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2014 1st Workshop on Pattern Recognition Techniques for Indirect Immunofluorescence Images最新文献

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HEp-2 Cell Image Classification with Convolutional Neural Networks 基于卷积神经网络的HEp-2细胞图像分类
Zhimin Gao, Jianjia Zhang, Luping Zhou, Lei Wang
The diagnosis of many autoimmune diseases can be greatly facilitated by automatic staining patterns classification of Human Epithelial-2 (HEp-2) cells within indirect immunofluorescence (IIF) images. In this paper, we propose a framework to classify the HEp-2 cells by utilizing the deep convolutional neural networks (CNNs). With carefully designed network architecture and optimized parameters, our networks extract features from raw pixels of cell images in a hierarchical manner and perform classification jointly, avoiding using hand-crafted features to represent a HEp-2 cell image. We evaluate our method on the training dataset of HEp-2 cells classification competition held by ICPR 2014. Our system achieves mean class accuracy of 96.7% on the held-out test set and it also obtains competitive performance on the ICPR 2012 cell dataset.
间接免疫荧光(IIF)图像中人类上皮-2 (HEp-2)细胞的自动染色模式分类可以极大地促进许多自身免疫性疾病的诊断。在本文中,我们提出了一个利用深度卷积神经网络(cnn)对HEp-2细胞进行分类的框架。通过精心设计的网络架构和优化的参数,我们的网络以分层的方式从细胞图像的原始像素中提取特征并共同进行分类,避免了使用手工制作的特征来表示HEp-2细胞图像。我们在ICPR 2014举办的HEp-2细胞分类大赛的训练数据集上对我们的方法进行了评估。我们的系统在hold -out测试集上达到了96.7%的平均分类准确率,在ICPR 2012单元数据集上也取得了具有竞争力的性能。
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引用次数: 41
HEp-2 Cells Classification Using Morphological Features and a Bundle of Local Gradient Descriptors 形态学特征和局部梯度描述符的HEp-2细胞分类
Ilias Theodorakopoulos, Dimitris Kastaniotis, G. Economou, S. Fotopoulos
A system for automatic classification of staining patterns in IIF imaging is presented. A full pipeline of pre-processing, feature extraction and classification stages is designed in order to overcome specific challenges posed by the nature of the data. In the preprocessing stage the images are subjected to normalization and de-noising using a sparse representation-based technique. A set morphological features, extracted using multi-level thresholding, is combined with a bundle of local gradient descriptors, selected so as to encode textural and structural information of the fluorescent patterns in multiple scales. The proposed method was evaluated using a dataset with over 10K images achieving over 90 percent of classification accuracy.
提出了一种用于IIF成像染色模式自动分类的系统。为了克服数据性质带来的具体挑战,设计了一个完整的预处理、特征提取和分类阶段管道。在预处理阶段,使用基于稀疏表示的技术对图像进行归一化和去噪。采用多级阈值法提取一组形态学特征,并结合一组局部梯度描述符进行选择,在多尺度上编码荧光图案的纹理和结构信息。使用超过10K图像的数据集对所提出的方法进行了评估,获得了超过90%的分类准确率。
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引用次数: 30
A Graph Cuts Image Segmentation Method for Quantifying Barrier Permeation in Bone Tissue 一种用于定量骨组织屏障渗透的图切割图像分割方法
Hironori Shigeta, T. Mashita, Takeshi Kaneko, J. Kikuta, S. Seno, H. Takemura, H. Matsuda, M. Ishii
Bio-imaging techniques have recently gotten a lot of attention since they have enabled in-vivo imaging. They are expected to contribute to drug discovery, understanding of disease mechanisms etc. However, data retrieved by bioimaging techniques have been increasing in volume, and it is not anymore feasible to analyze it manually. Therefore automatic extraction of characteristic of a huge amount of data have become important. Moreover, quantitative analysis methods are required for statistical reliability. In this paper we introduce a method for the analysis of a sequence of bone tissue images taken by a two-photon microscope to quantify blood permeability of bone marrow. This method segments the input image sequence to blood vessel, bone marrow and bone regions by graph cuts which we extended according to the images. Permeability is quantified by the intensity of the segmentation result. We also confirm that our method shows that quantification tendency is similar to ground truth data made by an expert.
