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

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Classification of breast-tissue microarray spots using colour and local invariants 利用颜色和局部不变量对乳腺组织微阵列斑点进行分类
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541167
Telmo Amaral, S. McKenna, K. Robertson, A. Thompson
{"title":"Classification of breast-tissue microarray spots using colour and local invariants","authors":"Telmo Amaral, S. McKenna, K. Robertson, A. Thompson","doi":"10.1109/ISBI.2008.4541167","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541167","url":null,"abstract":"Breast tissue microarrays facilitate the survey of very large numbers of tumours but their scoring by pathologists is time consuming, typically highly quantised and not without error. Automated segmentation of cells and intra-cellular compartments in such data can be problematic for reasons that include cell overlapping, complex tissue structure, debris, and variable appearance. This paper proposes a computationally efficient approach that uses colour and differential invariants to assign class posterior probabilities to pixels and then performs probabilistic classification of TMA spots using features analogous to the Quickscore system currently used by pathologists. It does not rely on accurate segmentation of individual cells. Classification performance at both pixel and spot levels was assessed using 110 spots from the adjuvant breast cancer (ABC) chemotherapy trial. The use of differential invariants in addition to colour yielded a small improvement in accuracy. Some reasons for classification results in disagreement with pathologist-provided labels are discussed and include noise in the class labels.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134454723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 16
Unsupervised segmentation of cell nuclei using geometric models 利用几何模型对细胞核进行无监督分割
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541099
Shaun Fitch, Trevor Jackson, Péter András, C. Robson
{"title":"Unsupervised segmentation of cell nuclei using geometric models","authors":"Shaun Fitch, Trevor Jackson, Péter András, C. Robson","doi":"10.1109/ISBI.2008.4541099","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541099","url":null,"abstract":"Fluorescent microscopy of biological samples allows non-invasive screening of specific molecular events in-situ. This approach is useful for investigating intricate signalling pathways and in the drug discovery process. The large volumes of data involved in image analysis are a limiting factor. As manual image interpretation relies on expensive manpower automated analysis is a far more appropriate solution. In this paper we discuss our approach to achieve reliable automated segmentation of individual cell nuclei from wide field images taken of prostate cancer cells. We present a novel analysis routine to accurately identify cell nuclei based upon intensity clustering and morphological validation using a data derived geometric model. This approach is shown to consistently outperform the standard analysis technique using real data.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130320405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Iterative nonlinear least squares algorithms for direct reconstruction of parametric images from dynamic PET 动态PET直接重建参数图像的迭代非线性最小二乘算法
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541175
Guobao Wang, J. Qi
{"title":"Iterative nonlinear least squares algorithms for direct reconstruction of parametric images from dynamic PET","authors":"Guobao Wang, J. Qi","doi":"10.1109/ISBI.2008.4541175","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541175","url":null,"abstract":"Indirect and direct methods have been developed for reconstructing parametric images from dynamic PET data. Indirect methods are relatively simple and easy to implement because the reconstruction and kinetic modeling are performed in two separate steps. Direct methods estimate the parametric images directly from the dynamic PET data and are statistically more efficient, but the algorithms are often difficult to implement. This paper presents a simple, monotonically convergent iterative algorithm for direct reconstruction of parametric images. Each iteration of the proposed algorithm consists of two separate steps: reconstruction of dynamic images followed by a pixel-wise weighted nonlinear least squares fitting. This algorithm resembles the empirical iterative implementation of the indirect approach, but converges to the solution of the direct formulation.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"4 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114001309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 16
Fast nonlocal filtering applied to electron cryomicroscopy 快速非局部滤波在电子冷冻显微镜中的应用
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541250
J. Darbon, Alexandre Cunha, T. Chan, S. Osher, G. Jensen
