{"title":"Sparse magnetic resonance imaging using tagging RF pulses","authors":"V. Singh, A. Tewfik","doi":"10.1109/ISBI.2013.6556472","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556472","url":null,"abstract":"Few fast magnetic resonance (MR) imaging techniques have proposed modifications to the MR signal encoding formulation in order to improve the performance guarantees of image recovery using compressed sensing. A limitation of the previously proposed encoding formulations is their difficult realization on the physical hardware. The deviation of realizable formulation from the theoretical model leads to operating characteristics which are clinically infeasible. In this paper, a novel MR signal encoding formulation using tagging radio-frequency pulses is proposed. The proposed formulation uses tagging pulses to uniquely modulate the longitudinal magnetization in the field-of-view for each MR excitation. The modulation of magnetization leads to mixing of information in the spatial Fourier space which improves the incoherence between the sensing and the sparsifying basis. The physical realization of the proposed formulation is promising due to the use of clinically active RF pulses. The preliminary results for image recovery experiments using the proposed formulation on an in-vivo dataset are comparably close and at times better than the results of the difficult-to-realize state-of-the-art formulation.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"104 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131551600","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}
Yuanjie Zheng, B. Vanderbeek, Ebenezer Daniel, D. Stambolian, M. Maguire, D. Brainard, J. Gee
{"title":"An automated drusen detection system for classifying age-related macular degeneration with color fundus photographs","authors":"Yuanjie Zheng, B. Vanderbeek, Ebenezer Daniel, D. Stambolian, M. Maguire, D. Brainard, J. Gee","doi":"10.1109/ISBI.2013.6556807","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556807","url":null,"abstract":"We present a system of automated drusen detection from color fundus photographs with our ultimate goal being to automatically assess the risk for the development of Age-related Macular Degeneration (AMD). Our system incorporates learning based drusen detection and includes fundus image analysis techniques for image denoising, illumination correction and color transfer. In contrast to previous work, we incorporate both optimal color descriptors and robust multiscale local image descriptors in our drusen detection process. Our system was evaluated with color fundus photographs from two AMD clinical studies [1, 2]. By comparing our results to those obtained via manual drusen segmentation, we show that our system outperforms two state-of-the-art techniques.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"103 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131653951","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}
N. Duggan, Hayden Schaeffer, C. L. Guyader, E. Jones, M. Glavin, L. Vese
{"title":"Boundary detection in echocardiography using a Split Bregman edge detector and a topology preserving level set approach","authors":"N. Duggan, Hayden Schaeffer, C. L. Guyader, E. Jones, M. Glavin, L. Vese","doi":"10.1109/ISBI.2013.6556415","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556415","url":null,"abstract":"In the current paper a novel approach for echocardiographic segmentation is proposed based on a combination of the Geometric Active Contour Split Bregman (GSB) method with a topology preserving level set method. The proposed method was tested against manual delineations on 20 frames across 2 datasets and achieved an average Hausdorff distance of 4.01 ± 1.06 mm and Mean Absolute distance of 1.62 ± 0.3 mm, which represented an enhanced performance when compared with intensity gradient and region based methods.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130796648","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}
{"title":"Efficient extraction of 3D bone cells descriptors from micro-CT images","authors":"Pei Dong, S. Haupert, P. Gouttenoire, F. Peyrin","doi":"10.1109/ISBI.2013.6556817","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556817","url":null,"abstract":"While cell analysis is conventionally performed on 2D slices, novel micro and nano-CT system opens new perspectives in this area. Here, we show that synchrotron radiation (SR) micro-CT is well suited to analyze the 3D distribution of osteocyte lacunae in bone tissue. Osteocytes are receiving increasing interest in the comprehension of bone diseases. Here, we propose a fast automated method to extract 3D quantitative morphological descriptors on these cells. To this aim, after a fast connected component analysis applied on the segmented image, a moment-based approach and intrinsic volumes are calculated to derive 3D descriptors on each object. The segmentation is refined by eliminating artifacts according to some descriptors. Validation of segmentation and experimental results on twelve bone samples are presented. This method is efficient and is believed to open new perspectives to quantify physiopathologic changes at the cell level.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"93 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131015238","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}
S. Vijayan, S. Klein, E. F. Hofstad, F. Lindseth, B. Ystgaard, T. Langø
{"title":"Validation of a non-rigid registration method for motion compensation in 4D ultrasound of the liver","authors":"S. Vijayan, S. Klein, E. F. Hofstad, F. Lindseth, B. Ystgaard, T. Langø","doi":"10.1109/ISBI.2013.6556594","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556594","url":null,"abstract":"Future therapy using focused ultrasound (FUS) to treat tumors in abdominal organs, such as the liver, must incorporate motion tracking of these organs due to breathing and drift caused by gravity and intestines (peristalsis). Motion tracking of the target (e.g. tumor) is needed to ensure accurately located sonications. We have performed a quantitative validation of a methodology for motion tracking of the liver with 4D (3D+time) ultrasound. The offline analysis was done using a recently published non-rigid registration algorithm that was specifically designed for motion estimation from dynamic imaging data. The method registers the entire 4D sequence in a group-wise optimization fashion, thus avoiding a bias towards a specifically chosen reference time point. Both spatial and temporal smoothness of the transformations are enforced by using a 4D free-form B-spline deformation model. For our evaluation, three healthy volunteers were scanned over several breath cycles from three different positions and angles on the abdomen (totally nine 4D scans). A skilled physician performed the scanning and manually annotated well-defined anatomic landmarks for assessment of the automatic algorithm. Four engineers each annotated these points in all time frames, the mean of which was taken as a gold standard. The error of the automatic motion estimation method was compared with inter-observer variability. The registration method estimated liver motion better than the observers and had an error (75% percentile over all datasets) of 1 mm. We conclude that the methodology was able to accurately track the motion of the liver in the 4D ultrasound data.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131242862","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}