生物成像技术最近得到了很多关注,因为它们使体内成像成为可能。他们有望为药物发现、疾病机制的理解等做出贡献。然而,通过生物成像技术获取的数据量越来越大,人工分析已不再可行。因此,对海量数据特征的自动提取就显得十分重要。此外,统计可靠性需要定量分析方法。本文介绍了一种分析双光子显微镜拍摄的一系列骨组织图像的方法,以量化骨髓的血液通透性。该方法对输入图像序列进行图切割,并根据图像进行扩展,将输入图像序列分割为血管、骨髓和骨骼区域。渗透率通过分割结果的强度来量化。我们还证实,我们的方法表明量化趋势类似于专家所做的地面真实数据。
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引用次数: 7
HEp-2 Cell Classification with Heterogeneous Classes-Processes Based on K-Nearest Neighbours 基于k近邻的HEp-2细胞异质分类过程
Cascio Donato, Taormina Vincenzo, Cipolla Marco, Fauci Francesco, Vasile Simone Maria, Raso Giuseppe
We present a scheme for the feature extraction and classification of the fluorescence staining patterns of HEp-2 cells in IIF images. We propose a set of complementary processes specific to each class of patterns to search. Our set of processes consists of preprocessing, features extraction and classification. The choice of methods, features and parameters was performed automatically, using the Mean Class Accuracy (MCA) as a figure of merit. We extract a large number (108) of features able to fully characterize the staining pattern of HEp-2 cells. We propose a classification approach based on two steps: the first step follows the one-against-all (OAA) scheme, while the second step follows the one-against-one (OAO) scheme. To do this, we needed to implement 21 KNN classifiers: 6 OAA and 15 OAO. Leave-one-out image cross validation method was used for the evaluation of the results.
我们提出了一种IIF图像中HEp-2细胞荧光染色模式的特征提取和分类方案。我们针对每一类要搜索的模式提出了一组互补的过程。我们的过程包括预处理、特征提取和分类。方法、特征和参数的选择是自动进行的,使用平均类精度(MCA)作为优点的数字。我们提取了大量(108)个能够充分表征HEp-2细胞染色模式的特征。我们提出了一种基于两步的分类方法:第一步遵循一对一(OAA)方案,第二步遵循一对一(OAO)方案。为此,我们需要实现21个KNN分类器:6个OAA和15个OAO。采用留一图像交叉验证法对结果进行评价。
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引用次数: 16
Class-Specific Hierarchical Classification of HEp-2 Cell Images: The Case of Two Classes HEp-2细胞图像的类特异性分级分类:以两类为例
Krati Gupta, Vibha Gupta, A. Sao, A. Bhavsar, A. D. Dileep
We propose and analyze a novel framework for classification of HEp-2 cell images. It is based upon two important aspects. First, we propose to utilize the expert knowledge about the visual characteristics of classes to formulate class-specific image features. Secondly, realizing that the problem involves a small number of classes, we treat the classification task as hierarchical verification subtasks. Thus, the overall classification problem is posed as a verification of each class, using its class-specific features. The current study reports the results using the Nuclear Membrane and Golgi classes. We demonstrate that our framework yields high classification rate with simple and efficient feature definitions, and only (20%) of the data for training. We also analyze important aspects such as comparison with non-hierarchical approach, and performance on low-contrast images which are important for early disease detection.
