:上述研究结果表明,在皮层水平上,复杂性和连通性是识别 SCZ 的有效生物标志物。这弥补了峰值电位和脑电图之间的差距。这可能有助于理解精神分裂症患者大脑皮层的病理生理机制。
{"title":"Investigating cortical complexity and connectivity in rats with schizophrenia.","authors":"Zongya Zhao, Yifan Feng, Menghan Wang, Jiarong Wei, Tao Tan, Ruijiao Li, Heshun Hu, Mengke Wang, Peiqi Chen, Xudong Gao, Yinping Wei, Chang Wang, Zhixian Gao, Wenshuai Jiang, Xuezhi Zhou, Mingcai Li, Chong Wang, Ting Pang, Yi Yu","doi":"10.3389/fninf.2024.1392271","DOIUrl":"10.3389/fninf.2024.1392271","url":null,"abstract":"<p><strong>Background: </strong>The above studies indicate that the SCZ animal model has abnormal gamma oscillations and abnormal functional coupling ability of brain regions at the cortical level. However, few researchers have focused on the correlation between brain complexity and connectivity at the cortical level. In order to provide a more accurate representation of brain activity, we studied the complexity of electrocorticogram (ECoG) signals and the information interaction between brain regions in schizophrenic rats, and explored the correlation between brain complexity and connectivity.</p><p><strong>Methods: </strong>We collected ECoG signal from SCZ rats. The frequency domain and time domain functional connectivity of SCZ rats were evaluated by magnitude square coherence and mutual information (MI). Permutation entropy (PE) and permutation Lempel-Ziv complexity (PLZC) were used to analyze the complexity of ECoG, and the relationship between them was evaluated. In addition, in order to further understand the causal structure of directional information flow among brain regions, we used phase transfer entropy (PTE) to analyze the effective connectivity of the brain.</p><p><strong>Results: </strong>Firstly, in the high gamma band, the complexity of brain regions in SCZ rats is higher than that in normal rats, and the neuronal activity is irregularity. Secondly, the information integration ability of SCZ rats decreased and the communication of brain network information was hindered at the cortical level. Finally, compared with normal rats, the causal relationship between brain regions of SCZ rats was closer, but the information interaction center was not clear.</p><p><strong>Conclusion: </strong>The above findings suggest that at the cortical level, complexity and connectivity are valid biomarkers for identifying SCZ. This bridges the gap between peak potentials and EEG. This may help to understand the pathophysiological mechanisms at the cortical level in schizophrenics.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"18 ","pages":"1392271"},"PeriodicalIF":2.5,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11358091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Corrigendum: Building a realistic, scalable memory model with independent engrams using a homeostatic mechanism. 更正:利用同态机制建立一个具有独立刻痕的现实的、可扩展的记忆模型。
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-08-09 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1461597
Marvin Kaster, Fabian Czappa, Markus Butz-Ostendorf, Felix Wolf

[This corrects the article DOI: 10.3389/fninf.2024.1323203.].

[此处更正了文章 DOI:10.3389/fninf.2024.1323203.]。
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引用次数: 0
Editorial: Neuromodulation using spatiotemporally complex patterns. 社论:利用时空复杂模式进行神经调控
IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-08-05 eCollection Date: 2024-01-01 DOI: 10.3389/fninf.2024.1454834
Peter A Tass, Hemant Bokil
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引用次数: 0
Exploring white matter dynamics and morphology through interactive numerical phantoms: the White Matter Generator 通过交互式数字模型探索白质动态和形态:白质生成器
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-31 DOI: 10.3389/fninf.2024.1354708
Sidsel Winther, Oscar Peulicke, Mariam Andersson, Hans M. Kjer, Jakob A. Bærentzen, Tim B. Dyrby
Brain white matter is a dynamic environment that continuously adapts and reorganizes in response to stimuli and pathological changes. Glial cells, especially, play a key role in tissue repair, inflammation modulation, and neural recovery. The movements of glial cells and changes in their concentrations can influence the surrounding axon morphology. We introduce the White Matter Generator (WMG) tool to enable the study of how axon morphology is influenced through such dynamical processes, and how this, in turn, influences the diffusion-weighted MRI signal. This is made possible by allowing interactive changes to the configuration of the phantom generation throughout the optimization process. The phantoms can consist of myelinated axons, unmyelinated axons, and cell clusters, separated by extra-cellular space. Due to morphological flexibility and computational advantages during the optimization, the tool uses ellipsoids as building blocks for all structures; chains of ellipsoids for axons, and individual ellipsoids for cell clusters. After optimization, the ellipsoid representation can be converted to a mesh representation which can be employed in Monte-Carlo diffusion simulations. This offers an effective method for evaluating tissue microstructure models for diffusion-weighted MRI in controlled bio-mimicking white matter environments. Hence, the WMG offers valuable insights into white matter's adaptive nature and implications for diffusion-weighted MRI microstructure models, and thereby holds the potential to advance clinical diagnosis, treatment, and rehabilitation strategies for various neurological disorders and injuries.
