Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193263
Q. Xue, M. Leake
Automated tracking of fluorescent particles in living cells is vital for subcellular stoichoimetry analysis [1, 2]. Here, a new automatic tracking algorithm is described to track multiple particles, based on minimal path optimization. After linking feature points frame-by-frame, spatio-temporal data from time-lapse microscopy are combined together to construct a transformed 3D volume. The trajectories are then generated from the minimal energy path as defined by the solution of the time-dependent partial differential equation using a gray weighted distance transform dynamic programming method. Results from simulated and experimental data demonstrate that our novel automatic method gives sub-pixel accuracy even for very noisy images.
{"title":"A novel multiple particle tracking algorithm for noisy in vivo data by minimal path optimization within the spatio-temporal volume","authors":"Q. Xue, M. Leake","doi":"10.1109/ISBI.2009.5193263","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193263","url":null,"abstract":"Automated tracking of fluorescent particles in living cells is vital for subcellular stoichoimetry analysis [1, 2]. Here, a new automatic tracking algorithm is described to track multiple particles, based on minimal path optimization. After linking feature points frame-by-frame, spatio-temporal data from time-lapse microscopy are combined together to construct a transformed 3D volume. The trajectories are then generated from the minimal energy path as defined by the solution of the time-dependent partial differential equation using a gray weighted distance transform dynamic programming method. Results from simulated and experimental data demonstrate that our novel automatic method gives sub-pixel accuracy even for very noisy images.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115196831","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193253
Thierry Dorval, C. Moraes, Arnaud Ogier, Lucio Freitas Junior, Auguste Genovesio
In this paper we present a framework for correcting the spatial drift that can occur in 3D optical fluorescence microscopy images. These shifts happen during long time acquisition and can corrupt further analysis. This artifact has to be taken into account especially if the application requires an high spatial detection accuracy. Our correction method is based on the use of a microsphere located within the biological assay. As the bead does not provide the same correction quality for each Z-slice, we propose here, to include a level of confidence depending on the depth in a Kalman filtering process. This framework allows then to extend the motion compensation along the complete 3D images. This method is validated on real data and provides an easy and accurate way to correct 3D images corrupted along Z by a XY motion.
{"title":"3D spatial drift correction using Kalman filtering for fluorescence based imaging","authors":"Thierry Dorval, C. Moraes, Arnaud Ogier, Lucio Freitas Junior, Auguste Genovesio","doi":"10.1109/ISBI.2009.5193253","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193253","url":null,"abstract":"In this paper we present a framework for correcting the spatial drift that can occur in 3D optical fluorescence microscopy images. These shifts happen during long time acquisition and can corrupt further analysis. This artifact has to be taken into account especially if the application requires an high spatial detection accuracy. Our correction method is based on the use of a microsphere located within the biological assay. As the bead does not provide the same correction quality for each Z-slice, we propose here, to include a level of confidence depending on the depth in a Kalman filtering process. This framework allows then to extend the motion compensation along the complete 3D images. This method is validated on real data and provides an easy and accurate way to correct 3D images corrupted along Z by a XY motion.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"56 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114531009","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193309
P. Besson, C. Delmaire, V. Thuc, S. Lehéricy, F. Pasquier, X. Leclerc
The graph theory is increasingly used and provides powerful tools for studying complex biological networks problems. They were able to characterize the small-worldness of the brain connectivity network and were accurate enough to observe topological differences between healthy and diseased brain graphs. However, these methods relied on topological characteristics implying that differences could be observed between two groups only if corresponding graphs topologies were different.
