Biyomedikal Mühendisliği Enstitüsü

Director : Ahmet Ademoğlu

Assistant Directors : Bora Garipcan, Esin Öztürk Işık

Professors : Ahmet Ademoğlu, Albert Güveniş, Bora Garipcan, Burak Güçlü, Can Ali Yücesoy, Cengizhan Öztürk, Duygu Ege, Esin Öztürk Işık, Mehmed Özkan

Associate Professors : Banu İyisan, Daniela Schulz, Mustafa Kemal Ruhi

Assistant Professors : E. Sümeyra Turalı Emre, Mehmet Saadeddin Öztürk, Pınar Özbay, Yasin Çotur

Instructors : Prof. Dr. Naime Hale Saybaşılı*

Assistants : Ayşe Işık, Ayşe İrem Çetin, Belal Tavashi, Beste İmamoğlu Yıldırım, Dilan Avşar Akdeniz, Emir Kulakoğlu, Hüden Neşe, Meryem Torlak, Şeyma Soykan, Şirin Yağmur Abacı, Tansu Gölcez Köse, Yağmur Zengin, Zeynep İrem Özcan

*Part-time
•Adjunct

Objectives of the Institute

Biomedical Engineering (BME) is concerned with the application of engineering technology and scientific methods to the analysis of biological, physiological and health care problems.

The Institute of Biomedical Engineering offers interdisciplinary graduate programs for the MS and PhD degrees in BME.

The Institute's objective is to provide specialized academic training and research opportunities infrastructure for graduate students in specific areas of Biomedical Engineering.

MASTER OF SCIENCE DEGREE

Master of Science courses are designed in an interdisciplinary framework. Students graduated from engineering, science or medical disciplines are admitted to the program and MS course packages are tailored to every student’s individual needs and background. There are three proposed areas of concentration: “Biomechanics & Neuroengineering”, “Biomedical Instrumentation & Imaging” and “Biomaterials & Biophotonics”. Students must choose a specific BME Area of Concentration from which they select four courses focusing on their studies. Additionally, four Complementary Electives must be selected from the courses offered by the Institute of BME and/or other programs to complement the students background. Students must complete a minimum of 24 credit hours (min. 60 ECTS from courses) and complete a Master's thesis (60 ECTS). Students are suggested to take eight courses and the Graduate Seminar according to the following curriculum table spanning two semesters.

MS Program Curriculum

First Semester		Cr.	ECTS
BM -- --	BME Areas of Concentration*	3	8
BM -- --	BME Areas of Concentration*	3	8
BM -- --	Complementary Elective **	3	8
BM -- --	Complementary Elective ***	3	8
BM 579	Graduate Seminar	0	1
TOTAL		12	33

Second Semester		Cr.	ECTS
BM -- --	BME Areas of Concentration*	3	8
BM -- --	BME Areas of Concentration*	3	8
BM -- --	Complementary Elective **	3	8
BM -- --	Complementary Elective **	3	8
TOTAL		12	32

*BME Areas of Concentration: courses offered in the BME Concentration area selected.

** Complementary Elective: courses offered by the Institute of BME and/or other programs to complement the students background.

		Cr.	ECTS
BM 690	MS Thesis	0	60
TOTAL		0	60

TOTAL: min. 24 credit hours + Graduate Seminar + MS Thesis
ECTS: 125 (min. 120 ECTS required for graduation)

DOCTOR OF PHILOSOPHY DEGREE

Students holding an MS degree in engineering, science or medical disciplines are admitted to the PhD program. Each PhD student determines a curriculum of study with his/her appointed advisor. Students holding an MS degree in a field other than Biomedical Engineering may be required to complete a remedial period of study. Related to their doctoral research topic, students are required to complete six courses, at least three of which must be selected from the courses offered by the Institute of BME. The remaining courses may also be chosen from other programs to complement the students background. Additionally, the Guided Research course and the Graduate Seminar must be completed in the PhD Program for the fulfillment of course requirement with a minimum of 22 credit hours (min. 61 ECTS). After completing the course work, students must pass the Qualifying Exam (30 ECTS), and prepare a Thesis Proposal (30 ECTS). Students start working on their PhD Thesis studies (120 ECTS) after their proposals are approved. Students are suggested to take six courses, Guided Research course and the Graduate Seminar according to the following curriculum table spanning two semesters.

