{"title":"Life Sciences Research Center and Data Management","authors":"F. Akal","doi":"10.1109/BIYOMUT.2017.8479197","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8479197","url":null,"abstract":"Life Sciences Research Centers are bodies that provide researchers in this domain with laboratuaries, hardware and consultancy support they need. Such centers allows that resources can be managed centrally, researchers in similar areas can be gathered together and data produced in scientific works can be stored and processed properly. This paper outlines a research center that provides all these functionality.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125737041","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}
Enes Çakar, A. Türker, Emre Güleryüz, Ahmet Karaca
{"title":"Detection of Candidate Nodules in Lung Tomography by Image Processing Techniques","authors":"Enes Çakar, A. Türker, Emre Güleryüz, Ahmet Karaca","doi":"10.1109/BIYOMUT.2017.8478990","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8478990","url":null,"abstract":"In this project, the data set generated from the data of the National Cancer Institute (NCI) derived from DICOMformatted lung cancer data has been converted to PNG format to make it suitable for the operation of image processing algorithms. The converted data is filtered by a second-order median filter to prevent noise. A laplacian filter was applied to clarify the boundaries of the candidate nodules. The threshold must be determined according to the histogram value of each view. To select a different threshold for each image was subjected to the determination threshold Otsu method. In Otsu threshold selection method determines the point at which the minimum-class variance and between-class variance is a maximum, and determines the threshold value. In the availability of candidate nodules, nodule diameter is intended for detection of the large nodules than 2 mm. To meet this requirement, the Otsu thresholding method was applied on the MATLAB platform to sieve nodules smaller than 2 mm in diameter and candidate nodules were detected. By determining the morphological characteristics of the identified candidate nodules in MATLAB platform, candidate nodule; Major features such as area, major axis length, minor axis length, and perimeters are extracted. The boundaries of the identified candidate nodules are bounded by the edge detection algorithm and numerically ordered.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130958687","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}
A. Bozdogan, Sebnem Seherler, Tugba Arzu Ozal Ildeniz, I. Anac, F. N. Kok
{"title":"Surface Plasmon Florescence Spectroscopy Based Biosensor for Cholera Toxin Detection","authors":"A. Bozdogan, Sebnem Seherler, Tugba Arzu Ozal Ildeniz, I. Anac, F. N. Kok","doi":"10.1109/BIYOMUT.2017.8479292","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8479292","url":null,"abstract":"Diseases and epidemics caused by pathogens in drinking water supplies not only cause deaths but also lead to an important economic and labor loss. Rapid and easy detection of these pathogens on water sources will help us to prevent the diseases associated with them. In this study, the aim is to achieve the detection of low amount of toxins by amplification of the signal by surface plasmon fluorescence spectroscopy (SPFS) and to minimize the need for sample preparation. Cholera toxin B (ChB), a truncated form of cholera toxin, was chosen as the model toxin. Capture antibody that will assure specific binding of the toxin was immobilized to the sensor surface by different methods and measurement conditions were optimized.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121125877","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}
Ecem Bozkurt, Mustafa Utkur, Yavuz Muslu, E. Saritas
{"title":"Effects of Drive Field Parameters in Magnetic Particle Imaging: A Relaxometer Study","authors":"Ecem Bozkurt, Mustafa Utkur, Yavuz Muslu, E. Saritas","doi":"10.1109/BIYOMUT.2017.8478888","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8478888","url":null,"abstract":"In Magnetic Particle Imaging (MPI), it is possible to acquire signal from the nanoparticles via applying oscillating magnetic fields in the 1 kHz -150 kHz frequency range . Though 25 kHz is commonly used, there are not enough studies on determining the optimal excitation frequency and excitation strength for obtaining images of high quality. In this study, we observed nanoparticles’ response and the effect on the point spread functions (PSF) at various field amplitudes and at 10 kHz, 25 kHz and 148.5 kHz excitation frequencies. Accordingly, at 10 kHz and 25 kHz both the harmonic response of the nanoparticles and the PSFs are largely similar. On the other hand, the frequency components at 148.5 kHz are decreasing rapidly at increasing harmonics. The larger full-width at half-maximum of the obtained PSF indicates that the image resolution of this image will be lower at this frequency.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123771687","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}
