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2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro最新文献

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CUDA: Scalable parallel programming for high-performance scientific computing CUDA:用于高性能科学计算的可扩展并行编程
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541126
D. Luebke
Graphics processing units (GPUs) originally designed for computer video cards have emerged as the most powerful chip in a high-performance workstation. Unlike multicore CPU architectures, which currently ship with two or four cores, GPU architectures are "manycore" with hundreds of cores capable of running thousands of threads in parallel. NVIDIA's CUDA is a co-evolved hardware-software architecture that enables high-performance computing developers to harness the tremendous computational power and memory bandwidth of the GPU in a familiar programming environment - the C programming language. We describe the CUDA programming model and motivate its use in the biomedical imaging community.
最初为计算机显卡设计的图形处理单元(gpu)已经成为高性能工作站中最强大的芯片。与多核CPU架构不同的是,目前的多核CPU架构只有两个或四个核心,而GPU架构是“多核”的,拥有数百个核心,能够并行运行数千个线程。NVIDIA的CUDA是一种共同发展的硬件软件架构,使高性能计算开发人员能够在熟悉的编程环境(C编程语言)中利用GPU的巨大计算能力和内存带宽。我们描述了CUDA编程模型,并激励其在生物医学成像社区的使用。
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引用次数: 205
Assessment of ventricle volume from serial MRI scans in communicating hydrocephalus 通讯性脑积水患者脑室容积的MRI连续扫描评估
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4540929
J. Butman, M. Linguraru
Postoperative communicating hydrocephalus has been recognized in patients with brain tumors. The associated changes in ventricle volume can be difficult to identify, particularly over short time intervals. Potentially, accurate ventricle volume estimates could provide for a better understanding of communicating hydrocephalus, and lead to more confident diagnoses. Our method evaluates ventricle size from serial brain MRI examinations, we (1) combined serial images to increase SNR (2) segmented this image to generate a ventricle template using fats marching methods and geodesic active contours, and (3) propagate the segmentation using deformable registration of the original MRI datasets. By applying this deformation to the ventricle template, serial volume estimates were obtained in a robust manner.
脑肿瘤患者术后沟通性脑积水已被确认。心室容积的相关变化很难识别,特别是在短时间间隔内。潜在地,准确的脑室容积估计可以更好地了解沟通性脑积水,并导致更自信的诊断。我们的方法从连续的脑MRI检查中评估脑室大小,我们(1)将连续图像组合以提高信噪比(2)使用脂肪行军方法和测地线活动轮廓对该图像进行分割以生成心室模板(3)使用原始MRI数据集的可变形配准传播分割。通过将这种变形应用于心室模板,以鲁棒的方式获得了序列体积估计。
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引用次数: 12
Non-parametric regression for patch-based fluorescence microscopy image sequence denoising 基于斑块的荧光显微镜图像序列去噪的非参数回归
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541104
J. Boulanger, J. Sibarita, C. Kervrann, P. Bouthemy
We present a non-parametric regression method for denoising fluorescence video-microscopy volume sequences. The designed method aims at using the 3D+t information in order to restore acquired data contaminated by Poisson and Gaussian noise. We propose to use a variance stabilization transform to deal with the combination of Poisson and Gaussian noise. Consequently, we further propose an adaptive patch-based framework able to preserve space-time discontinuities and reduce significantly noise level using the 3D+t space-time context. This approach lead to an algorithm whose parameters are calibrated and then ready for intensive use. The performance of the proposed method are then demonstrated on both synthetic and real image sequences using quantitative as well as qualitative criteria.