First Semester		Cr.	ECTS
BM --	BME Elective*	3	8
-- --	BME Elective*	3	8
-- --	BME Elective*	3	8
-- --	Complementary Elective **	3	8
BM 700	Graduate Seminar	0	1
Total		12	33

Second Semester		Cr	ECTS
-- --	Complementary Elective **	3	8
-- --	Complementary Elective **	3	8
BM 699	Guided Research	4	12
		10	28

*BME Elective: courses offered by the Institute of BME.

** Complementary Elective: courses offered by the Institute of BME and/or other programs to complement the students background.

		Cr.	ECTS
-- --	Qualifying Exam	0	30
-- --	Thesis Proposal	0	30
BM 790	PhD Thesis	0	120
Total		0	180

Total: min. 22 Credit Hours + Graduate Seminar + Qualifying Exam +Thesis Proposal + PhD Thesis

ECTS : min. 241

GENERAL COURSES

Code Course Title	Hours/Week	Cr	ECTS
BM 501 Biology of Living Systems	3+2+0	3	8
BM 502 Human Physiology	3+2+0	3	8
BM 503 Basic Mathematics for Biomedical Science	3+0+0	3	8
BM 504 Systems Theory for Biomedical Science	3+2+0	3	8
BM 506 Biostatistical Methods	3+0+0	3	8
BM 531 Numerical Methods and C Programming	3+0+0	3	8
BM 600 Advanced Research Methods	3+0+0	3	8

MATHEMATICS FOR BME

Code Course Title	Hours/Week	Cr	ECTS
BM 503 Basic Mathematics for Biomedical Science	3+0+0	3	8
BM 504 Systems Theory for Biomedical Science	3+0+2	4	9
BM 506 Biostatistical Methods	3+0+0	3	8
BM 531 Numerical Methods and C Programming	3+0+0	3	8
BM 533 Neural Networks	3+0+0	3	8

LIFE SCIENCES FOR BME

Code Course Title	Hours/Week	Cr	ECTS
BM 501 Biology of Living Systems	3+0+0	3	8
BM 502 Human Physiology	3+0+2	4	9
BM 530 Fundamentals of Neuroscience	3+0+0	3	8
BM 632 Sensory Systems	3+0+0	3	8

BIOMEDICAL ENGINEERING ‘AREAS OF CONCENTRATION’

BIOMATERIALS & BIOPHOTONICS focuses on biocompatible materials and light-based technologies for the development of prosthetics, implants, and artificial organs to advance medical interventions and biological material interactions.

Code Course Title	Hours/Week	Cr	ECTS
BM 505 Characterization of Nanoscale Particles	3+0+0	3	8
BM 507 Bioactive Polymer Nanoparticles	3+0+0	3	8
BM 515 Laser-Tissue Interaction Mechanisms	3+0+0	3	8
BM 516 Biophotonics	3+0+0	3	8
BM 517 Novel Applications in Biomedical Optics	3+0+0	3	8
BM 519 Biosensors	3+0+0	3	8
BM 521 Optical Methods for Detection & Treatment of Cancer	3+0+0	3	8
BM 523 Cell Culture Techniques	3+0+0	3	8
BM 541 Biomaterials*	3+0+0	3	8
BM 545 Characterization of Biomedical Samples	3+0+0	3	8
BM 546 Tissue-Biomaterials Interactions	3+0+0	3	8
BM 547 Biomedical Nanostructures	3+0+0	3	8

BIOMECHANICS & NEUROENGINEERING integrates mechanical principles and neuro-technologies to analyze the structure and function of neural systems to understand, repair, or enhance them for their functional restoration.