M. Gangeh, A. Sadeghi-Naini, M. Kamel, G. Czarnota
{"title":"Assessment of cancer therapy effects using texton-based characterization of quantitative ultrasound parametric images","authors":"M. Gangeh, A. Sadeghi-Naini, M. Kamel, G. Czarnota","doi":"10.1109/ISBI.2013.6556788","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556788","url":null,"abstract":"This paper proposes the application of texton-based approach for textural characterization of quantitative ultrasound parametric maps, in order to assess noninvasively the progressive effects of cancer treatment in preclinical animal models. Xenograft tumour-bearing animals were treated with chemotherapy. Ultrasound data were acquired from tumours prior to, and at different times after exposure, and quantitative ultrasound spectral parametric maps were generated. Texton-based features were extracted from 0-MHz Intercept parametric maps and applied to differentiate between preand posttreatment states. The classification error was then translated into a quantitative measure of the treatment effects. Obtained results demonstrated a very good agreement with histological observations, and suggested that the proposed approach can be used noninvasively to evaluate the progressive effects of cancer treatment.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133335990","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}
Mei Hui Tan, Ying Sun, S. Ong, Jiang Liu, M. Baskaran, T. Aung, T. Wong
{"title":"Automatic notch detection in retinal images","authors":"Mei Hui Tan, Ying Sun, S. Ong, Jiang Liu, M. Baskaran, T. Aung, T. Wong","doi":"10.1109/ISBI.2013.6556805","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556805","url":null,"abstract":"This paper presents a new method to detect notching in the optic cup using retinal images. Optic cup notching is an important feature in differentiating normal from glaucomatous eyes. The proposed notching detection method comprises four steps: disc and vessel segmentation, vessel bend detection at key regions, feature points selection and automatic classification. The key step of vessel bend detection involves computing the local curvature of the vessels, then ranking them based on the angle of vessel bend and the local gradient in the neighborhood region. The algorithm was tested on a set of color fundus images and achieved a notching detection rate of 88.9%, a false alarm rate of 4.0%, and an overall accuracy of 95.4%.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132669872","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}
{"title":"3D Haar-like elliptical features for object classification in microscopy","authors":"F. Amat, Philipp J. Keller","doi":"10.1109/ISBI.2013.6556694","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556694","url":null,"abstract":"Object detection and classification are key tasks in computer vision that can facilitate high-throughput image analysis of microscopy data. We present a set of local image descriptors for three-dimensional (3D) microscopy datasets inspired by the well-known Haar wavelet framework. We add orientation, illumination and scale information by assuming that the neighborhood surrounding points of interests in the image can be described with ellipsoids, and we increase discriminative power by incorporating edge and shape information into the features. The calculation of the local image descriptors is implemented in a Graphics Processing Unit (GPU) in order to reduce computation time to 1 millisecond per object of interest. We present results for cell division detection in 3D time-lapse fluorescence microscopy with 97.6% accuracy.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134480147","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}
X. Descombes, G. Malandain, C. Fonta, László Négyessy, R. Mokso
{"title":"Automatic dendrite spines detection from x-ray tomography volumes","authors":"X. Descombes, G. Malandain, C. Fonta, László Négyessy, R. Mokso","doi":"10.1109/ISBI.2013.6556505","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556505","url":null,"abstract":"We consider the problem of dendritic spine detection from X-ray micro-tomographic volumes that allow huge volume of tissue visualization. To compensate for the noise in data that induces false positives in the spine detection process, we first segment the dendrites. This segmentation is obtained by computing the medial axis and approximating the results by segments obtained with a 3D Hough transform. Dendrites are then reconstructed and a spine mask is obtained using the typical diameter of dendrites and distance between spine and dendrites. A point process is then optimized on this mask, thus providing the spine detection.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131689129","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}
{"title":"Functional connectivity eigennetworks reveal different brain dynamics in multiple sclerosis patients","authors":"Nora Leonardi, J. Richiardi, D. Ville","doi":"10.1109/ISBI.2013.6556528","DOIUrl":"https://doi.org/10.1109/ISBI.2013.6556528","url":null,"abstract":"Resting state functional connectivity is defined as correlations in brain activity measured by functional magnetic resonance imaging without any stimulation paradigm. Such connectivity is dynamic, even over the course of minutes, and the development of tools for its analysis is an important challenge in neuroscience. We propose a novel data-driven technique to extract connectivity patterns from dynamic whole-brain networks of multiple subjects. Our technique is based on singular value decomposition and decomposes a collection of networks into linearly independent “eigennetworks” and associated time courses. To deal with the temporal redundancy of networks, we propose a novel subsampling method based on the standard deviation of the connectivity strength. We apply the proposed technique to dynamic resting-state networks of healthy subjects and multiple sclerosis patients, and show its potential to detect aberrant connectivity patterns in patients.","PeriodicalId":178011,"journal":{"name":"2013 IEEE 10th International Symposium on Biomedical Imaging","volume":"115 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124588396","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}