{"title":"Graph wavelet applied to human brain connectivity","authors":"P. Besson, C. Delmaire, V. Thuc, S. Lehéricy, F. Pasquier, X. Leclerc","doi":"10.1109/ISBI.2009.5193309","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193309","url":null,"abstract":"The graph theory is increasingly used and provides powerful tools for studying complex biological networks problems. They were able to characterize the small-worldness of the brain connectivity network and were accurate enough to observe topological differences between healthy and diseased brain graphs. However, these methods relied on topological characteristics implying that differences could be observed between two groups only if corresponding graphs topologies were different.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"101 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124788158","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193204
Xiaofeng Niu, Yongyi Yang, M. Wernick
Recently we developed an image reconstruction procedure aimed to unify gated imaging and dynamic imaging in nuclear cardiac imaging. It can yield a single image sequence to show simultaneously both cardiac motion and tracer distribution change over the course of imaging. In this work, we further develop and investigate the feasibility of our gated dynamic imaging procedure for perfusion defect detection in cardiac SPECT imaging, where the challenge is even greater without using fast camera rotations. We study the saliency of temporal kinetic information derived from the reconstructed dynamic images for differentiating defects from normal cardiac perfusion. We also propose several metrics to characterize the salient kinetic information in gated dynamic images. The proposed development was demonstrated using simulated gated cardiac imaging with the NCAT phantom and Tc99m-Teboroxime as the imaging agent.
{"title":"Detectability of perfusion defect in gated dynamic cardiac SPECT images","authors":"Xiaofeng Niu, Yongyi Yang, M. Wernick","doi":"10.1109/ISBI.2009.5193204","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193204","url":null,"abstract":"Recently we developed an image reconstruction procedure aimed to unify gated imaging and dynamic imaging in nuclear cardiac imaging. It can yield a single image sequence to show simultaneously both cardiac motion and tracer distribution change over the course of imaging. In this work, we further develop and investigate the feasibility of our gated dynamic imaging procedure for perfusion defect detection in cardiac SPECT imaging, where the challenge is even greater without using fast camera rotations. We study the saliency of temporal kinetic information derived from the reconstructed dynamic images for differentiating defects from normal cardiac perfusion. We also propose several metrics to characterize the salient kinetic information in gated dynamic images. The proposed development was demonstrated using simulated gated cardiac imaging with the NCAT phantom and Tc99m-Teboroxime as the imaging agent.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"240 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124823004","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193102
K. Wilamowska, L. Shapiro, C. Heike
Given a set of labeled 3D meshes acquired from stereo imaging of heads, the goal of this research is to develop a successful methodology for discriminating between individuals with 22q11.2 deletion syndrome and the general population. Although many approaches for such discrimination exist in the medical and computer vision literature, the goal is to develop methods that focus on shape-based morphological differences of facial features.
{"title":"Classification of 3D face shape in 22q11.2 deletion syndrome","authors":"K. Wilamowska, L. Shapiro, C. Heike","doi":"10.1109/ISBI.2009.5193102","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193102","url":null,"abstract":"Given a set of labeled 3D meshes acquired from stereo imaging of heads, the goal of this research is to develop a successful methodology for discriminating between individuals with 22q11.2 deletion syndrome and the general population. Although many approaches for such discrimination exist in the medical and computer vision literature, the goal is to develop methods that focus on shape-based morphological differences of facial features.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125025668","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193184
J. Moltz, M. Schwier, H. Peitgen
In follow-up CT examinations of cancer patients, therapy success is evaluated by estimating the change in tumor size from diameter or volume comparison between corresponding lesions. We present an algorithm that automatizes the detection of matching lesions, given a baseline segmentation mask. It is generally applicable and does not need an organ mask or CAD findings, only a coarse registration of the datasets is required. In the first step, lesion candidates are identified in a local area based on gray value filtering and detection of circular structures using a Hough transform. On all candidate voxels, a template matching is performed minimizing normalized cross-correlation. The method was evaluated on clinical follow-up data comprising 94 lung nodules, 107 liver metastases, and 137 lymph nodes. The ratio of correctly detected lesions was 96%, 84% and 85%, respectively, at an average computation time of 0.9 s per lesion on a standard PC.