Code Course Title	Hours/Week	Cr	ECTS
BM 510 Advanced Muscle Mechanics	3+0+0	3	8
BM 513 Human Cognition and Behavior	3+0+0	3	8
BM 522 Skeletal Muscle Mechanics	3+0+0	3	8
BM 525 Tissue Biomechanics	3+0+0	3	8
BM 526 Motion Biomechanics	3+0+0	3	8
BM 530 Fundamentals of Neuroscience	3+0+0	3	8
BM 533 Neural Networks	3+0+0	3	8
BM 538 Computational Neuroscience	3+0+0	3	8
BM 571 Biomedical Signal Processing	3+0+0	3	8
BM 632 Sensory Systems	3+0+0	3	8
BM 633 Dynamics of Neural Systems	3+0+0	3	8

BIOMEDICAL INSTRUMENTATION & IMAGING merges the design and development of innovative hardware and software systems for therapeutic and diagnostic purposes, while utilizing specialized techniques to improve research accuracy and clinical outcomes.

Code Course Title	Hours/Week	Cr	ECTS
BM 508 Medical Image Processing and Analysis	3+0+0	3	8
BM 512 Magnetic Resonance Image Reconstruction	3+0+0	3	8
BM 514 Multimodal Brain Imaging	3+0+0	3	8
BM 536 Principles of Neuroimaging	3+0+0	3	8
BM 560 Introduction to Medical Device and Implant Design	3+0+0	3	8
BM 563 Medical Imaging	3+0+0	3	8
BM 564 Biomedical Instrumentation and Measurement	3+2+0	3	8
BM 570 Magnetic Resonance Spectroscopic Imaging	3+0+0	3	8
BM 573 Cardiovascular Imaging	3+0+0	3	8
BM 602 Deep Learning in Medical Imaging	3+0+0	3	8
BM 611 Nuclear Biomedical Instrumentation	3+0+0	3	8
BM 641 Magnetic Resonance Imaging Principles	3+0+0	3	8

CLINICAL ENGINEERING is primarily concerned with the optimization of healthcare delivery through quality management of medical devices and systems.

Code Course Title	Hours/Week	Cr	ECTS
BM 561 Quality Assurance in Diagnostic Radiology	3+0+0	3	8
BM 563 Medical Imaging	3+0+0	3	8
BM 564 Biomedical Instrumentation and Measurement	3+0+2	4	9

* Compulsory course(s) of the area of concentration.

MEDICAL IMAGING studies various imaging modalities for diagnostic and research purposes.

Code Course Title	Hours/Week	Cr	ECTS
BM 536 Principles of Neuroimaging	3+0+0	3	8
BM 563 Medical Imaging*	3+0+0	3	8
BM 570 Magnetic Resonance Spectroscoping Imaging	3+0+0	3	8
BM 571 Biomedical Signal Processing	3+0+0	3	8
BM 573 Cardiovascular Imaging	3+0+0	3	8
BM 611 Nuclear Biomedical Instrumentation	3+0+0	3	8
BM 641 Magnetic Resonance Imaging Principles	3+0+0	3	8

* Compulsory course(s) of the area of concentration.

NEUROENGINEERING is a discipline that uses engineering techniques to understand, repair, replace, or enhance neural systems.

Code Course Title	Hours/Week	Cr	ECTS
BM 530 Fundamentals of Neuroscience*	3+0+0	3	8
BM 536 Principles of Neuroimaging	3+0+0	3	8
BM 538 Computational Neuroscience	3+0+0	3	8
BM 571 Biomedical Signal Processing	3+0+0	3	8
BM 632 Sensory Systems	3+0+0	3	8
BM 633 Dynamics of Neural Systems	3+0+0	3	8

* Compulsory course(s) of the area of concentration.

BIOPHOTONICS deals with the interaction between biological systems and photons. This area focuses on the medical applications of lasers and near infrared spectroscopy.

Code Course Title	Hours/Week	Cr	ECTS
BM 515 Laser-Tissue Interaction Mechanisms	3+0+0	3	8
BM 516 Biophotonics*	3+0+0	3	8
BM 517 Novel Applications in Biomedical Optics	3+0+0	3	8

* Compulsory course(s) of the area of concentration.

