Biomedical Image Processing / Medical Image Processing
Mehdi Delavari; Amir Hosein Foruzan; Ben Vi Chen
Volume 8, Issue 3 , September 2014, , Pages 213-227
Abstract
Statistical Shape Models are used to interpret shapes. They include mean and variance of corresponding points of training shapes. One of the most important challenges in building statistical shape models is to establish correct correspondences among landmarks in a training set. In this paper, the ...
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Statistical Shape Models are used to interpret shapes. They include mean and variance of corresponding points of training shapes. One of the most important challenges in building statistical shape models is to establish correct correspondences among landmarks in a training set. In this paper, the non-rigid CPD (Coherent Point Drift) method is used to find correct correspondences among points. This method uses both Deterministic Annealing and a non-rigid scheme to register two shapes simultaneously. Then, the statistical shape model is built using a rigid transformation. The proposed method is evaluated using Compactness, Generalization ability and Specificity measures. The built model is compared to models created using the ICP (Iterative Closest Point), TPS-RPM (Thin Plate Spline – Robust Point Matching) and MDL (Minimum Descreption Length) methods by these metrics. The results show that the proposed method performs like the MDL regarding Specificity measure (0.21±0.06). The Compactness and Generalization ability measures of the proposed method are very similar to those for the MDL method. The run-time of our proposed method is about 68 seconds which is faster than non-rigid TPS-RPM and MDL approaches (390 and 3600 seconds respectively). Our results are superior to the ICP and TPS-RPM algorithms.
Cardiovascular Biomechanics
Farzad Forouzandeh; Mahdie Haji-Bozorgi; Behrooz Meshkat; Nasser Fatouraee
Volume 8, Issue 3 , September 2014, , Pages 241-248
Abstract
Coronary Artery Diseases are one of the main reasonsof mortality. When these arteries occlude, usually a CoronaryArtery Bypass Graft (CABG) surgery is performed. Sine humanSaphenous Veins (SV) is used for CABG, they are of interest forresearchers. In this study human SV samples undergo inflationtest, ...
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Coronary Artery Diseases are one of the main reasonsof mortality. When these arteries occlude, usually a CoronaryArtery Bypass Graft (CABG) surgery is performed. Sine humanSaphenous Veins (SV) is used for CABG, they are of interest forresearchers. In this study human SV samples undergo inflationtest, using an inflation test device. Displacements of the samplesfor different pressures are analyzed, and average values are usedas input of a computational method. In the numerical simulationthe tissue is assumed as an elastic, isotropic, and homogenoussolid material, and its output is Young’s Modulus (E) ofthetissue. Results show that E of the SV increases linearly with thedistension pressure. Although simplifications were applied in thisstudy, it can be helpful for giving a basic insight aboutmechanical properties of human Saphenous Vein, which can befollowed by more realistic studies in the future.
Biomedical Image Processing / Medical Image Processing
Malihe Miri; Mohammad Taghi Sadeghi; Vahid Abootalebi
Volume 8, Issue 1 , March 2014, , Pages 45-56
Abstract
Successful outcomes of Sparse Representation-based Classifier (SRC) and Sparse Subspace Clustering (SSC) in many applications motivated us to combine these methods and propose a hierarchical classifier. The main idea behind the SRC and SSC algorithms is to represent a data using a sparse linear combination ...
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Successful outcomes of Sparse Representation-based Classifier (SRC) and Sparse Subspace Clustering (SSC) in many applications motivated us to combine these methods and propose a hierarchical classifier. The main idea behind the SRC and SSC algorithms is to represent a data using a sparse linear combination of elementary signals so that those elementary signals which are similar to the data contribute mainly in the representation. In this paper, the performance of a sparse representation based classifier is improved by pre-clustering of training samples using the SSC algorithm. A twostage SRC is then designed using the resulting clusters. A test data is classified by first determining the most similar cluster. The data label is subsequently found using the second stage classifier. The performance of the proposed method is evaluated considering cancer classification problem using the 14-Tumors microarray dataset. Due to low number of data samples per each class and high dimensionality of the data, this is a challenging problem. Curse of dimensionality, overfitting of the classifier to the training data and computational complexity are the possible related problems. Our experimental results show that the proposed method outperforms some other state of the art classifiers.
Cardiovascular Biomechanics
Mohammad Shafigh; Nasser Fatouraee; Amir Saeed Seddighi
Volume 5, Issue 4 , June 2011, , Pages 297-304
Abstract
Understanding of mechanical properties of healthy brain arteries is a key element in the development of clinical diagnosis and prevention.For this reason we make biaxial measurements to have appropriate parameters for the underlying material models. To acquire these properties, eight samples were obtained ...