{"title":"Fast nonlocal filtering applied to electron cryomicroscopy","authors":"J. Darbon, Alexandre Cunha, T. Chan, S. Osher, G. Jensen","doi":"10.1109/ISBI.2008.4541250","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541250","url":null,"abstract":"We present an efficient algorithm for nonlocal image filtering with applications in electron cryomicroscopy. Our denoising algorithm is a rewriting of the recently proposed nonlocal mean filter. It builds on the separable property of neighborhood filtering to offer a fast parallel and vectorized implementation in contemporary shared memory computer architectures while reducing the theoretical computational complexity of the original filter. In practice, our approach is much faster than a serial, non-vectorized implementation and it scales linearly with image size. We demonstrate its efficiency in data sets from Caulobacter crescentus tomograms and a cryoimage containing viruses and provide visual evidences attesting the remarkable quality of the nonlocal means scheme in the context of cryoimaging. With such development we provide biologists with an attractive filtering tool to facilitate their scientific discoveries.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114141143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 280
Exact reconstruction formula for diffuse optical tomography using simultaneous sparse representation 同时稀疏表示的漫射光学层析成像精确重建公式
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541323
J. C. Ye, Su Yeon Lee, Y. Bresler
{"title":"Exact reconstruction formula for diffuse optical tomography using simultaneous sparse representation","authors":"J. C. Ye, Su Yeon Lee, Y. Bresler","doi":"10.1109/ISBI.2008.4541323","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541323","url":null,"abstract":"Diffuse optical tomography (DOT) is a sensitive and relatively low cost imaging modality. However, the inverse problem of reconstructing optical parameters from scattered light measurements is highly nonlinear due to the nonlinear coupling between the optical coefficients and the photon flux in the diffusion equation. Even though nonlinear iterative methods have been commonly used, such iterative processes are computationally expensive especially for the three dimensional imaging scenario with massive number of detector elements. The main contribution of this paper is a novel non-iterative and exact inversion algorithm when the optical inhomogeneities are sparsely distributed. We show that the problem can be converted into simultaneous sparse representation problem with multiple measurement vectors from compressed sensing framework. The exact reconstruction formula is obtained using simultaneous orthogonal matching pursuit (S-OMP) and a simple two step approach without ever calculating the diffusion equation. Simulation results also confirm our theory.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114804408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 23
Automated MAP-MRF EM labelling for volume determination in PET 用于PET体积测定的自动MAP-MRF EM标记
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4540917
Hugh Gribben, P. Miller, Hongbin Wang, K. Carson, A. Hounsell, A. Zatari
{"title":"Automated MAP-MRF EM labelling for volume determination in PET","authors":"Hugh Gribben, P. Miller, Hongbin Wang, K. Carson, A. Hounsell, A. Zatari","doi":"10.1109/ISBI.2008.4540917","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4540917","url":null,"abstract":"An automated, unsupervised Maximum a Posterior - Markov Random Field Expectation Maximisation (MAP- MRF EM) Labelling technique, based upon a Bayesian framework, for volume of interest (VOI) determination in Positron Emission Tomography (PET) imagery is proposed. The segmentation technique incorporates MAP-MRF modelling into a mixture modelling approach using the EM algorithm, to consider both the structural and statistical nature of the data. The performance of the algorithm has been assessed on a set of PET phantom data. Investigations revealed improvements over a simple statistical approach using the EM algorithm, and improvements over a MAP- MRF approach, using the output from the EM algorithm as an initial estimate. Improvement is also shown over a standard semi-automated thresholding method, and an automated Fuzzy Hidden Markov Chain (FHMC) approach; particularly for smaller object volume determination, as the FHMC method loses some spatial correlation. A deblurring pre-processing stage was also found to provide improved results.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"270 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114448260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
Support vector machine for data on manifolds: An application to image analysis 流形上数据的支持向量机:在图像分析中的应用
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541216
S. Sen, M. Foskey, J. Marron, M. Styner