COURSE DESCRIPTIONS: BM 501 Biology of Living Systems (3+2+0) 3 ECTS 8
(Canlı Sistemlerin Biyolojisi)Cell structure and organelles. Phospholipids, aminoacids and proteins, nucleotides and nucleic acids. Transport mechanisms: active and passive transports, osmosis. PH and buffers. Feedback control. Enzymes and coenzymes: glycolysis and Krebs cycle, oxidative phosphorylation, chemical energy production. Genetic coding: replication, transcription (mRNA synthesis) and translation (protein synthesis), post-translational modification.

BM 502 Human Physiology (3+0+2) 4 ECTS 9
(İnsan Fizyolojisi)
Review of Cell Physiology. Physiology of Organ Systems: Nerve and Muscle; Physical Work; Autonomic Nervous System; Blood; Respiration; Acid-Base Homeostasis; Kidneys, Salt and Water Balance, Cardiovascular System, Thermal Balance and Thermoregulation, Nutrition and Digestion, Hormones, Central Nervous System, Special Senses. Electrocardiography, Blood Pressure, Heart Sounds.

BM 503 Basic Mathematics for Biomedical Science (3+0+0) 3 ECTS 8
(Biyotıp Bilimleri için Temel Matematik)
Mathematical methods in biomedical sciences. Series and convergence, functions, differential and integral calculus, matrix algebra, solution of linear system of equations, first- and second-order ordinary differential equations; multivariable calculus; introduction to optimization; numerical methods for solution of differential equations, data analysis, and visualization.

BM 504 Systems Theory for Biomedical Science (3+0+2) 3 ECTS 8
(Biyotıp Bilimleri için Sistem Kuramı)
State models and numerical solutions. Response characteristics of linear system. Convolution and deconvolution. Feedback systems. Frequency response. Modulation and demodulation. Sampling, signal averaging and filtering. MATLAB basics, oscilloscope, signal generation, and analog/digital filters.
Prerequisite: BM 503 or consent of the instructor.

BM 505 Characterization of Nanoscale Particles (3+0+0) 3 ECTS 8 (Nano Ölçekli Parçacıkların Karakterizasyonu)

Characterization techniques for determining the properties and functions of nanoparticles in biomedical applications. Colloidal and morphological characterization, thermal analysis, characterization of nanoparticle–biomolecule interactions, quantification of cargo (e.g. drug, imaging agents) loading and release, and characterization techniques for cellular viability and uptake

BM 506 Biostatistical Methods (3+0+0) 3 ECTS 8
(Biyoistatistiksel Yöntemler)Numerical data sampling in biomedical applications; measures of central tendency and dispersion in biomedical data; interval; nominal and ordinal quantification and estimation; Gaussian models; hypothesis testing; unpaired and paired t-test; analysis of variance; repeated measures analysis of variance; linear regression models; product-moment correlation analysis; Bland-Altman test; Spearman rank correlation models; Chi-square analysis of contingency tables; McNemar's analysis; Mann-Whitney rank sum test; Kruskal Wallis statistic; Wilcoxon signed rank test; Friedman statistical analysis for small sample sizes; survival analysis; log-rank test; and Gehan's modeling of survival data.

BM 507 Bioactive Polymer Nanoparticles (Biyoaktif Polimer Nanoparçacıklar
General outlook for polymer and hybrid nanoparticles. Introduction to biocompatible and smart polymers for formulation of nanomedicines. Synthesis and fabrication methods by focusing on nanocapsule formation. Large scale fabrication tools to manufacture polymer nanoparticles. Stability of nanoparticle dispersions. Stimuli responsive and functional nanoparticle design in the scope of nanomedicine and synthetic biology.