我们提出了一种非参数回归方法去噪荧光视频显微镜体积序列。所设计的方法旨在利用三维+t信息来恢复被泊松和高斯噪声污染的采集数据。我们提出使用方差稳定变换来处理泊松噪声和高斯噪声的组合。因此,我们进一步提出了一种基于补丁的自适应框架,该框架能够使用3D+t时空上下文来保持时空不连续并显着降低噪声水平。这种方法产生了一种算法,其参数经过校准,然后准备好大量使用。然后使用定量和定性标准在合成和真实图像序列上证明了所提出方法的性能。
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引用次数: 7
Automated localisation of retinal optic disk using Hough transform 基于霍夫变换的视网膜视盘自动定位
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541312
S. Sekhar, W. Al-Nuaimy, A. Nandi
The retinal fundus photograph is widely used in the diagnosis and treatment of various eye diseases such as diabetic retinopathy and glaucoma. Medical image analysis and processing has great significance in the field of medicine, especially in non-invasive treatment and clinical study. Normally fundus images are manually graded by specially trained clinicians in a time-consuming and resource-intensive process. A computer-aided fundus image analysis could provide an immediate detection and characterisation of retinal features prior to specialist inspection. This paper describes a novel method to automatically localise one such feature: the optic disk. The proposed method consists of two steps: in the first step, a circular region of interest is found by first isolating the brightest area in the image by means of morphological processing, and in the second step, the Hough transform is used to detect the main circular feature (corresponding to the optical disk) within the positive horizontal gradient image within this region of interest. Initial results on a database of fundus images show that the proposed method is effective and favourable in relation to comparable techniques.
视网膜眼底照片广泛应用于糖尿病视网膜病变、青光眼等多种眼病的诊断和治疗。医学图像分析与处理在医学领域,特别是在无创治疗和临床研究中具有重要意义。通常眼底图像是由经过专门培训的临床医生手动分级的,这是一个耗时且资源密集的过程。计算机辅助眼底图像分析可以在专家检查之前提供视网膜特征的即时检测和表征。本文提出了一种自动定位视盘特征的新方法。该方法分为两步:第一步,首先通过形态学处理分离图像中最亮的区域,找到感兴趣的圆形区域;第二步,使用霍夫变换检测该感兴趣区域内正水平梯度图像中的主要圆形特征(对应于光盘)。在眼底图像数据库上的初步结果表明,与同类技术相比,该方法是有效和有利的。
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引用次数: 140
Liver tumor assessment with DCE-MRI 肝肿瘤DCE-MRI评估
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541118
L. Caldeira, J. Sanches
Dynamic-contrast enhanced MRI (DCE-MRI) is used in clinical practice to assess liver tumor malignancy. An algorithm to get information for automatic classification of tumors is presented. The Maximum value and WashIn and WashOut rates, obtained from the perfusion curves measured from the DCE-MRI images, are used in the classification process. The perfusion curves are described by a linear discrete pharmacokinetic (PK) model, based on multi-compartment paradigm where the input is the bolus injection. The arterial input function (AIF) that is usually estimated in the closest artery is assumed here to be the response of a second order linear system to the bolus injection. Therefore, the complete chain is modeled as a third order system with a single zero. The alignment procedure is performed by using the Mutual Information (MI) criterion with a non-rigid transformation to compensate the displacements occurred during the acquisition process. It is shown that the Maximum values and the WashIn and WashOut rates of the perfusion curves in malignant tumors are higher than in healthy tissues. This fact is used to classify them. Furthermore, it is also shown, that inside the tumor, the parameters associated with the perfusion curves for each pixel (time courses) present a higher variance than in the healthy tissues, which may also be used to increase the accuracy of the classifier. Examples using real data are presented.
