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    A hybrid segmentation framework for computer-assisted dental procedures

    , Article IEICE Transactions on Information and Systems ; Volume E92-D, Issue 10 , 2009 , Pages 2137-2151 ; 09168532 (ISSN) Hosntalab, M ; Aghaeizadeh Zoroofi, R ; Abbaspour Tehrani Fard, A ; Shirani, G ; Asharif, M. R ; Sharif University of Technology
    Teeth segmentation in computed tomography (CT) images is a major and challenging task for various computer assisted procedures. In this paper, we introduced a hybrid method for quantification of teeth in CT volumetric dataset inspired by our previous experiences and anatomical knowledge of teeth and jaws. In this regard, we propose a novel segmentation technique using an adaptive thresholding, morphological operations, panoramic re-sampling and variational level set algorithm. The proposed method consists of several steps as follows: first, we determine the operation region in CT slices. Second, the bony tissues are separated from other tissues by utilizing an adaptive thresholding technique... 

    A surface registration technique for estimation of 3-D kinematics of joints

    , Article Studies in Health Technology and Informatics, 19 January 2009 through 22 January 2009 ; Volume 142 , 2009 , Pages 204-206 ; 09269630 (ISSN) ; 9781586039646 (ISBN) Mostafavi, K ; Jafari, A ; Farahmand, F ; Sharif University of Technology
    This study proposes a new technique for registration of complicated freeform surfaces. The relationship between the initial and transferred location/orientation of a points cloud is formulated and then generalized within the framework of the influence surface modeling approach using least squares method. Results of case studies for estimation of the transformation matrix of articular surface of the knee joint in two scenes of MR images indicated high accuracies of ±1 mm and ±1 degree  

    Refractive index correction in optical coherence tomography images of multilayer tissues

    , Article Journal of Biomedical Optics ; Volume 23, Issue 7 , 2018 ; 10833668 (ISSN) Turani, Z ; Fatemizadeh, E ; Xu, Q ; Daveluy, S ; Mehregan, D ; Nasiriavanaki, M ; Sharif University of Technology
    SPIE  2018
    We propose an algorithm to compensate for the refractive index error in the optical coherence tomography (OCT) images of multilayer tissues, such as skin. The performance of the proposed method has been evaluated on one-and two-layer solid phantoms, as well as the skin of rat paw. © 2018 Society of Photo-Optical Instrumentation Engineers (SPIE)  

    A three-dimensional statistical volume element for histology informed micromechanical modeling of brain white matter

    , Article Annals of Biomedical Engineering ; Volume 48, Issue 4 , 2020 , Pages 1337-1353 Hoursan, H ; Farahmand, F ; Ahmadian, M. T ; Sharif University of Technology
    Springer  2020
    This study presents a novel statistical volume element (SVE) for micromechanical modeling of the white matter structures, with histology-informed randomized distribution of axonal tracts within the extracellular matrix. The model was constructed based on the probability distribution functions obtained from the results of diffusion tensor imaging as well as the histological observations of scanning electron micrograph, at two structures of white matter susceptible to traumatic brain injury, i.e. corpus callosum and corona radiata. A simplistic representative volume element (RVE) with symmetrical arrangement of fully alligned axonal fibers was also created as a reference for comparison. A... 

    An Approach for Cancer Diagnosis Based on Graph Modeling

    , M.Sc. Thesis Sharif University of Technology Taghizadeh, Ghasem (Author) ; Habibi, Jafar (Supervisor)
    Digital image analysis of histological datasets is a currently expanding field of research. Histological images are inherently complex in nature and contain a wide variety of visual information. Graph-based methods have recently gained immense popularity, as these methods can effectively describe tissue architecture and provide adequate numeric information for subsequent computer-based analysis. Graphs have the ability to represent spatial arrangements and neighborhood relationships of different tissue components, which are essential characteristics observed visually by pathologists during the investigation of specimens. In this thesis, we proposed an automatic approach for classification... 

    Domain Generalization in Deep Learning Models for Histopathology

    , M.Sc. Thesis Sharif University of Technology Sadeghi, Reyhaneh (Author) ; Rohban, Mohammad Hossein (Supervisor)
    Domain shift is an inevitable issue when histopathological images are analyzed in a standard laboratory. This is due to the variations in tissue handling, manual procedures for sample preparation, and differences in scanners. This can result in reduced performance of machine learning algorithms trained on images from one laboratory when applied to another. In this framework, the goal of utilizing domain generalization techniques in machine learning is to develop models that perform well in different domains. This research examines various methods of dealing with the domain shift challenges within the context of detecting mitotic cells, and proposes algorithms to improve domain generalization... 