BM 508 Medical Image Processing and Analysis (3+0+0) 3 ECTS 8 (Medikal Görüntü İşleme ve Analizi)
Medical image processing and analysis; magnetic resonance imaging; MR image contrast and pulse sequences; brain imaging; data anonymization; personal data protection; image filtering; image transformations; MRI modalities and modality-specific processing; magnetic resonance spectroscopic imaging; perfusion-weighted imaging; diffusion-weighted imaging; arterial spin labeling MRI; image registration; image segmentation; thresholding; region growing; morphological operators; quantitative biomarker production; statistical analysis of biomarkers; radiomics analysis; network attached storage; GitHub.

BM 510 Advanced Muscle Mechanics (3+0+0) 3 ECTS 8 (İleri Kas Mekaniği)
Research techniques for muscle mechanics: Animal experiments; Histological techniques; Computational analyses using finite element modeling for characterizing force and motion production mechanisms; Intraoperative experiments in human subjects; Imaging analyses using MRI and DTI for in vivo local tissue deformation assessments, tissue structure and elastography. In vivo muscle and joint mechanics using 3D motion analyses, surface EMG and dynamometer. Novel motion assistive device technology development coupled with neurotechnology.

BM 512 Magnetic Resonance Image Reconstruction (3+0+0) 3 ECTS 8 (Manyetik Rezonans Görüntü Geriçatması)Medical image reconstruction; computed tomography backprojection; magnetic resonance image (MRI) reconstruction; MRI data acquisition; k-space; undersampling; partial Fourier methods; homodyne reconstruction; conjugate synthesis; projection onto convex sets; non Cartesian reconstruction; echo planar imaging; spiral imaging; radial imaging; rosette trajectories; convolution regridding; density compensation; parallel imaging; SENSE; SMASH and variants; GRAPPA; compressed sensing; time-series imaging reconstruction; deep learning based MRI reconstruction.

BM 513 Human Cognition and Behavior (3+0+0) 3 ECTS 8 (İnsan Bilişi ve Davranışı)Human brain development, Human nervous system, Brain imaging techniques, Brain and physiology, Biology of behavior, Sensory areas, Emotions; stress, fear, pain, Attention, Consciousness, Alertness, Brain rhythms and sleep, Memory and learning, Decision making, Addiction, Cognitive impairment

BM 514 Multimodal Brain Imaging (3+0+0) 3 ECTS 8( Çok Modlu Beyin Görüntüleme)The basics of MRI and functional MRI (fMRI), Neurobiological principles of fMRI, Experiment design, data acquisition, and preprocessing, Physiological signals, Spatiotemporal brain patterns, Simultaneous EEG-fMRI, EEG artifacts, EEG data preprocessing, EEG data analysis, Multimodal brain imaging in clinics, Hands-on analyses with AFNI and EEGLAB

BM 515 Laser-Tissue Interaction Mechanisms (3+0+0) 3 ECTS 8
(Laser-Doku Etkileşim Mekanizmaları)
Physical principles of therapeutic uses of lasers in medicine. Optical properties of biological tissues and measurement techniques; photochemical, thermal, photoablative interaction mechanisms and their applications in photodynamic therapy; biostimulation, coagulation, vaporization, ablation, photodistruption, plasma formation, and shock wave generation; clinical applications of lasers.

BM 516 Biophotonics (3+0+0) 3 ECTS 8
(Biyofotonik)
Principles of optics and lasers in medicine, the interaction of light with biological tissues, and the applications of light in biomedicine. Electromagnetic waves and the nature of light, geometrical optics, optical instruments, physical optics, incoherent light sources, basic laser theory, optical fibers, interaction of light with biological materials; laser Doppler flowmetry, colorimetry, flame photometry, spectrophotometry, optical flow cytometry, ultraviolet and visible absorption spectroscopy, infrared spectroscopy, optical coherence tomography.

BM 517 Novel Applications in Biomedical Optics (3+0+0) 3 ECTS 8
(Biyomedikal Optikte Yeni Uygulamalar)
New research studies on bioimaging, confocal and multiphoton microscopy, optical coherent tomography, spectroscopic diagnostics, tissue engineering with light, laser tweezers and scissors, photodynamic therapy and biostimulation.