动态对比增强MRI (DCE-MRI)用于临床评估肝脏肿瘤的恶性程度。提出了一种用于肿瘤自动分类的信息获取算法。从DCE-MRI图像测量的灌注曲线中获得的最大值和WashIn和WashOut率用于分类过程。灌注曲线由线性离散药代动力学(PK)模型描述,该模型基于多室范式,其中输入是大剂量注射。通常在最近的动脉中估计的动脉输入函数(AIF)在这里被假设为二阶线性系统对大剂量注射的响应。因此,完整链被建模为具有单零的三阶系统。对准过程采用互信息(MI)准则和非刚性变换来补偿在采集过程中发生的位移。结果表明,恶性肿瘤灌注曲线的最大值和WashIn、WashOut率均高于健康组织。这一事实被用来对它们进行分类。此外,研究还表明,在肿瘤内部,与每个像素(时间过程)的灌注曲线相关的参数比在健康组织中呈现更高的方差,这也可用于提高分类器的准确性。给出了使用实际数据的实例。
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引用次数: 3
A new detection scheme for multiple object tracking in fluorescence microscopy by joint probabilistic data association filtering 基于联合概率数据关联滤波的荧光显微镜多目标跟踪检测新方案
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4540983
Ihor Smal, W. Niessen, E. Meijering
Tracking of multiple objects in biological image data is a challenging problem due largely to poor imaging conditions and complicated motion scenarios. Existing tracking algorithms for this purpose often do not provide sufficient robustness and/or are computationally expensive. In this paper we propose a new object detection scheme, based on importance sampling from image intensity distributions, and show how it can be easily incorporated into a probabilistic tracking framework based on Kalman or particle filtering. Experiments on synthetic as well as real fluorescence microscopy image data from different biological studies show that the resulting tracking algorithm yields smaller localization errors at much lower execution times compared to other available methods.
生物图像数据中多目标的跟踪是一个具有挑战性的问题,主要是由于成像条件差和运动场景复杂。用于此目的的现有跟踪算法通常不能提供足够的鲁棒性和/或计算成本很高。在本文中,我们提出了一种新的目标检测方案,基于图像强度分布的重要性采样,并展示了如何将其轻松地纳入基于卡尔曼或粒子滤波的概率跟踪框架。对不同生物学研究的合成和真实荧光显微镜图像数据的实验表明,与其他可用方法相比,所得到的跟踪算法在更短的执行时间内产生更小的定位误差。
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引用次数: 64
Surface-based modeling of white matter fasciculi with orientation encoding 基于方向编码的白质束状体表面建模
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541094
Hui Zhang, Paul Yushkevich, T. Simon, J. Gee
In this paper, we describe a novel technique for modeling sheet-like white matter (WM) fasciculi using continuous medial representation (cm-rep). In the cm-rep framework, the skeleton of a fasciculus is described by a parametric surface patch. This modeling scheme is particularly appropriate for sheet-like structures, because the shapes of such objects can be effectively captured by their skeletons. We show that dimensionality reduction can be achieved without much loss of spatial specificity by projecting data along the "less interesting" thickness direction onto the skeletons. We demonstrate that local fiber orientation of the modeled fasciculi can be encoded in our framework and show how this information can be leveraged for deriving and analyzing brain connectivity patterns on the skeleton themselves.
在本文中,我们描述了一种使用连续内侧表示(cm-rep)来建模片状白质(WM)束状体的新技术。在cm-rep框架中,束的骨架由参数表面贴片描述。这种建模方案特别适用于片状结构,因为这类物体的形状可以通过它们的骨架有效地捕获。我们表明,通过将数据沿着“不那么有趣”的厚度方向投影到骨架上,可以在不损失太多空间特异性的情况下实现降维。我们证明了局部神经束的纤维方向可以在我们的框架中编码,并展示了如何利用这些信息来推导和分析骨骼本身的大脑连接模式。
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引用次数: 1
High throughput multiplex image analyses for androgen receptor function 雄激素受体功能的高通量多重图像分析
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4540997
Adam T. Szafran, M. Marcelli, M. Mancini
Evidence suggest that a subgroup of patients affected by either prostate cancer or androgen insensitivity syndrome harbor mutations within the androgen receptor that may contribute to the disease phenotype. To characterize the effects of these AR mutations, we have developed a high content screening assay able to determine AR transcriptional activity, cellular distribution, and cellular patterning simultaneously at the single cell level. We demonstrate that two mutations (F764L, R840C) isolated from AIS patients retain the ability to achieve similar levels of transcriptional activity, nuclear translocation, and nuclear hyperspeckling as wild type receptor, but require significantly higher levels of agonist. Differences in responses seen between the different compounds tested also suggest that the assay could be amendable to agonist screening for personalized patient drug selection.