{"title":"Support vector machine for data on manifolds: An application to image analysis","authors":"S. Sen, M. Foskey, J. Marron, M. Styner","doi":"10.1109/ISBI.2008.4541216","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541216","url":null,"abstract":"The Support Vector Machine (SVM) is a powerful tool for classification. We generalize SVM to work with data objects that are naturally understood to be lying on curved manifolds, and not in the usual d-dimensional Euclidean space. Such data arise from medial representations (m-reps) in medical images, Diffusion Tensor-MRI (DT-MRI), diffeomorphisms, etc. Considering such data objects to be embedded in higher dimensional Euclidean space results in invalid projections (on the separating direction) while Kernel Embedding does not provide a natural separating direction. We use geodesic distances, defined on the manifold to formulate our methodology. This approach addresses the important issue of analyzing the change that accompanies the difference between groups by implicitly defining the notions of separating surface and separating direction on the manifold. The methods are applied in shape analysis with target data being m-reps of 3 dimensional medical images.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"120 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114561312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 15
Atlas based segmentation of white matter fiber bundles in DTMRI using fractional anisotropy and principal eigen vectors 利用分数各向异性和主特征向量对DTMRI白质纤维束进行基于图谱的分割
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541137
E. Davoodi-bojd, H. Soltanian-Zadeh
{"title":"Atlas based segmentation of white matter fiber bundles in DTMRI using fractional anisotropy and principal eigen vectors","authors":"E. Davoodi-bojd, H. Soltanian-Zadeh","doi":"10.1109/ISBI.2008.4541137","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541137","url":null,"abstract":"In this work, we develop an atlas based method for automatic segmentation of white matter fiber bundles. To this end, we propose a new method for registration of diffusion tensor (DT) images using DTI information which is also used in the fiber tracking process, and we also propose a strategy for segmenting the fiber bundles using the new registration method and a probabilistic white matter atlas. We apply the registration method to 13 real DTI data sets and evaluate the results by comparing the level of alignment of all fibers. Then, we use the proposed strategy to segment 10 major fiber bundles in one of the subjects. One of the advantages of such a method is the robustness of the results thanks to using prior knowledge. The segmented results can be used for comparing and evaluating other fiber bundle segmentation methods.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"151 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114732724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Texture analysis of 3D bladder cancer CT images for improving radiotherapy planning 三维膀胱癌CT图像纹理分析对放疗规划的指导意义
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541080
W. Nailon, A. Redpath, D. McLaren
{"title":"Texture analysis of 3D bladder cancer CT images for improving radiotherapy planning","authors":"W. Nailon, A. Redpath, D. McLaren","doi":"10.1109/ISBI.2008.4541080","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541080","url":null,"abstract":"At present no single texture analysis approach can provide automatic classification to the accuracy required for radiotherapy applications. The method presented was developed to classify areas within the gross tumor volume (GTV), and other clinically relevant regions, on computerized tomography (CT) images. For eight bladder cancer patients, CT information was acquired at the radiotherapy planning stage and thereafter at regular intervals during treatment. Textural features (N=27) were calculated on regions extracted within the bladder, rectum and a region identified as clinically relevant. The sequential forward search (SFS) method was used to reduce the feature set (N=3). The results demonstrate the significant sensitivity of the reduced feature set for classification of any orthogonal CT image and the potential of the approach for radiotherapy applications.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115135158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Innovation modelling and wavelet analysis of fractal processes in bio-imaging 生物成像中分形过程的创新建模与小波分析
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro Pub Date : 2008-05-14 DOI: 10.1109/ISBI.2008.4541293
P. D. Tafti, D. Ville, M. Unser
{"title":"Innovation modelling and wavelet analysis of fractal processes in bio-imaging","authors":"P. D. Tafti, D. Ville, M. Unser","doi":"10.1109/ISBI.2008.4541293","DOIUrl":"https://doi.org/10.1109/ISBI.2008.4541293","url":null,"abstract":"Growth and form in biology are often associated with some level of fractality. Fractal characteristics have also been noted in a number of imaging modalities. These observations make fractal modelling relevant in the context of bio-imaging. In this paper, we introduce a simple and yet rigorous innovation model for multi-dimensional fractional Brownian motion (fBm) and provide the computational tools for the analysis of such processes in a multi-resolution framework. The key point is that these processes can be whitened by application of the appropriate fractional Lapla-cian operator which has a corresponding polyharmonic wavelet. We examine the case of MRI and mammography images through comparison with theoretical results, which underline the suitability of fractal models in the study of bio-textures.","PeriodicalId":184204,"journal":{"name":"2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"198 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115163576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
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