BM 519 Biosensors (3+0+0) 3 ECTS 8
(Biyoalgılayıcılar)
Biological components involved in biosensors, immobilization of biological components to transducers; principal performance characteristics, fabrication and biomedical applications of electrochemical, optical, piezoelectric and thermistor based biosensors.

BM 521 Optical Methods for Detection & Treatment of Cancer (3+0+0) 3 ECTS 8(Kanserin Tanı ve Tedavisinde Optik Yöntemler)
Optical methods for cancer detection and treatment; basic principles of optical imaging and therapy; current clinical applications in oncology; latest research developments in biomedical optics; fluorescence-guided tumor resection; photodynamic therapy.

BM 522 Skeletal Muscle Mechanics (3+0+0) 3 ECTS 8
(İskelet Kası Mekaniği)
Skeletal muscle architecture: morphology, uni- and multipennate muscles, mono- and multiarticular muscles. Mechanism of activation and sliding filament theory. Force production in the sarcomere level in isometric and isokinetic conditions. Force production in the muscle level and muscle architecture variations in relation to force production. Muscle mechanics: Hill’s muscle equation, Hill type muscle models, constancy of muscle volume, constitutive models, mechanisms of transmission of muscle force. Finite element modeling of muscle. Experimental techniques.

BM 523 Cell Culture Techniques (3+0+0) 3 ECTS 8 (Hücre Kültürü Tekniği
Characterization techniques for assessing cellular responses and functionality in cell culture systems. Core approaches include evaluation of cell viability and cytotoxicity, analysis of cell morphology, adhesion, and proliferation under different culture conditions, and monitoring of cell differentiation and lineage commitment. Additional techniques encompass biochemical and molecular characterization methods such as enzyme activity assays (e.g. ALP), gene expression analysis (e.g. PCR), and protein quantification (e.g. Western blotting). The measurement of cellular microenvironment factors, including reactive oxygen species (ROS), as well as advanced techniques such as flow cytometry and organoid/spheroid-based models, further enable comprehensive understanding of cellular behavior in vitro.

BM 525 Tissue Biomechanics (3+0+0) 3 ECTS 8
(Doku Biyomekaniği)
Introduction to biomechanics and to the structures of the musculoskeletal system. Concepts of continuum mechanics, finite deformation analysis, viscoelasticity, anisotropy and inhomogeneity, used to describe the complex mechanical properties of biological tissues, with emphasis on the tissues comprising the musculoskeletal system.

BM 526 Motion Biomechanics (3+0+0) 3 ECTS 8
(Hareket Biyomekaniği)
Analysis of movement of the musculoskeletal system: anthropometry, link-segment models, kinematics, kineties. Active and passive mechanical properties of skeletal muscle in relation to its structure. Mechanisms of transmission of muscle force. Effects of myofascial force transmission on muscle function. Motor control and coordination of muscular activity: types of muscle fibers, motor units, size principle, sensory information.

BM 530 Fundamentals of Neuroscience (3+0+0) 3 ECTS 8
(Sinirbilimin Temelleri)
Functional parts and properties of a nerve cell. Signal integration in the central nervous system (CNS). Neurotransmitters and their action mechanisms. Receptors, structure and function of excitatory amino acid receptors. Plasticity in the nervous system. Mechanisms of learning and memory. Neuropathological diseases.

BM 531 Numerical Methods and C Programming (3+0+0) 3 ECTS 8
(Sayısal Yöntemler ve C Programlama)
An overview of C programming; variables, structures, type definitions, expressions, statements and functions. Data representations and machine precision. Using the C libraries for the solution of linear systems, approximation and interpolation, integration, optimization, solution of ordinary and partial differential equations. Fundamentals of Object Oriented Programming; inheritance, polymorphism and overloading. Class development for complex and matrix operations.

