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Weakly- and Semisupervised Probabilistic Segmentation and Quantification of Reverberation Artifacts. 混响伪像的弱和半监督概率分割和量化。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-02-25 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9837076
Alex Ling Yu Hung, Edward Chen, John Galeotti
Objective and Impact Statement. We propose a weakly- and semisupervised, probabilistic needle-and-reverberation-artifact segmentation algorithm to separate the desired tissue-based pixel values from the superimposed artifacts. Our method models the intensity decay of artifact intensities and is designed to minimize the human labeling error. Introduction. Ultrasound image quality has continually been improving. However, when needles or other metallic objects are operating inside the tissue, the resulting reverberation artifacts can severely corrupt the surrounding image quality. Such effects are challenging for existing computer vision algorithms for medical image analysis. Needle reverberation artifacts can be hard to identify at times and affect various pixel values to different degrees. The boundaries of such artifacts are ambiguous, leading to disagreement among human experts labeling the artifacts. Methods. Our learning-based framework consists of three parts. The first part is a probabilistic segmentation network to generate the soft labels based on the human labels. These soft labels are input into the second part which is the transform function, where the training labels for the third part are generated. The third part outputs the final masks which quantifies the reverberation artifacts. Results. We demonstrate the applicability of the approach and compare it against other segmentation algorithms. Our method is capable of both differentiating between the reverberations from artifact-free patches and modeling the intensity fall-off in the artifacts. Conclusion. Our method matches state-of-the-art artifact segmentation performance and sets a new standard in estimating the per-pixel contributions of artifact vs underlying anatomy, especially in the immediately adjacent regions between reverberation lines. Our algorithm is also able to improve the performance of downstream image analysis algorithms.
目标和影响声明。我们提出了一种弱监督和半监督的概率针状和混响伪影分割算法,以从叠加的伪影中分离出所需的基于组织的像素值。我们的方法对伪影强度的强度衰减进行建模,旨在最大限度地减少人为标记误差。介绍超声图像质量一直在不断提高。然而,当针头或其他金属物体在组织内操作时,产生的混响伪影会严重破坏周围的图像质量。这样的效果对于用于医学图像分析的现有计算机视觉算法是具有挑战性的。针形混响伪影有时很难识别,并在不同程度上影响各种像素值。这些人工制品的边界是模糊的,导致人类专家在标记人工制品时存在分歧。方法。我们基于学习的框架由三部分组成。第一部分是基于人类标签生成软标签的概率分割网络。这些软标签被输入到作为变换函数的第二部分中,其中生成用于第三部分的训练标签。第三部分输出量化混响伪影的最终掩模。后果我们证明了该方法的适用性,并将其与其他分割算法进行了比较。我们的方法能够区分来自无伪影补丁的反射,并对伪影中的强度衰减进行建模。结论我们的方法匹配了最先进的伪影分割性能,并在估计伪影与底层解剖结构的每像素贡献方面树立了一个新标准,尤其是在混响线之间的紧邻区域。我们的算法还能够提高下游图像分析算法的性能。
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引用次数: 2
Noninvasive Ultrasound Retinal Stimulation for Vision Restoration at High Spatiotemporal Resolution. 无创超声视网膜刺激用于高时空分辨率视觉恢复。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-02-21 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9829316
Xuejun Qian, Gengxi Lu, Biju B Thomas, Runze Li, Xiaoyang Chen, K Kirk Shung, Mark Humayun, Qifa Zhou

Objective. Retinal degeneration involving progressive deterioration and loss of function of photoreceptors is a major cause of permanent vision loss worldwide. Strategies to treat these incurable conditions incorporate retinal prostheses via electrically stimulating surviving retinal neurons with implanted devices in the eye, optogenetic therapy, and sonogenetic therapy. Existing challenges of these strategies include invasive manner, complex implantation surgeries, and risky gene therapy. Methods and Results. Here, we show that direct ultrasound stimulation on the retina can evoke neuron activities from the visual centers including the superior colliculus and the primary visual cortex (V1), in either normal-sighted or retinal degenerated blind rats in vivo. The neuron activities induced by the customized spherically focused 3.1 MHz ultrasound transducer have shown both good spatial resolution of 250 μm and temporal resolution of 5 Hz in the rat visual centers. An additional customized 4.4 MHz helical transducer was further implemented to generate a static stimulation pattern of letter forms. Conclusion. Our findings demonstrate that ultrasound stimulation of the retina in vivo is a safe and effective approach with high spatiotemporal resolution, indicating a promising future of ultrasound stimulation as a novel and noninvasive visual prosthesis for translational applications in blind patients.