有证据表明,受前列腺癌或雄激素不敏感综合征影响的患者亚组在雄激素受体内存在可能导致疾病表型的突变。为了表征这些AR突变的影响,我们开发了一种高含量筛选试验,能够在单细胞水平上同时确定AR转录活性、细胞分布和细胞模式。我们证明,从AIS患者中分离的两个突变(F764L, R840C)保留了与野生型受体相似的转录活性、核易位和核超斑点化水平的能力,但需要明显更高水平的激动剂。不同化合物测试之间的反应差异也表明,该分析可以用于激动剂筛选,以进行个性化的患者药物选择。
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引用次数: 2
Navigated nuclear probes for intra-operative functional imaging 导航核探针术中功能成像
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541266
Nassir Navab, J. Traub, T. Wendler, A. Buck, S. Ziegler
Since the 1920s, functional imaging has continuously contributed with novel methods in medical diagnostics. Its usage in the operation room has been limited in the past, although there is a great potential for localization of target structures and control of the surgery outcome. One example of functional information in the operation room is the use of nuclear probes. These devices are radiation detectors that provide a ID signal that allows the surgeons to get information about the distribution of a radioactive labeled structure. We extended nuclear probes with a spatial localization system in order to generate functional 3D surface images or functional tomographic images in the operating room. In this paper we summarize our methodology, discuss current limitations and possible remedies, and provide an outlook towards a new generation of image guided surgery based on anatomical and functional intraoperative imaging.
自20世纪20年代以来,功能成像不断为医学诊断提供新的方法。虽然在定位靶结构和控制手术结果方面有很大的潜力,但它在手术室中的应用在过去一直受到限制。手术室中功能性信息的一个例子是核探针的使用。这些设备是辐射探测器,可以提供ID信号,使外科医生能够获得有关放射性标记结构分布的信息。我们使用空间定位系统扩展核探针,以便在手术室中生成功能三维表面图像或功能层析图像。在本文中,我们总结了我们的方法,讨论了目前的局限性和可能的补救措施,并展望了基于解剖和功能术中成像的新一代图像引导手术。
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引用次数: 3
Three-dimensional reconstruction of serial histological mouse brain sections 小鼠连续脑组织的三维重建
Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541164
M. Chakravarty, B. Bedell, S. Zehntner, Alan C. Evans, D. Collins
Animal models are widely used to improve our understanding of the complex pathophysiological processes underlying diseases of the central nervous system (CNS), as well as a providing a means of evaluating the efficacy of new therapeutic agents. The advent of high-resolution, dedicated small animal magnetic resonance imaging and positron emission tomography scanners has greatly improved the value of animal imaging for such studies. However, the use of in vivo imaging markers requires extensive validation against gold standard, ex vivo tissue studies. In this paper, we describe methods for three-dimensional reconstruction of two-dimensional serial histological sections to create volumetric data, a major step in the use of ex vivo data for validating in vivo imaging techniques.
动物模型被广泛用于提高我们对中枢神经系统(CNS)疾病的复杂病理生理过程的理解,并提供了一种评估新药物疗效的手段。高分辨率、专用的小动物磁共振成像和正电子发射断层扫描扫描仪的出现大大提高了动物成像在这类研究中的价值。然而,体内成像标记的使用需要针对金标准、离体组织研究进行广泛的验证。在本文中,我们描述了二维连续组织学切片的三维重建方法,以创建体积数据,这是使用离体数据验证体内成像技术的主要步骤。
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引用次数: 13
期刊
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro
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