BM 533 Neural Networks (3+0+0) 3 ECTS 8
(Sinir Ağları)
Reverse engineering in the nervous system; anatomical, physiological and mathematical approaches. Computational action and interaction of brain networks; architecture, performance rules and learning rules. Dryware, wetware, connectivity. A biological neural network analysis of learning and memory. Computation modeling of neuronal network. Artificial implementations: VLSI, optical and holographic implementations, resistive networks for computer vision, silicon cortex. Static and dynamic networks. Pulse frequency modulation in the nervous system. Stability and periodic oscillations. Learning algorithms. Application examples.

BM 536 Principles of Neuroimaging (3+0+0) 3 ECTS 8
(Nörogörüntülemenin İlkeleri)
Overview of the Statistical Parameter Mapping, Computational aspects of preprocessing the anatomical images; registration, segmentation and spatial normalization, Statistical modeling of functional Magnetic Resonance Imageing (fMRI) data; convolution models for fMRI, general linear model, Contrast vectors and classical inference, Hierarchical models, Bayesian inference; expectation maximization, recursive maximum likelihood estimation, variational Bayes, EEG Source Imaging; forward and inverse models.

BM 538 Computational Neuroscience (3+0+0) 3 ECTS 8
(Hesaplamalı Nörobilim)
Neural spike trains and point processes. Spike rate and statistics. Neural encoding. Estimating firing rates. Reverse correlation methods. Static nonlinearities. Spatiotemporal receptive fields. Neural decoding. Discrimination. Spike-train decoding. Population decoding. Entropy and mutual information. Entropy maximization. Entropy and information in spike trains.

BM 541 Biomaterials (3+0+0) 3 ECTS 8
(Biyomalzemeler)
General properties of materials. Chemical, Physical and Mechanical Properties of Biomaterials. Biomaterial Degradation and Processing. Surface properties of Biomaterials. Metallic, ceramic, polymeric and composite materials for Biomedical Applications. Evaluation of standards used in Biomaterials.

BM 545 Characterization of Biomedical Samples (3+0+0) 3 ECTS 8
(Biyomedikal Malzemelerin Karakterizasyonu)
Surface analysis of biomaterials using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM). Chemical analysis of biomedical samples using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. Mechanical characterization of biomaterials using stress and strain analyses, examination of types of deformation, strengthening mechanisms and modes of fracture, and application of Mohr’s circle and failure criteria.

BM 546 Tissue-Biomaterials Interactions (3+0+0) 3 ECTS 8
(Doku-Malzeme Etkileşimleri)
Biomaterials, Proteins, Protein-Surface Interactions, Blood-Biomaterials Interactions and Coagulation, Inflammation and Infection, Immune System and Infection, Wound Healing, Surfaces of Biomaterials and Physiological Environment, Biocompatibility, Example Case Investigations.

BM 547 Biomedikal Nanostructures (3+0+0) 3 ECTS 8
(Biyomedikal Nanoyapılar)
Nanotechnology and Nanobiotechnology terms and their definitions, Synthesis and Characterization of Nanostructures, Nanoproduction, Nanostructures-Protein, Cell and Tissue Interactions, Biomedical and Clinical applications of Nanostructures.

BM 560 Introduction to Medical Device and Implant Design (3+0+0) 3 ECTS 8
(Medikal Cihaz ve İmplant Tasarımına Giriş)
Review on Selection of biocompatible materials, surface properties of biomaterials, host response, medical manufacturing technologies, design control, pre-clinical device testing for safety and efficiency and include the risk/benefit ratio assessment evaluation of clinical performance and design of clinical trials.

BM 563 Medical Imaging (3+0+0) 3 ECTS 8
(Tıbbi Görüntüleme)
Radiation quantities and units, radioactivity, x-ray production and x-ray tube, interaction of radiation with matter, scattered radiation, x-ray film, fluoroscopy, digital imaging system, angiography, ultrasound imaging, gamma camera, x-ray CT and image reconstruction, emission tomography: PET and SPECT, MR imaging, LASER imaging, electrical impedance tomography, bone densitometer, patient exposure and protection, quality assurance in radiology.