客观的视网膜变性涉及光感受器功能的逐渐退化和丧失,是世界范围内永久性视力丧失的主要原因。治疗这些不治之症的策略包括通过在眼睛中植入装置电刺激存活的视网膜神经元来进行视网膜修复、光遗传学治疗和声遗传学治疗。这些策略的现有挑战包括侵入性方式、复杂的植入手术和危险的基因治疗。方法和结果。在这里,我们发现,在体内正常视力或视网膜退化失明大鼠中,对视网膜的直接超声刺激可以引起包括上丘和初级视觉皮层(V1)在内的视觉中心的神经元活动。定制的球形聚焦3.1诱导的神经元活动 MHz超声换能器显示出250的良好空间分辨率 μm,时间分辨率为5 Hz。额外定制4.4 MHz螺旋换能器被进一步实现以产生字母形式的静态刺激模式。结论我们的研究结果表明,体内超声刺激视网膜是一种安全有效的高时空分辨率方法,这表明超声刺激作为一种新的非侵入性视觉假体在盲人患者中的平移应用前景广阔。
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引用次数: 12
Ultrasound-Mediated Drug Delivery: Sonoporation Mechanisms, Biophysics, and Critical Factors. 超声介导的药物递送:声蒸发机制、生物物理学和关键因素。
IF 5 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-29 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9807347
Juan Tu, Alfred C H Yu

Sonoporation, or the use of ultrasound in the presence of cavitation nuclei to induce plasma membrane perforation, is well considered as an emerging physical approach to facilitate the delivery of drugs and genes to living cells. Nevertheless, this emerging drug delivery paradigm has not yet reached widespread clinical use, because the efficiency of sonoporation is often deemed to be mediocre due to the lack of detailed understanding of the pertinent scientific mechanisms. Here, we summarize the current observational evidence available on the notion of sonoporation, and we discuss the prevailing understanding of the physical and biological processes related to sonoporation. To facilitate systematic understanding, we also present how the extent of sonoporation is dependent on a multitude of factors related to acoustic excitation parameters (ultrasound frequency, pressure, cavitation dose, exposure time), microbubble parameters (size, concentration, bubble-to-cell distance, shell composition), and cellular properties (cell type, cell cycle, biochemical contents). By adopting a science-backed approach to the realization of sonoporation, ultrasound-mediated drug delivery can be more controllably achieved to viably enhance drug uptake into living cells with high sonoporation efficiency. This drug delivery approach, when coupled with concurrent advances in ultrasound imaging, has potential to become an effective therapeutic paradigm.

超声汽化,或在空化核存在的情况下使用超声诱导质膜穿孔,被认为是一种新兴的物理方法,有助于将药物和基因输送到活细胞。尽管如此,这种新兴的药物递送模式尚未在临床上得到广泛应用,因为由于缺乏对相关科学机制的详细了解,超声汽化的效率通常被认为是平庸的。在这里,我们总结了目前关于声蒸发概念的观测证据,并讨论了对与声蒸发相关的物理和生物过程的普遍理解。为了便于系统理解,我们还介绍了声蒸发的程度如何取决于与声激励参数(超声频率、压力、空化剂量、暴露时间)、微气泡参数(大小、浓度、气泡到细胞的距离、外壳组成)和细胞特性(细胞类型、细胞周期、生物化学含量)相关的多种因素。通过采用科学支持的方法来实现声蒸发,可以更可控地实现超声介导的药物递送,从而以高的声蒸发效率有效地增强药物对活细胞的吸收。这种给药方法,再加上超声成像的同时发展,有可能成为一种有效的治疗模式。
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引用次数: 0
Automated Segmentation and Connectivity Analysis for Normal Pressure Hydrocephalus. 常压脑积水的自动分割和连通性分析。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-09 eCollection Date: 2022-01-01 DOI: 10.34133/2022/9783128
Angela Zhang, Amil Khan, Saisidharth Majeti, Judy Pham, Christopher Nguyen, Peter Tran, Vikram Iyer, Ashutosh Shelat, Jefferson Chen, B S Manjunath