我们提出并分析了一种新的HEp-2细胞图像分类框架。它基于两个重要方面。首先,我们建议利用关于类的视觉特征的专家知识来制定特定于类的图像特征。其次,考虑到问题涉及的类数量较少,我们将分类任务视为分层验证子任务。因此,整个分类问题被提出作为每个类的验证,使用其特定于类的特征。目前的研究报告了使用核膜和高尔基类的结果。我们证明了我们的框架通过简单有效的特征定义产生了很高的分类率,并且只有(20%)的数据用于训练。我们还分析了重要的方面,如与非分层方法的比较,以及对早期疾病检测重要的低对比度图像的性能。
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引用次数: 12
A Bag of Words Based Approach for Classification of HEp-2 Cell Images 基于词袋的HEp-2细胞图像分类方法
Shahab Ensafi, Shijian Lu, A. Kassim, C. Tan
In this work we present an automatic HEp-2 cell image classification technique that exploits different spatial scaled image representation and sparse coding of SIFT and SURF features. The proposed method is applied on the ICIP2013 dataset in the I3A workshop, which is held in ICPR 2014 conference. Experiments are designed to capture the accuracies on training set with cross validation method. Additionally, the prior information on positive and intensity levels of cells are used to boost the overall performance. Finally, different number of iterations on learning the dictionary is studied to find the optimum one.
在这项工作中,我们提出了一种自动HEp-2细胞图像分类技术,该技术利用不同的空间尺度图像表示和SIFT和SURF特征的稀疏编码。该方法在ICPR 2014会议I3A研讨会上对ICIP2013数据集进行了应用。实验采用交叉验证的方法来获取训练集上的准确率。此外,关于细胞的阳性和强度水平的先验信息被用来提高整体性能。最后,研究了不同迭代次数的字典学习,找到最优的字典。
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引用次数: 31
Biologically-Inspired Dense Local Descriptor for Indirect Immunofluorescence Image Classification 用于间接免疫荧光图像分类的生物启发密集局部描述子
Diego Gragnaniello, Carlo Sansone, L. Verdoliva
This work deals with the design of a classification method for cells extracted from Indirect Immunofluorescence images. In particular, we propose to use a dense local descriptor invariant both to scale changes and to rotations in order to classify the six categories of staining patterns of the cells. The descriptor is able to give a compact and discriminative representation and combines a log-polar sampling with spatially-varying gaussian smoothing applied on the gradients images in specific directions. Bag of Words is finally used to perform classification and experimental results show very good performance.
本工作涉及设计一种从间接免疫荧光图像中提取细胞的分类方法。特别是,我们建议使用密集的局部描述符不变量来缩放变化和旋转,以便对细胞的六种染色模式进行分类。该描述符能够给出紧凑的判别表示,并将对数极坐标采样与空间变化的高斯平滑相结合,应用于特定方向的梯度图像。最后使用Bag of Words进行分类,实验结果显示了很好的分类效果。
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引用次数: 28
Morphological and Texture Features for HEp-2 Cells Classification HEp-2细胞分类的形态学和纹理特征
L. Nanni, M. Paci, F. C. Santos, J. Hyttinen
This paper describes our texture descriptor ensemble aimed to compete for the Cell Level classification task (Task 1) in the "Contest on Performance Evaluation on Indirect Immunofluorescence Image Analysis Systems", hosted by the I3A Workshop on Pattern Recognition Techniques for Indirect Immunofluorescence Images. Our system is based on the combination of 4 descriptors based on Local Binary Pattern (LBP) and 1 morphological feature set: the multiscale Pyramid LBP, Local Configuration Pattern, Rotation Invariant Co-occurrence among adjacent LBP, Extended LBP and finally Strandmark morphological features. From each image a total of 2643 features are extracted. The corresponding 5 feature sets are classified using Support Vector Machines and results are combined according to the sum rule. By using a 10-fold cross validation testing protocol, the proposed ensemble obtains 60.9% of accuracy, outperforming many state-of-art stand-alone texture descriptors as well as other ensembles.