脑白质是一个动态的环境,会随着刺激和病理变化而不断适应和重组。尤其是神经胶质细胞,在组织修复、炎症调节和神经恢复中发挥着关键作用。神经胶质细胞的运动及其浓度变化会影响周围轴突的形态。我们引入了白质生成器(WMG)工具,以研究轴突形态如何受到此类动态过程的影响,以及这反过来又如何影响扩散加权磁共振成像信号。通过在整个优化过程中对模型生成的配置进行交互式更改,使这一研究成为可能。模型可由髓鞘轴突、无髓鞘轴突和细胞簇组成,并由细胞外空间分隔。由于形态上的灵活性和优化过程中的计算优势,该工具使用椭圆体作为所有结构的构建模块;轴突使用椭圆体链,细胞簇使用单个椭圆体。优化后,椭圆体表示法可转换为网格表示法,用于蒙特卡洛扩散模拟。这为在受控的生物模拟白质环境中评估用于扩散加权磁共振成像的组织微结构模型提供了一种有效的方法。因此,WMG 为了解白质的适应性及其对扩散加权磁共振成像微结构模型的影响提供了宝贵的见解,从而有望推动各种神经系统疾病和损伤的临床诊断、治疗和康复策略。
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引用次数: 0
LYNSU: automated 3D neuropil segmentation of fluorescent images for Drosophila brains LYNSU:果蝇大脑荧光图像的自动三维神经纤层分割
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-29 DOI: 10.3389/fninf.2024.1429670
Kai-Yi Hsu, Chi-Tin Shih, Nan-Yow Chen, Chung-Chuan Lo
The brain atlas, which provides information about the distribution of genes, proteins, neurons, or anatomical regions, plays a crucial role in contemporary neuroscience research. To analyze the spatial distribution of those substances based on images from different brain samples, we often need to warp and register individual brain images to a standard brain template. However, the process of warping and registration may lead to spatial errors, thereby severely reducing the accuracy of the analysis. To address this issue, we develop an automated method for segmenting neuropils in the Drosophila brain for fluorescence images from the FlyCircuit database. This technique allows future brain atlas studies to be conducted accurately at the individual level without warping and aligning to a standard brain template. Our method, LYNSU (Locating by YOLO and Segmenting by U-Net), consists of two stages. In the first stage, we use the YOLOv7 model to quickly locate neuropils and rapidly extract small-scale 3D images as input for the second stage model. This stage achieves a 99.4% accuracy rate in neuropil localization. In the second stage, we employ the 3D U-Net model to segment neuropils. LYNSU can achieve high accuracy in segmentation using a small training set consisting of images from merely 16 brains. We demonstrate LYNSU on six distinct neuropils or structures, achieving a high segmentation accuracy comparable to professional manual annotations with a 3D Intersection-over-Union (IoU) reaching up to 0.869. Our method takes only about 7 s to segment a neuropil while achieving a similar level of performance as the human annotators. To demonstrate a use case of LYNSU, we applied it to all female Drosophila brains from the FlyCircuit database to investigate the asymmetry of the mushroom bodies (MBs), the learning center of fruit flies. We used LYNSU to segment bilateral MBs and compare the volumes between left and right for each individual. Notably, of 8,703 valid brain samples, 10.14% showed bilateral volume differences that exceeded 10%. The study demonstrated the potential of the proposed method in high-throughput anatomical analysis and connectomics construction of the Drosophila brain.