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Understanding of mechanical properties of healthy brain arteries is a key element in the development of clinical diagnosis and prevention.For this reason we make biaxial measurements to have appropriate parameters for the underlying material models. To acquire these properties, eight samples were obtained from middle cerebral arteries of human cadavers, whose death were not due to injuries or diseases of cerebral vessels, and tested within twelve hours after resection. The changes of force and deformation until the vessel rupture were recorded. Thereafter, the stress-strain curves were plotted and fitted with a hyperelastic five-parameter Fung model parameters, according to the best fit, were determined. It was found that the arteries were remarkably stiffer in circumferential than in axial direction. It was also found that the use of multi-parameter hyperelastic constitutive models is applicable for mathematical description of behavior of cerebral vessel tissue. The reported material properties can be a proper reference for numerical simulation of cerebral arteries of healthy or diseased intracranial arteries.
Biomedical Image Processing / Medical Image Processing
Mohammad Hasan Moradi; Mohammad Sajad Manuchehri; Reza IraniRad
Volume 5, Issue 4 , June 2011, , Pages 313-331
Abstract
During the centuries, palpation has always been a crucial procedure in diagnosing the diseases. At first, these procedures were invasive, but nowadays numerous attempts by the name of elastographyhave been madeforreaching to noninvasive methods. Elastographys basic datais tissues relative displacement ...
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During the centuries, palpation has always been a crucial procedure in diagnosing the diseases. At first, these procedures were invasive, but nowadays numerous attempts by the name of elastographyhave been madeforreaching to noninvasive methods. Elastographys basic datais tissues relative displacement which is tracked by ultrasound waves. First in these systems in order to attain the displacements gradient, an image of tissue is taken and then it is compared to image of that same tissue after applying a small mechanical impulse into it. Mechanical strain is calculated by estimating the displacements gradient and demonstrated as an image with gray levels named elastogram (strains image) .Based on how the mechanical vibration is given, ultrasound-elastography will separate into four categories as follows: static, dynamic, shear-wave and passive elastography. In static-elastography, the force is applied manually by the clinician and therefore it depends on operators skill and cannot be considerable. In dynamic type the movement of tissue is constantly provided by an external vibrator, so in order to prevent the interference of impulses we must use a rapid imaging system that eventually will cost extra expense and unavailability. Shear-wave elastography which currently is the most common method used in elastography systems,has an external vibratorLike dynamic method, but due to momentary impulses, it skips the problem of impulse interference. In passive method, physiologic movements of body will be given to tissue as itsvibration. This technique is hypothetical yet.
Biomedical Image Processing / Medical Image Processing
Fateme Nazem; Alireza Ahmadian; Mohammad Javad Abolhasani; Nasim Dadashi; Masoume Gity; Mohammad Bagher Shiran
Volume 5, Issue 4 , June 2011, , Pages 351-358
Abstract
Abstract: Image guided liver surgery based on intra-operative ultrasound images has received much attention in recent years. Using an efficient point-based registration method to improve both the accuracy and computational time for registration of pre-deformation CT liver images to post-deformation Ultrasound ...
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Abstract: Image guided liver surgery based on intra-operative ultrasound images has received much attention in recent years. Using an efficient point-based registration method to improve both the accuracy and computational time for registration of pre-deformation CT liver images to post-deformation Ultrasound images is of great concern during surgical procedure. Although, Iterative Closest Point (ICP) algorithm is widely used in surface-based registration, its performance is strongly dependent on existence of noise and initial alignment. The registration technique based on the Unscented Kalman Filter (UKF) proposed recently can be a solution to overcome to noise and outliers on an incremental registration basis but it suffers from computational complexity. To overcome the limitations of ICP and UKF algorithms we proposed an incremental two-stage registration algorithm based on the combination of ICP and UKF algorithm to update the registration process based on arrival of intra-operative images. The two-stage algorithm is examined on phantom data sets. The results of phantom study confirm that the two-stage algorithm outperforms the accuracy of ICP and UKF by 23% and 13%, respectively and reduces the running time of UKF by 60%.
Biomedical Image Processing / Medical Image Processing
Effat Yahaghi; Yashar Nohi; Amir Movafeghi; Hamid Soltanian Zadeh
Volume 4, Issue 1 , June 2010, , Pages 1-11
Abstract
Magnetic resonance imaging (MRI) is a non-ionizing method for identification and evaluation of soft tissue lesions. Perfusion MRI evaluates soft tissues by measuring changes in magnetization of water molecules due to a contrast agent. To this end, concentration curves in the plasma and tissue are estimated ...