Zeeshan Rashid, U. C. Coskun, Y. Morova, B. Morova, A. A. Bozkurt, A. Erten, A. Jonáš, S. Aktürk, A. Kiraz
{"title":"Femtosecond Laser Ablated Tracks on Smart Surfaces for Droplet Manipulation Applications","authors":"Zeeshan Rashid, U. C. Coskun, Y. Morova, B. Morova, A. A. Bozkurt, A. Erten, A. Jonáš, S. Aktürk, A. Kiraz","doi":"10.1109/BIYOMUT.2017.8478903","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8478903","url":null,"abstract":"In droplet based microfluidics, ability of controlling the motion of the droplets insidechips have great importance for the applications such guiding, sorting, mixing and dividing of liquid droplets. In this study, we fabricated hydrophilic microchannels inside the chips by femtosecond laser ablation technique in order to control droplet motion. The laser beam focused on PDMS converts the irradiated regions to hydrophilic by ablating the coating entirely from the surface. Droplets follow the tracks because of the difference in wettability of ablated region and PDMS surfaces together with the topographical profile of the ablated tracks. Within this study, we investigated the manipulation of three kind of liquid droplets (water/surfactant mixture, pure water and pure etylene glycol) along microchannels with depths of 1μm, 1.5μm and 2μm. We verified the experimental results with simulations and analyzed the trajectories of the moving droplets with the different wettability along the tracks of different depths. Our results showed that, while topographical effects play role in droplet guiding for 1.5μm and 2μm tracks, for the case of 1μm depth of channel, surface energy modifications cause the guiding rather than the topographical step on the surface. These results will pioneer for sorting applications of different micro droplets mixed in the same microfluidic chip.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128237547","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":"Development of Artificial Neural Network Based Active Ankle Prosthesis Algorithm Using Gait Analysis Data","authors":"A. Keleş, Can A. Yücesoy","doi":"10.1109/BIYOMUT.2017.8478881","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8478881","url":null,"abstract":"Amputation is the removal of a part or all of a limb due to a disease, accident or trauma. In the United States, an average of 500 people loses at least one limb every day, of which about 65% is due to lower limb amputations. Since energetically active prostheses are costly, amputees usually continue to their daily lives using a wheelchair or a passive prosthesis. The aim of this study is to determine the optimum sensor needs of active ankle prostheses and to develop algorithm suitable for this sensor infrastructure, thus a device that is both easy to use and financially accessible to anyone can be built up. In this context, three neural networks structures with different inputs were developed and their performances were evaluated. As a result, it is determined that if a device in which only EMG signals are used as network inputs, a total of 5 signals should be collected from muscles that are responsible for hip, knee and wrist movements. It has been found that, when it is wanted to work with less EMG sensors, it is necessary to perform a force or torque feedback into the system. Three EMG signals collected from the dorsi and plantar flexor muscles of the ankle were found to be sufficient for such a system. These findings are important in order to determine the amount of the sensor needed by an active ankle prosthesis whose requirements can be variable according to the amputation level of the patient and the mechanical design flexibility.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128279453","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}
A. Atasoy, Berkay Erenay, E. Kaplanoglu, B. Garipcan, Burak Guclu, M. Ozkan
{"title":"Ionic Electroactive Polymer Actuated Prosthetic Finger Design","authors":"A. Atasoy, Berkay Erenay, E. Kaplanoglu, B. Garipcan, Burak Guclu, M. Ozkan","doi":"10.1109/BIYOMUT.2017.8479103","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8479103","url":null,"abstract":"The proposed work covers an ionic electroactive polymer actuator production for use in a prosthetic finger design. The best mechanical design will be possible if it considers anatomical features of the real finger/hand structure. A number of different finger movements for different purposes are formed by the antagonistic pairs of muscles. Ionic electroactive polymer actuators are intended to be used instead of intrinsic muscles, which enable precise movement of the hand beyond the force required for movement due to their low power consumption, low noise, high power/mass ratio.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124566624","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}