{"title":"A general framework for automatic detection of matching lesions in follow-up CT","authors":"J. Moltz, M. Schwier, H. Peitgen","doi":"10.1109/ISBI.2009.5193184","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193184","url":null,"abstract":"In follow-up CT examinations of cancer patients, therapy success is evaluated by estimating the change in tumor size from diameter or volume comparison between corresponding lesions. We present an algorithm that automatizes the detection of matching lesions, given a baseline segmentation mask. It is generally applicable and does not need an organ mask or CAD findings, only a coarse registration of the datasets is required. In the first step, lesion candidates are identified in a local area based on gray value filtering and detection of circular structures using a Hough transform. On all candidate voxels, a template matching is performed minimizing normalized cross-correlation. The method was evaluated on clinical follow-up data comprising 94 lung nodules, 107 liver metastases, and 137 lymph nodes. The ratio of correctly detected lesions was 96%, 84% and 85%, respectively, at an average computation time of 0.9 s per lesion on a standard PC.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121744699","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193280
Minsuok Kim, I. Larrabide, M. Villa-Uriol, Alejandro F Frangi
The aim of this study is to investigate the influence of stent axial orientation on saccular aneurysm hemodynamics. Two commercial stents, Neuroform stent (stent 1) and Zilver stent (stent 2) are modeled in this study. Both stents are virtually deployed with four different axial orientations to fit into the luminal surface of a patient-specific internal carotid artery (ICA) aneurysm model. Computational hemodynamic analyses are carried out in unstented and stented aneurysm models. The intra-aneurismal flows of stented aneurysm models show disturbed and complex flow patterns while the flow activities and the forces acting on the aneurysm wall are generally alleviated by stenting. The influence of the axial orientation of the stent on the aneurysm hemodynamics is more significant for stent 2 which has a larger strut size compared to stent 1. Interestingly, the flow activity in the aneurysm is rather increased when the intra-luminal scaffolding of stent is not sufficient.
{"title":"Hemodynamic alterations of a patient-specific intracranial aneurysm induced by virtual deployment of stents in various axial orientation","authors":"Minsuok Kim, I. Larrabide, M. Villa-Uriol, Alejandro F Frangi","doi":"10.1109/ISBI.2009.5193280","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193280","url":null,"abstract":"The aim of this study is to investigate the influence of stent axial orientation on saccular aneurysm hemodynamics. Two commercial stents, Neuroform stent (stent 1) and Zilver stent (stent 2) are modeled in this study. Both stents are virtually deployed with four different axial orientations to fit into the luminal surface of a patient-specific internal carotid artery (ICA) aneurysm model. Computational hemodynamic analyses are carried out in unstented and stented aneurysm models. The intra-aneurismal flows of stented aneurysm models show disturbed and complex flow patterns while the flow activities and the forces acting on the aneurysm wall are generally alleviated by stenting. The influence of the axial orientation of the stent on the aneurysm hemodynamics is more significant for stent 2 which has a larger strut size compared to stent 1. Interestingly, the flow activity in the aneurysm is rather increased when the intra-luminal scaffolding of stent is not sufficient.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122849814","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193287
Mohammad Matinfar, S. Iyer, E. Ford, J. Wong, P. Kazanzides
The purpose of the Small Animal Radiation Research Platform (SARRP) is to demonstrate computed tomography, conformal irradiation, and treatment planning capabilities for small animals. The SARRP is a portable system for precision irradiation with beam sizes down to approximately 0.5 mm and optimally planned radiation with on-board cone-beam CT (CBCT) guidance. This paper describes the utilization of the precision radiation beam on the SARRP for “dose painting” complex structures in the mouse brain. Pencil beam dose painting aims to target the tumor as accurately as possible and give it the highest dose of radiation while sparing normal tissue as much as possible.