Objective and Impact Statement. We propose an automated method of predicting Normal Pressure Hydrocephalus (NPH) from CT scans. A deep convolutional network segments regions of interest from the scans. These regions are then combined with MRI information to predict NPH. To our knowledge, this is the first method which automatically predicts NPH from CT scans and incorporates diffusion tractography information for prediction. Introduction. Due to their low cost and high versatility, CT scans are often used in NPH diagnosis. No well-defined and effective protocol currently exists for analysis of CT scans for NPH. Evans' index, an approximation of the ventricle to brain volume using one 2D image slice, has been proposed but is not robust. The proposed approach is an effective way to quantify regions of interest and offers a computational method for predicting NPH. Methods. We propose a novel method to predict NPH by combining regions of interest segmented from CT scans with connectome data to compute features which capture the impact of enlarged ventricles by excluding fiber tracts passing through these regions. The segmentation and network features are used to train a model for NPH prediction. Results. Our method outperforms the current state-of-the-art by 9 precision points and 29 recall points. Our segmentation model outperforms the current state-of-the-art in segmenting the ventricle, gray-white matter, and subarachnoid space in CT scans. Conclusion. Our experimental results demonstrate that fast and accurate volumetric segmentation of CT brain scans can help improve the NPH diagnosis process, and network properties can increase NPH prediction accuracy.

目标和影响声明。我们提出了一种通过CT扫描预测正常压力性脑积水(NPH)的自动方法。深度卷积网络从扫描中分割出感兴趣的区域。然后将这些区域与MRI信息相结合以预测NPH。据我们所知,这是第一种从CT扫描中自动预测NPH并结合扩散束成像信息进行预测的方法。介绍由于其低成本和高通用性,CT扫描经常用于NPH诊断。目前还没有明确有效的方案来分析NPH的CT扫描。Evans指数是使用一个2D图像切片对心室与大脑体积的近似值,已被提出,但并不稳健。所提出的方法是量化感兴趣区域的有效方法,并为预测NPH提供了一种计算方法。方法。我们提出了一种预测NPH的新方法,通过将CT扫描分割的感兴趣区域与连接体数据相结合,计算通过排除穿过这些区域的纤维束来捕捉心室增大影响的特征。分割和网络特征用于训练NPH预测的模型。后果我们的方法比目前最先进的方法高出9个精度点和29个召回点。我们的分割模型在CT扫描中分割心室、灰质和蛛网膜下腔方面优于目前最先进的分割模型。结论我们的实验结果表明,快速准确的CT脑扫描体积分割有助于改善NPH的诊断过程,网络特性可以提高NPH的预测精度。
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引用次数: 2
High-Frequency 3D Photoacoustic Computed Tomography Using an Optical Microring Resonator. 使用光学微环谐振器的高频三维光声计算机断层扫描。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.34133/2022/9891510
Qiangzhou Rong, Youngseop Lee, Yuqi Tang, Tri Vu, Carlos Taboada, Wenhan Zheng, Jun Xia, David A Czaplewski, Hao F Zhang, Cheng Sun, Junjie Yao

3D photoacoustic computed tomography (3D-PACT) has made great advances in volumetric imaging of biological tissues, with high spatial-temporal resolutions and large penetration depth. The development of 3D-PACT requires high-performance acoustic sensors with a small size, large detection bandwidth, and high sensitivity. In this work, we present a new high-frequency 3D-PACT system that uses a micro-ring resonator (MRR) as the acoustic sensor. The MRR sensor has a size of 80 μm in diameter, and was fabricated using the nanoimprint lithography technology. Using the MRR sensor, we have developed a transmission-mode 3D-PACT system that has achieved a detection bandwidth of ~23 MHz, an imaging depth of ~8 mm, a lateral resolution of 114 μm, and an axial resolution of 57 μm. We have demonstrated the 3D PACT's performance on in vitro phantoms, ex vivo mouse brain, and in vivo mouse ear and tadpole. The MRR-based 3D-PACT system can be a promising tool for structural, functional, and molecular imaging of biological tissues at depths.

