Danilov Viacheslav V, Laptev Vladislav V, Klyshnikov Kirill Yu, Stepanov Alexander D, Bogdanov Leo A, Antonova Larisa V, Krivkina Evgenia O, Kutikhin Anton G, Ovcharenko Evgeny A
Pompeu Fabra University, Barcelona, Spain.
Quantori, Cambridge, MA, United States.
Front Bioeng Biotechnol. 2024 Jun 26;12:1411680. doi: 10.3389/fbioe.2024.1411680. eCollection 2024.
The development of next-generation tissue-engineered medical devices such as tissue-engineered vascular grafts (TEVGs) is a leading trend in translational medicine. Microscopic examination is an indispensable part of animal experimentation, and histopathological analysis of regenerated tissue is crucial for assessing the outcomes of implanted medical devices. However, the objective quantification of regenerated tissues can be challenging due to their unusual and complex architecture. To address these challenges, research and development of advanced ML-driven tools for performing adequate histological analysis appears to be an extremely promising direction.
We compiled a dataset of 104 representative whole slide images (WSIs) of TEVGs which were collected after a 6-month implantation into the sheep carotid artery. The histological examination aimed to analyze the patterns of vascular tissue regeneration in TEVGs . Having performed an automated slicing of these WSIs by the Entropy Masker algorithm, we filtered and then manually annotated 1,401 patches to identify 9 histological features: arteriole lumen, arteriole media, arteriole adventitia, venule lumen, venule wall, capillary lumen, capillary wall, immune cells, and nerve trunks. To segment and quantify these features, we rigorously tuned and evaluated the performance of six deep learning models (U-Net, LinkNet, FPN, PSPNet, DeepLabV3, and MA-Net).
After rigorous hyperparameter optimization, all six deep learning models achieved mean Dice Similarity Coefficients (DSC) exceeding 0.823. Notably, FPN and PSPNet exhibited the fastest convergence rates. MA-Net stood out with the highest mean DSC of 0.875, demonstrating superior performance in arteriole segmentation. DeepLabV3 performed well in segmenting venous and capillary structures, while FPN exhibited proficiency in identifying immune cells and nerve trunks. An ensemble of these three models attained an average DSC of 0.889, surpassing their individual performances.
This study showcases the potential of ML-driven segmentation in the analysis of histological images of tissue-engineered vascular grafts. Through the creation of a unique dataset and the optimization of deep neural network hyperparameters, we developed and validated an ensemble model, establishing an effective tool for detecting key histological features essential for understanding vascular tissue regeneration. These advances herald a significant improvement in ML-assisted workflows for tissue engineering research and development.
下一代组织工程医疗器械的发展,如组织工程血管移植物(TEVG),是转化医学的一个主要趋势。显微镜检查是动物实验不可或缺的一部分,对再生组织进行组织病理学分析对于评估植入医疗器械的效果至关重要。然而,由于再生组织结构异常复杂,对其进行客观量化可能具有挑战性。为应对这些挑战,研发先进的机器学习驱动工具以进行充分的组织学分析似乎是一个极具前景的方向。
我们编制了一个包含104张TEVG代表性全切片图像(WSI)的数据集,这些图像是在将TEVG植入绵羊颈动脉6个月后收集的。组织学检查旨在分析TEVG中血管组织再生的模式。通过熵掩码算法对这些WSI进行自动切片后,我们对1401个切片进行了过滤并手动标注,以识别9种组织学特征:小动脉腔、小动脉中膜、小动脉外膜、小静脉腔、小静脉壁、毛细血管腔、毛细血管壁、免疫细胞和神经干。为了分割和量化这些特征,我们严格调整并评估了六种深度学习模型(U-Net、LinkNet、FPN、PSPNet、DeepLabV3和MA-Net)的性能。
经过严格的超参数优化,所有六种深度学习模型的平均骰子相似系数(DSC)均超过0.823。值得注意的是,FPN和PSPNet的收敛速度最快。MA-Net的平均DSC最高,为0.875,在小动脉分割方面表现出卓越性能。DeepLabV3在分割静脉和毛细血管结构方面表现良好,而FPN在识别免疫细胞和神经干方面表现出色。这三个模型的集成平均DSC达到0.889,超过了它们各自的性能。
本研究展示了机器学习驱动的分割在组织工程血管移植物组织学图像分析中的潜力。通过创建独特的数据集和优化深度神经网络超参数,我们开发并验证了一个集成模型,建立了一个有效的工具,用于检测理解血管组织再生所需的关键组织学特征。这些进展预示着机器学习辅助的组织工程研发工作流程将有显著改进。