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Magnetic resonance imaging (MRI) is a non-ionizing method for identification and evaluation of soft tissue lesions. Perfusion MRI evaluates soft tissues by measuring changes in magnetization of water molecules due to a contrast agent. To this end, concentration curves in the plasma and tissue are estimated by MRI and effective longitudinal relaxation time (T1eff) of the tissue was calculated. To interpret the results, the effects of water exchange on the effective longitudinal relaxation time should be studied. This work presents such a study in which the equations of two- and three-compartmental models of rat brain tissue are solved using Hion and Runge-Kutta numerical methods for different input functions and simulated by Monte Carlo method. Since the exchange of water and contrast agent among different tissue compartments is a diffusion phenomenon, Monte Carlo method is applicable. Results of the numerical methods were compared with those of Monte Carlo simulation. The results of the two methods were almost identical with a maximum relative difference of less than 1%. In this work, concentration of contrast agent in plasma is estimated from MRI of a rat brain tissue. This data is used in the Monte Carlo method to obtain T1eff and exchange rate constants. An advantage of our method is that T1eff is obtained from real data and not from the curve fitting method as commonly used. We derive concentration of contrast agent as a function of time in extravascular space for different constants (K). Then, the curves of simulated and real data were compared to obtain the exchange rate constant of each compartment. The results showed that K of an abnormal tissue was larger than that of the normal tissues. As such, this parameter may be used for diagnosis and treatment of the soft tissue diseases.
Biomedical Image Processing / Medical Image Processing
Mohammad Hosein Miranbeigi; Leila Mohammadi; Sahar Moghimi; Giti Torkaman
Volume 3, Issue 1 , June 2009, , Pages 15-24
Abstract
Collagen content and its configuration are considered to be among important criteria of healing in tissues. Therefore, developing a method to estimate these factors can benefit physicians in terms of valuable information. In this paper, we examine variation of collagens in tissue mimicking phantoms as ...
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Collagen content and its configuration are considered to be among important criteria of healing in tissues. Therefore, developing a method to estimate these factors can benefit physicians in terms of valuable information. In this paper, we examine variation of collagens in tissue mimicking phantoms as well as in vivo tissue taking advantage of applying image processing techniques on ultrasound images of samples. In phantoms, as the base tissue we have used agar-water matrix material and graphite to simulate collagen, respectively. We also have used different concentrations of graphite to simulate different contents of collagen according to attenuation coefficient of ultrasound waves in soft tissue and its correlation with weight ratio of graphite. Experimental and simulation results show that increase in concentration of graphite in phantoms results in higher energy and more contrast level in B-Mode images (r=0.99, p
Biomedical Image Processing / Medical Image Processing
Hamed Rakhshan; Hamid Behnam
Volume 3, Issue 1 , June 2009, , Pages 25-31
Abstract
Vibroacoustography is a relatively new elasticity imaging method that uses dynamic (oscillatory) radiation force of ultrasound to vibrate the tissue at low frequency (Kilo Hertz). The resulting acoustic emission is recorded with sensitive hydrophone to produce images that are related to the mechanical ...
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Vibroacoustography is a relatively new elasticity imaging method that uses dynamic (oscillatory) radiation force of ultrasound to vibrate the tissue at low frequency (Kilo Hertz). The resulting acoustic emission is recorded with sensitive hydrophone to produce images that are related to the mechanical properties of the tissue. This force is produced by two continuous overlapping ultrasound beams that have a slightly different frequency. Vibroacoustography has been applied to image breast and arteries microcalcification. The lateral resolution of this imaging method is about 0.7mm and its axial resolution is about 12 mm. In this paper two major methods of producing dynamic radiation force, Confocal and X-focal (consists of two concave transducers whose axes cross at their foci at an angle q), are analyzed. A new method for improving axial resolution using short duration pulses is introduced. Simulation results show that we have about 50% improvement in axial resolution using short duration pulses.
Biomedical Image Processing / Medical Image Processing
Mohammad Aboonajmi; Asadollah Akram; Seyed Kamaloddin Setarehdan; Ali Rajabipour
Volume 3, Issue 1 , June 2009, , Pages 55-65
Abstract
Ultrasound is a rapidly growing tool in the field of research, which shows an increasing use in the food industry for both analysis and modification of food products. Quality assessment of agricultural material has an important role in modern agriculture. This study demonstrates the possibility of non-destructive ...