    A meshless EFG-based algorithm for 3D deformable modeling of soft tissue in real-time

    , Article Studies in Health Technology and Informatics, 9 February 2012 through 11 February 2012 ; Volume 173 , February , 2012 , Pages 1-7 ; 09269630 (ISSN) ; 9781614990215 (ISBN) Abdi, E ; Farahmand, F ; Durali, M ; Sharif University of Technology
    The meshless element-free Galerkin method was generalized and an algorithm was developed for 3D dynamic modeling of deformable bodies in real time. The efficacy of the algorithm was investigated in a 3D linear viscoelastic model of human spleen subjected to a time-varying compressive force exerted by a surgical grasper. The model remained stable in spite of the considerably large deformations occurred. There was a good agreement between the results and those of an equivalent finite element model. The computational cost, however, was much lower, enabling the proposed algorithm to be effectively used in real-time applications  

    Laser induced breakdown spectroscopy and acoustic response techniques to discriminate healthy and cancerous breast tissues

    , Article Applied Optics ; Volume 55, Issue 29 , 2016 , Pages 8227-8235 ; 1559128X (ISSN) Ghasemi, F ; Parvin, P ; Hosseini Motlagh, N. S ; Amjadi, A ; Abachi, S ; Sharif University of Technology
    OSA - The Optical Society 
    Laser induced breakdown spectroscopy and subsequent acoustic response during microplasma formation are employed to identify cancerous human breast tissues. The characteristic optical emissions identify Ca, Na, and Mg rich species in cancerous tissues compared to those of healthy ones. Furthermore, we show that the characteristic parameters of the microplasma, generated on the unhealthy tissues, are elevated. We report higher decibel audio signals emanating from laser induced microplasma and a subsequent audio blueshift for malignant tissues. The higher abundance of trace elements in cancerous tissues as well as higher plasma temperature and electron density in laser induced microplasma... 

    Phenomenological contact model characterization and haptic simulation of an endoscopic sinus and skull base surgery virtual system

    , Article 4th RSI International Conference on Robotics and Mechatronics, ICRoM 2016, 26 October 2016 through 28 October 2016 ; 2017 , Pages 84-89 ; 9781509032228 (ISBN) Sadeghnejad, S ; Esfandiari, M ; Farahmand, F ; Vossoughi, G ; Sharif University of Technology
    During the endoscopic sinus and skull base training surgeries, the haptic perception of tool-tissue interaction and even transitions and ruptures in the tissues are fundamental which should be taken into account in a robotic control scheme. However, this problem is extremely complex given the nature and the variety of tissues involved in an ESS procedures. In this article, ex-vivo indentation and relaxation experiments associated with an offline model estimation of the interaction between tissues and a surgical tool are presented. The estimated parameters of the modified Kelvin-Voigt model are then used to provide a realistic tool-tissue interaction dynamic model. Finally, the principle of a... 

    A spatially-variant deconvolution method based on total variation for optical coherence tomography images

    , Article Progress in Biomedical Optics and Imaging - Proceedings of SPIE, 12 February 2017 through 14 February 2017 ; Volume 10137 , 2017 ; 16057422 (ISSN) ; 9781510607194 (ISBN) Almasganj, M ; Adabi, S ; Fatemizadeh, E ; Xu, Q ; Sadeghi, H ; Daveluy, S ; Nasiriavanaki, M ; Gimi, B ; Krol, A ; Sharif University of Technology
    Optical Coherence Tomography (OCT) has a great potential to elicit clinically useful information from tissues due to its high axial and transversal resolution. In practice, an OCT setup cannot reach to its theoretical resolution due to imperfections of its components, which make its images blurry. The blurriness is different alongside regions of image; thus, they cannot be modeled by a unique point spread function (PSF). In this paper, we investigate the use of solid phantoms to estimate the PSF of each sub-region of imaging system. We then utilize Lucy-Richardson, Hybr and total variation (TV) based iterative deconvolution methods for mitigating occurred spatially variant blurriness. It is... 

    Guiding medical needles using single-point tissue manipulation

    , Article Proceedings - IEEE International Conference on Robotics and Automation, 12 May 2009 through 17 May 2009, Kobe ; 2009 , Pages 2705-2710 ; 10504729 (ISSN); 9781424427895 (ISBN) Torabi, M ; Hauser, K ; Alterovitz, R ; Duindam, V ; Goldberg, K ; Sharif University of Technology
    This paper addresses the use of robotic tissue manipulation in medical needle insertion procedures to improve targeting accuracy and to help avoid damaging sensitive tissues. To control these multiple, potentially competing objectives, we present a phased controller that operates one manipulator at a time using closed-loop imaging feedback. We present an automated procedure planning technique that uses tissue geometry to select the needle insertion location, manipulation locations, and controller parameters. The planner uses a stochastic optimization of a cost function that includes tissue stress and robustness to disturbances. We demonstrate the system on 2D tissues simulated with a... 