Ozge Can Kaplan, Dilek Betul Arslan, Sevim Cengiz, Ani Kiçik, Emel Erdogdu, G. H. Hatay, Z. Tufekcioglu, B. Bilgiç, H. Hanagasi, H. Gurvit, T. Demiralp, A. Uluğ, E. O. Isik
{"title":"Determination of Diffusion Weighted Magnetic Resonance Imaging Based Biomarkers of Mild Cognitive Impairment in Parkinson’s Disease","authors":"Ozge Can Kaplan, Dilek Betul Arslan, Sevim Cengiz, Ani Kiçik, Emel Erdogdu, G. H. Hatay, Z. Tufekcioglu, B. Bilgiç, H. Hanagasi, H. Gurvit, T. Demiralp, A. Uluğ, E. O. Isik","doi":"10.1109/BIYOMUT.2017.8479249","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8479249","url":null,"abstract":"This study aims to specify biomarkers of Parkinson's disease mild cognitive impairment (PD-MCI) based on fractional anisotropy (FA) and mean diffusivity (MD) maps obtained from diffusion weighted magnetic resonance imaging (DWMRI). T1 and diffusion weighted MR images collected from 27 cognitively normal Parkinson's disease (PD-CN), 32 mild cognitively impaired Parkinson's disease (PD-MCI), and 18 healthy control (HC) volunteers, at a clinical 3T MR scanner, were processed using FMRIB Software Library (FSL)'s toolboxes. Average regional values of FA and MD maps and tract based spatial statistics (TBSS) were utilized to define statistically significant differences between the participant subject groups.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129896390","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}
Gençay Sevim, T. Mercan, Yigit Ali Uncu, M. Canpolat
{"title":"A new reconstruction technique used in Diffuse Optical Tomography System","authors":"Gençay Sevim, T. Mercan, Yigit Ali Uncu, M. Canpolat","doi":"10.1109/BIYOMUT.2017.8478965","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8478965","url":null,"abstract":"Several methods are used in the early diagnosis of breast cancer. Due to the disadvantages of these methods, the diffuse optical tomography (DOT) system is one of new methods have been developed to support these methods. In the DOT, the reconstruction technique used to create image is very important. Each reconstruction technique has some disadvantages. Thus, it is important to create an image by using the appropriate technique for DOT system. In this study, we have combined two algorithms called Truncated Conjugate Gradient (TCG) and Transpose Free Quasi Minimal Residual (TFQMR) to create a new algorithm named TCG-TFQMR. The reason of combining the two algorithms is low resolution of TCG and slow running of TFQMR. The new algorithm is first tested using simulation data created by Matlab. Then, in-vitro experiments were performed by acquiring DOT data from a breast phantom. The both reconstruction algorithms TCG and TCG-TFQMR were used to reconstruct the tissue phantom. It has been shown that TCG-TFQMR algorithm has better resolution than TCG.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"02 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129191241","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":"Variable-FOV Reconstruction for 3D Non-Cartesian Parallel Imaging","authors":"Celal Furkan Senel, T. Çukur","doi":"10.1109/BIYOMUT.2017.8479024","DOIUrl":"https://doi.org/10.1109/BIYOMUT.2017.8479024","url":null,"abstract":"Conventional parallel MRI reconstruction methods can be used in the case of variable-density non-Cartesian acquisitions, but they often require iterations with high complexity, which limits their applicability, especially for 3D reconstructions. A technique based on PILS that utilizes variable FOVs to obtain faster reconstructions for 2D non-Cartesian data has recently been proposed. Here we apply this new method to 3D variable density non-Cartesian data, and further process it using wavelet regularization to get rid of remaining artifacts. We compare the performance of using different parameters for regularization, and then, we compare the performance of the overall reconstruction technique to SOS conventional gridding, PILS, and ESPIRiT reconstructions. Results indicate that its performance is superior to the compared reconstruction methods for different acceleration values.","PeriodicalId":330319,"journal":{"name":"2017 21st National Biomedical Engineering Meeting (BIYOMUT)","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128402175","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}