本文描述了我们的纹理描述符集合,目的是在I3A间接免疫荧光图像模式识别技术研讨会主办的“间接免疫荧光图像分析系统性能评估竞赛”中竞争细胞水平分类任务(任务1)。该系统基于基于局部二值模式(LBP)的4个描述符和1个形态特征集的组合:多尺度金字塔型LBP、局部构型模式、相邻LBP之间的旋转不变共现、扩展LBP和最后的标志形态特征。从每张图像中共提取2643个特征。使用支持向量机对对应的5个特征集进行分类,并根据求和规则对结果进行组合。通过使用10倍交叉验证测试协议,所提出的集成获得了60.9%的准确率,优于许多最先进的独立纹理描述符以及其他集成。
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引用次数: 7
A Segmentation Method for Bone Marrow Cavity Imaging Using Graph Cuts 一种基于图切的骨髓腔图像分割方法
T. Mashita, Jun Usam, Hironori Shigeta, Yoshihiro Kuroda, J. Kikuta, S. Seno, M. Ishii, H. Matsuda, H. Takemura
The improvement of bioimaging technologies enables the observation of cellular dynamics invivo. Some new bioimaging technologies are expected to contribute to the discovery of new drugs and mechanisms of disease. To improve the contributions of bioimaging, it is required to extract a particular region or to detect a particular cell's motion within bioimages. Moreover, automatic extraction and detection with image processing is also required because the accurate and uniformed processing of a massive number of images manually is unrealistic. To help automate this process, we introduce a bone marrow cavity segmentation method for two-photon excitation microscopy images. Specialists of cellular dynamics define regions of bone marrow cavity by considering several criteria, including characteristics of intensity and blood flow. We take those criteria into our method as the energy function of graph cuts. Results of evaluations and comparison with normal graph cuts show that our proposed method that does not use hard constraints achieved a performance better than normal graph cuts with hard constraints.
生物成像技术的进步使在体内观察细胞动力学成为可能。一些新的生物成像技术有望有助于发现新的药物和疾病的机制。为了提高生物成像的贡献,需要在生物图像中提取特定区域或检测特定细胞的运动。此外,由于人工对大量图像进行准确、均匀的处理是不现实的,因此还需要通过图像处理实现自动提取和检测。为了使这一过程自动化,我们引入了一种双光子激发显微镜图像的骨髓腔分割方法。细胞动力学专家通过考虑几个标准来定义骨髓腔的区域,包括强度和血流的特征。我们将这些准则作为图切的能量函数纳入我们的方法。结果表明,不使用硬约束的法向图切比使用硬约束的法向图切具有更好的性能。
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引用次数: 5
Quadratic Recurrent Finite Impulse Response MLP for Indirect Immunofluorescence Image Recognition 间接免疫荧光图像识别的二次循环有限脉冲响应MLP
Cristinel Codrescu
The I3A2014 contest participants had to design and implement a pattern recognition system able to classify the cells belonging to HEp-2 images in one of six pattern classes. We propose the QR-FIRMLP architecture, an extension of the finite impulse response multilayer perceptron (FIRMLP). The FIRMLP is a multilayer perceptron where the static weights have been replaced by finite impulse response filters. We have extended this architecture by replacing some sigmoidal layers with quadratic ones and adding recurrent connections to the FIR neurons.
I3A2014竞赛的参与者必须设计并实现一个模式识别系统,该系统能够将属于HEp-2图像的细胞分类为六个模式类之一。我们提出了QR-FIRMLP结构,这是有限脉冲响应多层感知器(FIRMLP)的扩展。FIRMLP是一个多层感知器,其中静态权重已被有限脉冲响应滤波器所取代。我们扩展了这个结构,用二次元层替换了一些s型层,并向FIR神经元添加了循环连接。
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引用次数: 10
期刊
2014 1st Workshop on Pattern Recognition Techniques for Indirect Immunofluorescence Images
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