脑图谱可提供基因、蛋白质、神经元或解剖区域的分布信息,在当代神经科学研究中起着至关重要的作用。为了根据不同大脑样本的图像分析这些物质的空间分布,我们通常需要将单个大脑图像扭曲并配准到标准大脑模板上。然而,扭曲和配准过程可能会导致空间误差,从而严重降低分析的准确性。为了解决这个问题,我们开发了一种自动方法,用于根据 FlyCircuit 数据库中的荧光图像分割果蝇大脑中的神经线。这项技术使未来的脑图谱研究能够在个体水平上精确进行,而无需根据标准脑模板进行扭曲和对齐。我们的方法 LYNSU(通过 YOLO 定位和 U-Net 分割)包括两个阶段。在第一阶段,我们使用 YOLOv7 模型快速定位神经瞳孔,并快速提取小比例三维图像作为第二阶段模型的输入。这一阶段的神经瞳孔定位准确率达到 99.4%。在第二阶段,我们采用三维 U-Net 模型来分割神经瞳孔。LYNSU 只需使用由 16 个大脑图像组成的小型训练集,就能达到很高的分割准确率。我们在六种不同的神经瞳孔或结构上演示了 LYNSU,其分割准确率可与专业人工注释相媲美,三维交集-联合(IoU)高达 0.869。我们的方法只需 7 秒钟就能分割一个神经瞳孔,同时达到与人工标注相似的性能水平。为了演示 LYNSU 的使用案例,我们将其应用于 FlyCircuit 数据库中的所有雌果蝇大脑,以研究果蝇学习中心蘑菇体 (MB) 的不对称性。我们使用 LYNSU 对双侧蘑菇体进行分割,并比较每个个体的左右体积。值得注意的是,在 8703 个有效大脑样本中,10.14% 的样本显示双侧体积差异超过 10%。这项研究证明了所提出的方法在果蝇大脑高通量解剖分析和连接组学构建方面的潜力。
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引用次数: 0
M3: using mask-attention and multi-scale for multi-modal brain MRI classification M3:利用遮挡注意力和多尺度进行多模态脑磁共振成像分类
IF 3.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-07-29 DOI: 10.3389/fninf.2024.1403732
Guanqing Kong, Chuanfu Wu, Zongqiu Zhang, Chuansheng Yin, Dawei Qin
IntroductionBrain diseases, particularly the classification of gliomas and brain metastases and the prediction of HT in strokes, pose significant challenges in healthcare. Existing methods, relying predominantly on clinical data or imaging-based techniques such as radiomics, often fall short in achieving satisfactory classification accuracy. These methods fail to adequately capture the nuanced features crucial for accurate diagnosis, often hindered by noise and the inability to integrate information across various scales.MethodsWe propose a novel approach that mask attention mechanisms with multi-scale feature fusion for Multimodal brain disease classification tasks, termed M3, which aims to extract features highly relevant to the disease. The extracted features are then dimensionally reduced using Principal Component Analysis (PCA), followed by classification with a Support Vector Machine (SVM) to obtain the predictive results.ResultsOur methodology underwent rigorous testing on multi-parametric MRI datasets for both brain tumors and strokes. The results demonstrate a significant improvement in addressing critical clinical challenges, including the classification of gliomas, brain metastases, and the prediction of hemorrhagic stroke transformations. Ablation studies further validate the effectiveness of our attention mechanism and feature fusion modules.DiscussionThese findings underscore the potential of our approach to meet and exceed current clinical diagnostic demands, offering promising prospects for enhancing healthcare outcomes in the diagnosis and treatment of brain diseases.
导言脑部疾病,尤其是胶质瘤和脑转移瘤的分类以及脑卒中高血压的预测,给医疗保健带来了巨大挑战。现有的方法主要依赖临床数据或基于成像的技术(如放射组学),往往无法达到令人满意的分类准确性。这些方法未能充分捕捉到对准确诊断至关重要的细微特征,往往受到噪声和无法整合不同尺度信息的阻碍。方法我们提出了一种新方法,将注意力机制与多尺度特征融合,用于多模态脑疾病分类任务,称为 M3,旨在提取与疾病高度相关的特征。然后使用主成分分析法(PCA)对提取的特征进行降维处理,再使用支持向量机(SVM)进行分类,从而获得预测结果。结果我们的方法在脑肿瘤和脑卒中的多参数磁共振成像数据集上进行了严格测试。结果表明,在应对关键临床挑战方面,包括胶质瘤、脑转移瘤的分类以及出血性中风转变的预测方面,我们的方法都有了显著的改进。消融研究进一步验证了我们的注意机制和特征融合模块的有效性。 讨论这些发现强调了我们的方法在满足和超越当前临床诊断需求方面的潜力,为提高脑部疾病诊断和治疗的医疗效果提供了广阔的前景。
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引用次数: 0
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Frontiers in Neuroinformatics
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