{"title":"Image guided complex dose delivery for small animal radiotherapy","authors":"Mohammad Matinfar, S. Iyer, E. Ford, J. Wong, P. Kazanzides","doi":"10.1109/ISBI.2009.5193287","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193287","url":null,"abstract":"The purpose of the Small Animal Radiation Research Platform (SARRP) is to demonstrate computed tomography, conformal irradiation, and treatment planning capabilities for small animals. The SARRP is a portable system for precision irradiation with beam sizes down to approximately 0.5 mm and optimally planned radiation with on-board cone-beam CT (CBCT) guidance. This paper describes the utilization of the precision radiation beam on the SARRP for “dose painting” complex structures in the mouse brain. Pencil beam dose painting aims to target the tumor as accurately as possible and give it the highest dose of radiation while sparing normal tissue as much as possible.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122927758","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193211
A. Melbourne, D. Hawkes, D. Atkinson
The use of information theoretic cost functions in image registration is investigated, focusing on uncertainty coefficients. The theoretical derivation of the popular normalised mutual information cost function is presented and shown to be equivalent to a particular symmetrisation of relevant uncertainty coefficients. The use of uncertainty coefficients in image registration is investigated by recovering simulated deformations applied to MRI images showing that they may be used for image registration. A comparison of popular information theoretic cost functions is produced.
{"title":"Image registration using uncertainty coefficients","authors":"A. Melbourne, D. Hawkes, D. Atkinson","doi":"10.1109/ISBI.2009.5193211","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193211","url":null,"abstract":"The use of information theoretic cost functions in image registration is investigated, focusing on uncertainty coefficients. The theoretical derivation of the popular normalised mutual information cost function is presented and shown to be equivalent to a particular symmetrisation of relevant uncertainty coefficients. The use of uncertainty coefficients in image registration is investigated by recovering simulated deformations applied to MRI images showing that they may be used for image registration. A comparison of popular information theoretic cost functions is produced.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"91 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124211508","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}
Pub Date : 2009-06-28DOI: 10.1109/ISBI.2009.5193134
Zachary S Kelm, D. Blezek, B. Bartholmai, B. Erickson
Due to the rapid increase in use of CT imaging and the recently-heightened awareness of radiation-induced cancer, improving the diagnostic quality of low dose CT has become increasingly important. One potential method is to increase the signal-to-noise ratio of low dose images through denoising. Non-local means is a promising approach; however, it has many potentially adjustable parameters and application-specific areas of improvement. The filter uses a weighted average of similar regions to denoise each image pixel. Though the classic formulation uses only patches from the image being filtered, these patches can, in principle, be drawn from other images. In CT images, patches can be drawn from neighboring slices. We used that potential to increase the peak signal-to-noise ratio (PSNR) by over 4 dB when denoising low dose phantom CT images, and quantitatively demonstrated the filter's sensitivity to adjustment of each of its parameters.
{"title":"Optimizing non-local means for denoising low dose CT","authors":"Zachary S Kelm, D. Blezek, B. Bartholmai, B. Erickson","doi":"10.1109/ISBI.2009.5193134","DOIUrl":"https://doi.org/10.1109/ISBI.2009.5193134","url":null,"abstract":"Due to the rapid increase in use of CT imaging and the recently-heightened awareness of radiation-induced cancer, improving the diagnostic quality of low dose CT has become increasingly important. One potential method is to increase the signal-to-noise ratio of low dose images through denoising. Non-local means is a promising approach; however, it has many potentially adjustable parameters and application-specific areas of improvement. The filter uses a weighted average of similar regions to denoise each image pixel. Though the classic formulation uses only patches from the image being filtered, these patches can, in principle, be drawn from other images. In CT images, patches can be drawn from neighboring slices. We used that potential to increase the peak signal-to-noise ratio (PSNR) by over 4 dB when denoising low dose phantom CT images, and quantitatively demonstrated the filter's sensitivity to adjustment of each of its parameters.","PeriodicalId":272938,"journal":{"name":"2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","volume":"131 4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124248152","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}
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