    Three-dimensional bioprinting of functional skeletal muscle tissue using gelatin methacryloyl-alginate bioinks

    , Article Micromachines ; Volume 10, Issue 10 , 2019 ; 2072666X (ISSN) Seyedmahmoud, R ; Çelebi Saltik, B ; Barros, N ; Nasiri, R ; Banton, E ; Shamloo, A ; Ashammakhi, N ; Dokmeci, M. R ; Ahadian, S ; Sharif University of Technology
    MDPI AG  2019
    Skeletal muscle tissue engineering aims to fabricate tissue constructs to replace or restore diseased or injured skeletal muscle tissues in the body. Several biomaterials and microscale technologies have been used in muscle tissue engineering. However, it is still challenging to mimic the function and structure of the native muscle tissues. Three-dimensional (3D) bioprinting is a powerful tool to mimic the hierarchical structure of native tissues. Here, 3D bioprinting was used to fabricate tissue constructs using gelatin methacryloyl (GelMA)-alginate bioinks. Mechanical and rheological properties of GelMA-alginate hydrogels were characterized. C2C12 myoblasts at the density 8 × 106 cells/mL... 

    Single peak analysis of proton induced prompt gamma counts

    , Article Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms ; Volume 475 , 2020 , Pages 63-70 Saheli, F ; Vosoughi, N ; Riazi, Z ; Shahabinejad, H ; Rasouli, F. S ; Sharif University of Technology
    Elsevier B.V  2020
    Online elemental analysis of irradiated tissues is an important challenge in proton therapy for estimating the depth of the Bragg peak and monitoring the healing process. In the present study, the prompt gamma (PG) spectra of the most abundant elements of human tissues were obtained for two different incident protons of 30 MeV and 120 MeV using the Geant4 toolkit. Train phantoms were defined to study the elemental analysis of the tissue from PG spectra. It was found that the intensities of 7.12 and 3.91 MeV PG depend on the mass of 16O and 20Ca elements for both proton energies, respectively. Furthermore, multi-variable linear functions were presented for overlapping peaks like 4.44 and 2.31... 

    Multispectral brain MRI segmentation using genetic fuzzy systems

    , Article 2007 9th International Symposium on Signal Processing and its Applications, ISSPA 2007, Sharjah, 12 February 2007 through 15 February 2007 ; 2007 ; 1424407796 (ISBN); 9781424407798 (ISBN) Hasanzadeh, M ; Kasaei, S ; Sharif University of Technology
    Magnetic resonance imaging (MRI) techniques provide detailed anatomic information non-invasively and without the use of ionizing radiation. The development of new pulse sequences in MRI has allowed obtaining images with high clinical importance and thus joint analysis (multispectral MRI) is required for interpretation of these images. Fuzz rule-based systems can combine many inputs from widely varying sources so that they can be useful for description of tissues in MRI. In a fuzzy system an error free and optimized classifier can be obtained by genetic algorithms. In this paper, we have utilized a genetic fuzzy system for modeling different tissues in brain MRI and proposed a statistical... 

    A three-dimensional micromechanical model of brain white matter with histology-informed probabilistic distribution of axonal fibers

    , Article Journal of the Mechanical Behavior of Biomedical Materials ; Volume 88 , 2018 , Pages 288-295 ; 17516161 (ISSN) Yousefsani, S. A ; Farahmand, F ; Shamloo, A ; Sharif University of Technology
    Elsevier Ltd  2018
    This paper presents a three-dimensional micromechanical model of brain white matter tissue as a transversely isotropic soft composite described by the generalized Ogden hyperelastic model. The embedded element technique, with corrected stiffness redundancy in large deformations, was used for the embedment of a histology-informed probabilistic distribution of the axonal fibers in the extracellular matrix. The model was linked to a multi-objective, multi-parametric optimization algorithm, using the response surface methodology, for characterization of material properties of the axonal fibers and extracellular matrix in an inverse finite element analysis. The optimum hyperelastic... 