三维光声计算机断层扫描技术(3D- pact)在生物组织的体积成像方面取得了很大进展,具有高时空分辨率和大穿透深度。3D-PACT的发展需要体积小、探测带宽大、灵敏度高的高性能声学传感器。在这项工作中,我们提出了一种新的高频3D-PACT系统,该系统使用微环谐振器(MRR)作为声传感器。MRR传感器的直径为80 μm,采用纳米压印光刻技术制备。利用MRR传感器,我们开发了一种传输模式3D-PACT系统,该系统的检测带宽为~23 MHz,成像深度为~8 mm,横向分辨率为114 μm,轴向分辨率为57 μm。我们在离体小鼠模型、离体小鼠大脑、离体小鼠耳朵和蝌蚪上展示了三维PACT的性能。基于核磁共振的3D-PACT系统是一种很有前途的工具,可用于深层生物组织的结构、功能和分子成像。
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引用次数: 7
Molecular Computational Anatomy: Unifying the Particle to Tissue Continuum via Measure Representations of the Brain. 分子计算解剖学:通过大脑的测量表征统一粒子到组织连续体。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.34133/2022/9868673
Michael Miller, Daniel Tward, Alain Trouvé

Objective: The objective of this research is to unify the molecular representations of spatial transcriptomics and cellular scale histology with the tissue scales of computational anatomy for brain mapping.

Impact statement: We present a unified representation theory for brain mapping based on geometric varifold measures of the microscale deterministic structure and function with the statistical ensembles of the spatially aggregated tissue scales.

Introduction: Mapping across coordinate systems in computational anatomy allows us to understand structural and functional properties of the brain at the millimeter scale. New measurement technologies in digital pathology and spatial transcriptomics allow us to measure the brain molecule by molecule and cell by cell based on protein and transcriptomic functional identity. We currently have no mathematical representations for integrating consistently the tissue limits with the molecular particle descriptions. The formalism derived here demonstrates the methodology for transitioning consistently from the molecular scale of quantized particles-using mathematical structures as first introduced by Dirac as the class of generalized functions-to the tissue scales with methods originally introduced by Euler for fluids.

Methods: We introduce two mathematical methods based on notions of generalized functions and statistical mechanics. We use geometric varifolds, a product measure on space and function, to represent functional states at the micro-scales-electrophysiology, molecular histology-integrated with a Boltzmann-like program to pass from deterministic particle descriptions to empirical probabilities on the functional states at the tissue scales.

Results: Our space-function varifold representation provides a recipe for traversing from molecular to tissue scales in terms of a cascade of linear space scaling composed with nonlinear functional feature mapping. Following the cascade implies every scale is a geometric measure so that a universal family of measure norms can be introduced which quantifies the geodesic connection between brains in the orbit independent of the probing technology, whether it be RNA identities, Tau or amyloid histology, spike trains, or dense MR imagery.

Conclusions: We demonstrate a unified brain mapping theory for molecular and tissue scales based on geometric measure representations. We call the consistent aggregation of tissue scales from particle and cellular scales, molecular computational anatomy.

目的:本研究的目的是将空间转录组学和细胞尺度组织学的分子表征与计算解剖学的组织尺度相统一,用于脑制图。影响陈述:我们提出了一种统一的表征理论,该理论基于微观尺度确定性结构和功能的几何变分度量,具有空间聚集组织尺度的统计集合。在计算解剖学中,跨坐标系统的映射使我们能够在毫米尺度上理解大脑的结构和功能特性。数字病理学和空间转录组学的新测量技术使我们能够基于蛋白质和转录组功能同一性来测量脑分子和细胞。我们目前还没有数学表示来一致地整合组织极限与分子粒子描述。这里导出的形式化展示了从量子化粒子的分子尺度(使用狄拉克首先引入的数学结构作为一类广义函数)到组织尺度(最初由欧拉引入的流体方法)的一致过渡的方法。方法:介绍了基于广义函数和统计力学的两种数学方法。我们使用几何变量,空间和功能的乘积度量,来表示微尺度上的功能状态-电生理学,分子组织学-与类似玻尔兹曼的程序相结合,从确定性粒子描述传递到组织尺度上功能状态的经验概率。结果:我们的空间函数变量表示提供了一种从分子尺度到组织尺度的方法,该方法是由非线性功能特征映射组成的线性空间尺度级联。遵循级联意味着每个尺度都是一个几何测量,因此可以引入一个通用的测量规范家族,量化轨道中大脑之间的测地连接,而不依赖于探测技术,无论是RNA身份,Tau或淀粉样蛋白组织,尖峰序列还是密集的MR图像。结论:我们展示了基于几何测量表征的分子和组织尺度的统一脑映射理论。我们把粒子和细胞尺度的组织尺度的一致聚集称为分子计算解剖学。
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引用次数: 3
A Review of Deep Learning Applications in Lung Ultrasound Imaging of COVID-19 Patients. 深度学习在新冠肺炎患者肺部超声成像中的应用综述
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.34133/2022/9780173
Lingyi Zhao, Muyinatu A Lediju Bell

