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机器学习识别物种间的中风特征。

Machine learning identifies stroke features between species.

机构信息

Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tuebingen, Tuebingen, Germany.

Department of Nuclear Medicine and Clinical Molecular Imaging, Eberhard Karls University Tuebingen, Tuebingen, Germany.

出版信息

Theranostics. 2021 Jan 1;11(6):3017-3034. doi: 10.7150/thno.51887. eCollection 2021.


DOI:10.7150/thno.51887
PMID:33456586
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7806470/
Abstract

Identification and localization of ischemic stroke (IS) lesions is routinely performed to confirm diagnosis, assess stroke severity, predict disability and plan rehabilitation strategies using magnetic resonance imaging (MRI). In basic research, stroke lesion segmentation is necessary to study complex peri-infarction tissue changes. Moreover, final stroke volume is a critical outcome evaluated in clinical and preclinical experiments to determine therapy or intervention success. Manual segmentations are performed but they require a specialized skill set, are prone to inter-observer variation, are not entirely objective and are often not supported by histology. The task is even more challenging when dealing with large multi-center datasets, multiple experimenters or large animal cohorts. On the other hand, current automatized segmentation approaches often lack histological validation, are not entirely user independent, are often based on single parameters, or in the case of complex machine learning methods, require vast training datasets and are prone to a lack of model interpretation. We induced IS using the middle cerebral artery occlusion model on two rat cohorts. We acquired apparent diffusion coefficient (ADC) and T2-weighted (T2W) images at 24 h and 1-week after IS induction. Subsets of the animals at 24 h and 1-week post IS were evaluated using histology and immunohistochemistry. Using a Gaussian mixture model, we segmented voxel-wise interactions between ADC and T2W parameters at 24 h using one of the rat cohorts. We then used these segmentation results to train a random forest classifier, which we applied to the second rat cohort. The algorithms' stroke segmentations were compared to manual stroke delineations, T2W and ADC thresholding methods and the final stroke segmentation at 1-week. Volume correlations to histology were also performed for every segmentation method. Metrics of success were calculated with respect to the final stroke volume. Finally, the trained random forest classifier was tested on a human dataset with a similar temporal stroke on-set. Manual segmentations, ADC and T2W thresholds were again used to evaluate and perform comparisons with the proposed algorithms' output. In preclinical rat data our framework significantly outperformed commonly applied automatized thresholding approaches and segmented stroke regions similarly to manual delineation. The framework predicted the localization of final stroke regions in 1-week post-stroke MRI with a median Dice similarity coefficient of 0.86, Matthew's correlation coefficient of 0.80 and false positive rate of 0.04. The predicted stroke volumes also strongly correlated with final histological stroke regions (Pearson correlation = 0.88, P < 0.0001). Lastly, the stroke region characteristics identified by our framework in rats also identified stroke lesions in human brains, largely outperforming thresholding approaches in stroke volume prediction (P<0.01). Our findings reveal that the segmentation produced by our proposed framework using 24 h MRI rat data strongly correlated with the final stroke volume, denoting a predictive effect. In addition, we show for the first time that the stroke imaging features can be directly translated between species, allowing identification of acute stroke in humans using the model trained on animal data. This discovery reduces the gap between the clinical and preclinical fields, unveiling a novel approach to directly co-analyze clinical and preclinical data. Such methods can provide further biological insights into human stroke and highlight the differences between species in order to help improve the experimental setups and animal models of the disease.

摘要

对缺血性中风(IS)病变的识别和定位通常用于确认诊断、评估中风严重程度、预测残疾和制定康复策略,方法是使用磁共振成像(MRI)。在基础研究中,需要对中风病变进行分割,以研究复杂的梗死周围组织变化。此外,最终的中风体积是临床和临床前实验中评估的关键结果,用于确定治疗或干预的成功。可以进行手动分割,但需要专门的技能集,容易受到观察者之间差异的影响,不是完全客观的,并且通常不受组织学支持。当涉及到大的多中心数据集、多个实验者或大型动物队列时,任务甚至更加具有挑战性。另一方面,当前的自动分割方法通常缺乏组织学验证,不是完全独立于用户的,通常基于单一参数,或者在复杂的机器学习方法的情况下,需要大量的训练数据集,并且容易缺乏模型解释。我们使用大脑中动脉闭塞模型在两个大鼠队列中诱导 IS。我们在诱导 IS 后 24 小时和 1 周时获得了表观扩散系数(ADC)和 T2 加权(T2W)图像。在诱导 IS 后 24 小时和 1 周时,部分动物使用组织学和免疫组织化学进行评估。我们使用高斯混合模型,在其中一个大鼠队列中使用 24 小时的 ADC 和 T2W 参数之间的体素级交互进行分割。然后,我们使用这些分割结果训练随机森林分类器,并将其应用于第二个大鼠队列。算法的中风分割与手动中风描绘、T2W 和 ADC 阈值方法以及 1 周时的最终中风分割进行了比较。对于每种分割方法,还进行了与组织学的体积相关性分析。根据最终中风体积计算了成功的度量标准。最后,我们在具有类似时间中风发作的人类数据集中测试了训练有素的随机森林分类器。再次使用手动分割、ADC 和 T2W 阈值来评估和进行与所提出的算法输出的比较。在临床前大鼠数据中,我们的框架显著优于常用的自动阈值方法,并与手动描绘相似地分割中风区域。该框架以中位数 Dice 相似系数为 0.86、马修相关系数为 0.80 和假阳性率为 0.04,预测了 1 周后中风 MRI 的最终中风区域定位。预测的中风体积也与最终的组织学中风区域强烈相关(Pearson 相关系数=0.88,P<0.0001)。最后,我们框架在大鼠中识别的中风区域特征也在人类大脑中识别出中风病变,在中风体积预测方面大大优于阈值方法(P<0.01)。我们的发现表明,使用 24 小时 MRI 大鼠数据生成的框架分割与最终中风体积强烈相关,表明具有预测作用。此外,我们首次表明,可以在物种之间直接转换中风成像特征,从而使用基于动物数据训练的模型识别人类急性中风。这一发现缩小了临床和临床前领域之间的差距,为直接分析临床和临床前数据提供了一种新方法。这种方法可以为人类中风提供进一步的生物学见解,并突出物种之间的差异,以帮助改进疾病的实验设置和动物模型。

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[5]
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[6]
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[7]
Deep Learning in Ischemic Stroke Imaging Analysis: A Comprehensive Review.

Biomed Res Int. 2022

[8]
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Mol Imaging Biol. 2023-4

[9]
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[10]
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