    Fabrication and characterization of an injectable reinforced composite scaffold for cartilage tissue engineering: An in vitro study

    , Article Biomedical Materials (Bristol) ; Volume 16, Issue 4 , 2021 ; 17486041 (ISSN) Khozaei Ravari, M ; Mashayekhan, S ; Zarei, F ; Sayyahpour, F. A ; Taghiyar, L ; Eslaminejad, M. B ; Sharif University of Technology
    IOP Publishing Ltd  2021
    There are limitations in current medications of articular cartilage injuries. Although injectable bioactive hydrogels are promising options, they have decreased biomechanical performance. Researchers should consider many factors when providing solutions to overcome these challenges. In this study, we created an injectable composite hydrogel from chitosan and human acellular cartilage extracellular matrix (ECM) particles. In order to enhance its mechanical properties, we reinforced this hydrogel with microporous microspheres composed of the same materials as the structural building blocks of the scaffold. Articular cartilage from human donors was decellularized by a combination of physical,... 

    Disc size markedly influences concentration profiles of intravenously administered solutes in the intervertebral disc: A computational study on glucosamine as a model solute

    , Article European Spine Journal ; Vol. 23, issue. 4 , April , 2014 , p. 715-723 Motaghinasab, S ; Shirazi-Adl, A ; Parnianpour, M ; Urban, J. P. G ; Sharif University of Technology
    Purpose: Tests on animals of different species with large differences in intervertebral disc size are commonly used to investigate the therapeutic efficacy of intravenously injected solutes in the disc. We hypothesize that disc size markedly affects outcome. Methods: Here, using a small non-metabolized molecule, glucosamine (GL) as a model solute, we calculate the influence of disc size on transport of GL into rat, rabbit, dog and human discs for 10 h post intravenous-injection. We used transient finite element models and considered an identical GL supply for all animals. Results: Huge effects of disc size on GL concentration profiles were found. Post-injection GL concentration in the rat... 

    Analysis of different material theories used in a FE model of a lumbar segment motion

    , Article Acta of Bioengineering and Biomechanics ; Volume 15, Issue 2 , 2013 , Pages 33-41 ; 1509409X (ISSN) Gohari, E ; Nikkhoo, M ; Haghpanahi, M ; Parnianpour, M ; Sharif University of Technology
    In this study, a nonlinear poroelastic model of intervertebral disc as an infrastructure was developed. Moreover, a new element was defined consisting a disc (Viscoelastic Euler Beam Element) and a vertebra (Rigid Link) as a unit element. Using the new element, three different viscoelastic finite element models were prepared for lumbar motion segment (L4/L5). Prolonged loading (short-term and long-term creep) and cyclic loading were applied to the models and the results were compared with results of in vivo tests. Simplification of the models by using the new element leads to reduction of the runtime of the models in dynamic analyses to few minutes without losing the accuracy in the results  

    Tool-tissue force estimation in laparoscopic surgery using geometric features

    , Article Studies in Health Technology and Informatics ; Volume 184 , 2013 , Pages 225-229 ; 09269630 (ISSN) Kohani, M ; Behzadipour, S ; Farahmand, F ; Sharif University of Technology
    IOS Press  2013
    This paper introduces three geometric features, from deformed shape of a soft tissue, which demonstrate good correlation with probing force and maximum local stress. Using FEM simulation, 2D and 3D model of an in vivo porcine liver was built for different probing tasks. Maximum deformation angle, maximum deformation depth and width of displacement constraint of the reconstructed shape of the deformed body were calculated. Two neural networks were trained from these features and the calculated interaction forces. The features are shown to have high potential to provide force estimation either for haptic devices or to assess the damage to the tissue in large deformations of up to 40%  

    Magnetic graphene oxide mesoporous silica hybrid nanoparticles with dendritic pH sensitive moieties coated by PEGylated alginate-co-poly (acrylic acid) for targeted and controlled drug delivery purposes

    , Article Journal of Polymer Research ; Volume 22, Issue 8 , 2015 ; 10229760 (ISSN) Pourjavadi, A ; Shakerpoor, A ; Tehrani, Z. M ; Bumajdad, A ; Sharif University of Technology
    Kluwer Academic Publishers  2015
    In this study synthesis of a drug delivery system (DDS) is described which has several merits over its counterparts. In order to synthesize this nano-carrier, graphene oxide nano-sheets are used to accommodate MCM-41 nanoparticles. Furthermore Fe3O4 nanoparticles are introduced to this nano-material to produce a traceable nanoparticle. Since cancerous tissues have lower pH than healthy tissues, pH-sensitive oligomers are attached to this nano-material. Finally the nano-carrier is wrapped by a biocompatible shell (PEGylated sodium alginate); this polymeric shell makes the DDS capable of a more controllable drug release. By measuring in vitro situation, ‘loading content%’...