The massive and continuous spread of COVID-19 has motivated researchers around the world to intensely explore, understand, and develop new techniques for diagnosis and treatment. Although lung ultrasound imaging is a less established approach when compared to other medical imaging modalities such as X-ray and CT, multiple studies have demonstrated its promise to diagnose COVID-19 patients. At the same time, many deep learning models have been built to improve the diagnostic efficiency of medical imaging. The integration of these initially parallel efforts has led multiple researchers to report deep learning applications in medical imaging of COVID-19 patients, most of which demonstrate the outstanding potential of deep learning to aid in the diagnosis of COVID-19. This invited review is focused on deep learning applications in lung ultrasound imaging of COVID-19 and provides a comprehensive overview of ultrasound systems utilized for data acquisition, associated datasets, deep learning models, and comparative performance.

COVID-19的大规模持续传播促使世界各地的研究人员积极探索、了解和开发新的诊断和治疗技术。尽管与x射线和CT等其他医学成像方式相比,肺部超声成像是一种不太成熟的方法,但多项研究表明,它有望诊断COVID-19患者。同时,建立了许多深度学习模型来提高医学成像的诊断效率。这些最初平行的努力的整合导致多名研究人员报告了深度学习在COVID-19患者医学成像中的应用,其中大多数显示了深度学习在帮助COVID-19诊断方面的杰出潜力。这篇特邀综述的重点是深度学习在COVID-19肺部超声成像中的应用,并全面概述了用于数据采集、相关数据集、深度学习模型和比较性能的超声系统。
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引用次数: 18
Highly Integrated Multiplexing and Buffering Electronics for Large Aperture Ultrasonic Arrays. 用于大孔径超声阵列的高度集成多路复用和缓冲电子器件。
IF 5 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 Epub Date: 2022-06-30 DOI: 10.34133/2022/9870386
Robert Wodnicki, Haochen Kang, Di Li, Douglas N Stephens, Hayong Jung, Yizhe Sun, Ruimin Chen, Lai-Ming Jiang, Nestor E Cabrera-Munoz, Josquin Foiret, Qifa Zhou, Katherine W Ferrara

Large aperture ultrasonic arrays can be implemented by tiling together multiple pretested modules of high-density acoustic arrays with closely integrated multiplexing and buffering electronics to form a larger aperture with high yield. These modular arrays can be used to implement large 1.75D array apertures capable of focusing in elevation for uniform slice thickness along the axial direction which can improve image contrast. An important goal for large array tiling is obtaining high yield and sensitivity while reducing extraneous image artifacts. We have been developing tileable acoustic-electric modules for the implementation of large array apertures utilizing Application Specific Integrated Circuits (ASICs) implemented using 0.35 μ m high voltage (50 V) CMOS. Multiple generations of ASICs have been designed and tested. The ASICs were integrated with high-density transducer arrays for acoustic testing and imaging. The modules were further interfaced to a Verasonics Vantage imaging system and were used to image industry standard ultrasound phantoms. The first-generation modules comprise ASICs with both multiplexing and buffering electronics on-chip and have demonstrated a switching artifact which was visible in the images. A second-generation ASIC design incorporates low switching injection circuits which effectively mitigate the artifacts observed with the first-generation devices. Here, we present the architecture of the two ASIC designs and module types as well imaging results that demonstrate reduction in switching artifacts for the second-generation devices.

大孔径超声阵列可以通过将高密度声学阵列的多个预测试模块与紧密集成的多路复用和缓冲电子器件拼接在一起来实现,从而以高产率形成更大的孔径。这些模块化阵列可用于实现大的1.75D阵列孔径,该阵列孔径能够在仰角上聚焦以沿着轴向方向获得均匀的切片厚度,这可以提高图像对比度。大阵列拼接的一个重要目标是获得高产量和高灵敏度,同时减少多余的图像伪影。我们一直在开发可平铺的声电模块,用于利用0.35μm高压(50V)CMOS实现的专用集成电路(ASIC)实现大阵列孔径。已经设计并测试了多代ASIC。ASIC与高密度换能器阵列集成,用于声学测试和成像。这些模块进一步连接到Verasonics Vantage成像系统,并用于对行业标准超声模型进行成像。第一代模块包括芯片上具有多路复用和缓冲电子器件的ASIC,并且已经证明了在图像中可见的切换伪像。第二代ASIC设计结合了低开关注入电路,其有效地减轻了用第一代器件观察到的伪影。在这里,我们介绍了两种ASIC设计的架构和模块类型,以及成像结果,这些结果证明了第二代设备的开关伪影的减少。
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引用次数: 0
Recent Advances in the Science of Burst Wave Lithotripsy and Ultrasonic Propulsion. 爆破波碎石与超声推进技术的最新进展。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.34133/2022/9847952
Dima Raskolnikov, Michael R Bailey, Jonathan D Harper