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Ultrasound is a rapidly growing tool in the field of research, which shows an increasing use in the food industry for both analysis and modification of food products. Quality assessment of agricultural material has an important role in modern agriculture. This study demonstrates the possibility of non-destructive prediction of the main quality indices of the commercial eggs by processing a short ultrasound burst passing through the egg material and calculating the ultrasound phase velocity. For this purpose a set of three hundred samples of commercial eggs (Boris Brown, 33 weeks age) from the first day of egg lying were purchased from a farm and classified in two groups. The first group was kept in the room temperature (22-25°C) while the second group was kept within the refrigerator (4-5°C). 25 eggs were picked every week from each groups (room and refrigerator) were first subjected to the nondestructive ultrasound test at room temperature. Each day, the ultrasound signal is recorded from the eggs first. Then, immediately after that, the air cell, the thick albumen heights, the Haugh unit and the yolk index of the eggs were also determined destructively for comparison purposes. Significant differences at 5% level between the means of the destructive analysis at different days of storage of the eggs were found using ANOVA. Both the Haugh unit and yolk index decreased by time over 5 weeks in storage at room and refrigerator while the air cell height increased. The lower is the Haugh unit for the eggs in the refrigerator the lower is the phase velocity (1573 m/s at first day compared to 1540 m/s after 3 weeks). Similar changes of the phase velocity are found for the eggs in the room temperature (1571 m/s at first day compared to 1514 m/s after 3 weeks).
Cardiovascular Biomechanics
Mansour Alizadeh; Iman Mohebbi Nejad
Volume 2, Issue 4 , June 2008, , Pages 317-324
Abstract
Mechanical characteristic of arteries is very important for stent producing and cardiovascular implants. In this study mechanical behavior of a piece of left anterior descending coronary artery with specified dimension and separated layers which was prepared by holtzapfel and tested under tensile test ...
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Mechanical characteristic of arteries is very important for stent producing and cardiovascular implants. In this study mechanical behavior of a piece of left anterior descending coronary artery with specified dimension and separated layers which was prepared by holtzapfel and tested under tensile test bas been considered. Ogden hyperelastic model has been implemented for the experimental data and related parameters were obtained. These parameters have been optimized. The obtained results showed that by using the same experimental data the Ogden model can be fitted well with holtzapfel model and the errors fall within acceptable range.
Cardiovascular Biomechanics
Mehdi Maerefat; Asghar Khoushkar Shalmani; Manije Mokhtari Dizaji
Volume 1, Issue 2 , June 2007, , Pages 95-104
Abstract
Modeling of blood flow and arterial wall in large arteries such as carotid artery, using ultrasonic measurements, allows non-invasive evaluation of clinically interesting homodynamic variables. In this study, a nonlinear mathematical model for the pulsatile arterial flow is proposed using the approximation ...
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Modeling of blood flow and arterial wall in large arteries such as carotid artery, using ultrasonic measurements, allows non-invasive evaluation of clinically interesting homodynamic variables. In this study, a nonlinear mathematical model for the pulsatile arterial flow is proposed using the approximation of “local flow” theory. The blood velocity profile, the pressure gradient and the elastic modulus can be calculated using the model by measuring instantaneous radius and center-line blood velocity. An original mathematical model of pressure gradient in a tapered and elastic tube, using center-line blood velocity, is presented. A Newtonian incompressible Navier-Stokes solver coupled with elastic or visco-elastic arterial wall model is developed to solve the equations of model. The results of modeling and simulation indicate that the approach can estimate the elastic modulus of arterial wall from ultrasonic data. There is a good agreement between the computed arterial wall elasticity and the measured one. The method presented is relatively simple to implement clinically and can be taken as a new diagnostic tool for detecting local vascular change.
Tissue Engineering
Farhad Farmanzad; Siamak Najarian; Mohammad Reza Eslami; Amir Saeed Seddighi
Volume 1, Issue 4 , June 2007, , Pages 281-288
Abstract
Two different types of computer modeling, i.e., the elastic and hyperelastic plane strain models were employed and compared with each other. Using finite element analysis, we determined a suitable model for describing the biomechanical behavior of the brain, especially the deformation and displacement ...