Nephrolithiasis is a common, painful condition that requires surgery in many patients whose stones do not pass spontaneously. Recent technologic advances have enabled the use of ultrasonic propulsion to reposition stones within the urinary tract, either to relieve symptoms or facilitate treatment. Burst wave lithotripsy (BWL) has emerged as a noninvasive technique to fragment stones in awake patients without significant pain or renal injury. We review the preclinical and human studies that have explored the use of these two technologies. We envision that BWL will fill an unmet need for the noninvasive treatment of patients with nephrolithiasis.

肾结石是一种常见的、痛苦的疾病,许多结石不能自行排出的患者需要手术治疗。最近的技术进步使超声推进技术能够在尿路内重新定位结石,从而缓解症状或促进治疗。Burst wave lithotripsy (BWL)是一种无创碎石技术,可以在没有明显疼痛或肾脏损伤的清醒患者中粉碎结石。我们回顾了临床前和人类研究,探索了这两种技术的使用。我们设想BWL将填补肾结石患者无创治疗的未满足需求。
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引用次数: 2
Jointly Optimized Spatial Histogram UNET Architecture (JOSHUA) for Adipose Tissue Segmentation 联合优化空间直方图UNET架构(JOSHUA)用于脂肪组织分割
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-11-22 DOI: 10.1101/2021.11.22.469463
Joshua Peeples, Julie F. Jameson, Nisha M Kotta, J. Grasman, W. Stoppel, A. Zare
Objective We quantify adipose tissue deposition at surgical sites as a function of biomaterial implantation. Impact Statement To our knowledge, this study is the first investigation to apply convolutional neural network (CNN) models to identify and segment adipose tissue in histological images from silk fibroin biomaterial implants. Introduction When designing biomaterials for the treatment of various soft tissue injuries and diseases, one must consider the extent of adipose tissue deposition. In this work, we implant silk fibroin biomaterials in a rodent subcutaneous injury model. Current strategies for quantifying adipose tissue after biomaterial implantation are often tedious and prone to human bias during analysis. Methods We used CNN models with novel spatial histogram layer(s) that can more accurately identify and segment regions of adipose tissue in hematoxylin and eosin (H&E) and Masson’s Trichrome stained images, allowing for determination of the optimal biomaterial formulation. We compared the method, Jointly Optimized Spatial Histogram UNET Architecture (JOSHUA), to the baseline UNET model and an extension of the baseline model, Attention UNET, as well as to versions of the models with a supplemental “attention”-inspired mechanism (JOSHUA+ and UNET+). Results The inclusion of histogram layer(s) in our models shows improved performance through qualitative and quantitative evaluation. Conclusion Our results demonstrate that the proposed methods, JOSHUA and JOSHUA+, are highly beneficial for adipose tissue identification and localization. The new histological dataset and code for our experiments are publicly available.
目的定量研究手术部位脂肪组织沉积与生物材料植入的关系。据我们所知,本研究是首次应用卷积神经网络(CNN)模型在丝素生物材料植入物的组织学图像中识别和分割脂肪组织的研究。在设计用于治疗各种软组织损伤和疾病的生物材料时,必须考虑脂肪组织沉积的程度。在这项工作中,我们将丝素蛋白生物材料植入啮齿动物皮下损伤模型。目前对生物材料植入后的脂肪组织进行量化的策略往往是繁琐的,而且在分析过程中容易受到人为的偏见。方法采用具有新颖空间直方图层的CNN模型,可以更准确地识别和分割苏木精和伊红(H&E)和马松三色染色图像中的脂肪组织区域,从而确定最佳生物材料配方。我们将联合优化空间直方图UNET架构(JOSHUA)方法与基线UNET模型和基线模型的扩展Attention UNET,以及具有补充“注意力”启发机制的模型版本(JOSHUA+和UNET+)进行了比较。结果通过定性和定量评价,直方图层在我们的模型中得到了改善。结论我们的研究结果表明,JOSHUA和JOSHUA+方法对脂肪组织的识别和定位非常有益。新的组织学数据集和我们实验的代码是公开的。
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引用次数: 4
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