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Two different types of computer modeling, i.e., the elastic and hyperelastic plane strain models were employed and compared with each other. Using finite element analysis, we determined a suitable model for describing the biomechanical behavior of the brain, especially the deformation and displacement of the brain ventricles. The CT-Scan of an epidural hematoma patient was modeled using both approaches. Then, by varying the mechanical parameters of the tissue (i.e., C10, C01, E, and v) and the internal ventricular pressure, the displacement rate of the corresponding points in the ventricles was simulated. Finally, the results of the simulation were compared with those of the actual ventricles, and then, the data set with the least amount of error was identified. For various types of loadings and with different pressure gradients, the results of the simulation show that if the effect of an increase in the internal pressure of the ventricles is neglected, it will lead to unrealistic results. Particularly, in unidirectional strain loading with a pressure gradient of zero (AP= 0), the walls of the ventricle adjacent to the hematoma will collapse completely. The best results were obtained for the elastic model where ΔP = 9.4 mmHg (1.25 kPa) and for the hyperelastic model where ΔP = 7.5 mmHg (1.00 kPa). These findings are consistent with the clinical conditions of the patient. In the plane strain biomechanical modeling, for unidirectional strain loading (conditions which are similar to the application of navigation systems in surgeries), neglecting the geometry and the variation of the internal pressure of the ventricles will not lead to acceptable results. Taking into account the abovementioned parameters in describing the mechanical behavior of the brain (for epidural hematoma lesions), the elastic model (88.7% average relative accuracy) brings about better results compared with those of the hyperclastic model (86.9% average relative accuracy).
Biomedical Image Processing / Medical Image Processing
Ladan Amini; Hamid Soltanian Zadeh; Caro Lucas; Masoume Giti
Volume -2, Issue 1 , July 2005, , Pages 17-34
Abstract
Based on a discrete dynamic contour model, a method for segmentation of brain structures like thalamus and red nucleus from magnetic resonance images (MRI) is developed. A new method for solving common problems in extracting the discontinuous boundary of a structure from a low contrast image is presented. ...
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Based on a discrete dynamic contour model, a method for segmentation of brain structures like thalamus and red nucleus from magnetic resonance images (MRI) is developed. A new method for solving common problems in extracting the discontinuous boundary of a structure from a low contrast image is presented. External and internal forces deform the dynamic contour model. Internal forces are obtained from local geometry of the contour, which consist of vertices and edges, connecting adjacent vertices. The image data and desired image features such as image energy are utilized to obtain external forces. The problem of low contrast image data and unclear edges in the image energy is overcome by the proposed algorithm that uses several methods like thresholding, unsupervised clustering methods such as fuzzy C-means (FCM), edge-finding filters like Prewitt, and morphological operations. We also present a method for generating an initial contour for the model from the image data automatically. Evaluation and validation of the methods are conducted by comparing radiologist and automatic segmentation results. The average of the similarity between segmentation results is 0.8 for the left and right thalami indicating excellent performance of the new method. Additional noise and intensity inhomogeneity changed the evaluation results slightly illustrating the robustness of the proposed method to the image noise and intensity inhomogeneity.
Tissue Engineering
Giti Torkamaan; Ali Akbar Sharafi; Ali Fallah; Hamid Reza Katouzian; Mahmoud Mofid
Volume -1, Issue 1 , June 2004, , Pages 93-100
Abstract
Pressure ulcers are areas of tissue necrosis that tend to develop when tissue is compressed between a bony prominence and an external surface. Normal structure and physiological function of tissue viability are recognized but mechanism of tissue breakdown is unknown. In this study, an attempt has been ...
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Pressure ulcers are areas of tissue necrosis that tend to develop when tissue is compressed between a bony prominence and an external surface. Normal structure and physiological function of tissue viability are recognized but mechanism of tissue breakdown is unknown. In this study, an attempt has been made to recognize the tissue mechanical changes after pressure application using 61 male albino guinea pigs, 4-6 months old, weighing 300-450 g. A computer controlled indentor system was developed to induce pressure sore. This system is capable of monitoring and adjusting the applied pressure, friction and shearing force throughout the experiment. The applied force remained within ±10g of desired target force. The applied pressures were at 291 and 387 mmHg for 1,3 or 5 hours over the trochanter region of animal hind limb. The tissue was removed and blood was taken immediately, 2 and 7 days after pressure release. Uniaxial tensile test was performed using deformation rate of 20 mm/min. In this test, the contralateral site on the experimental animal served as intra-animal control. Full- thickness biopsy was taken and stained with H & E, trichrome and orcein for histological examination. Results of tensile tests showed that the maximum tensile strength (Fmax), stress and the area under load-deformation curve (work) have decreased significantly 7 days after pressure application (P<0.05). Histological study immediately and 2 days after force release, showed an increase in cellularity and inflammatory cells infiltration. Muscle necrosis and reduction of the skin fibers density were observed 7 days after load release. Serum CPK (2 days after) was increased. The amount of lactic acid as well as phosphorus immediately and 2 days after pressure also increased (P<0.05). Finally it was distinguished that pressure changed the biomechanical properties of skin and muscle. Decrease of tissue resistance was consistent with the histological findings as well as elevation of muscle specific enzymes in blood. It was also observed that pressure resulted in the tissue ischemia and breakdown.