BM 564 Biomedical Instrumentation and Measurement (3+0+2) 3 ECTS 8
(Biyomedikal Cihazlar ve Ölçümler)
Biomedical sensors, transducers and electrodes. Instrumentation amplifiers and their applications. Electrical safety. Electrocardiography (ECG), electroencephalography (EEG), electromyography (EMG), and electroretinography. Body temperature measurement. Pulse Oximetry, blood pressure and flow measurements, cardiac output measurements. Measurements of the respiratory system.

BM 570 Magnetic Resonance Spectroscopic Imaging (3+0+0) 3 ECTS 8
(Manyetik Rezonans Spektroscopic Görüntüleme)
Magnetic Resonance Spectroscopic Imaging (MRSI), spin-spin interactions, nuclear magnetic resonance chemical structure identification, molecular spectroscopy, metabolism, MRSI data acquisition protocols, MRSI data processing and analysis, clinical applications including cancer, neurological disorders, and pediatric diseas.

BM 571 Biomedical Signal Processing (3+0+0) 3 ECTS 8
(Biyomedikal İşaret İşleme)
Introduction to systems theory. Signals in time and transform domains; Fourier and ztransforms. Discrete time signals in the transform domain; Fourier and z-transforms. Digital filter design. Overview of probability, statistics and random processes. Signal Modeling: AR, ARMA, Prony Methods. Optimal filtering; Wiener and Kalman Approach. Fourier based power spectrum estimation. Parametric power spectrum estimation based on AR and ARMA modeling. Eigenanalysis based power spectrum estimation. Adaptive transversal filters. Application to Bioelectric Signals; ECG, EMG, EEG, HRV, fMRI-BOLD and others.

BM 573 Cardiovascular Imaging (3+0+0) 3 ECTS 8
(Kardiyovasküler Görüntüleme)
Cardiovascular imaging from a biomedical engineering perspective. A short review of cardiovascular physiology. An overview of cardiac diseases which are the focus of advanced imaging systems. Detailed comparative analysis of specific imaging modalities like US, PET, MRI. Investigation of various applications through projects that stress special challenges of cardiovascular imaging with emphasis on cardiac MRI.

BM 579 Graduate Seminar (0+1+0) 0 P/F ECTS 1
(Lisansüstü Seminer)
Seminars offered by faculty, guest speakers and/or graduate students designed to widen students' perspectives on specific topics of interest and to expand their range of scientific research techniques and publication ethics.

BM 580-589 Special Studies (3+0+0) 3 ECTS 8
(Özel Çalışmalar)
Study of specific Biomedical Engineering subjects in biomechanics, biocybernetics, bioelectronics or prosthetics and artificial organs.

BM 590-599 Selected Topics (3+0+0) 3 ECTS 8
(Seçilmiş Konular)
In depth study of a selected topic in the field of Biomedical Engineering.

BM 600 Advanced Research Methods (3+0+0) 3 ECTS 8
(İleri Araştırma Teknikleri)
Scientific concepts and practice of writing a research proposal, including the sections of the background and significance, problem statement, central goal and hypothesis, specific aims, objectives, approach and impact. Comparison of project proposal writing versus high impact manuscript writing. Author ethics, including guidelines to prevent plagiarism and ethical guidelines for human and animal research. Writing an ethics committee application based on students' research proposals. Communicating research results in posters and talks. Delivery of scientific talk based on students' research proposals.

BM 602 Deep Learning in Medical Imaging (3+0+0) 3 ECTS 8(Medikal Görüntülemede Derin Öğrenme)
Deep learning in medical imaging; classical machine learning algorithms; backpropagation; feature selection; regularization and optimization; convolutional neural networks; recurrent neural networks; attention mechanisms and transformers; transfer learning; self-supervised learning; generative models; medical image classification; medical image reconstruction; super-resolution; image segmentation; explainable AI; human-centered AI.

BM 611 Nuclear Biomedical Instrumentation (3+0+0) 3 ECTS 8
(Nükleer Biyomedikal Cihazlar)
Radioactivity, radioisotopes, radiation dosage, scanning with radionucleides, data presentation techniques, focusing, collimators, scintillation counters, rectilinear scanners, gamma camera, tomography and positron camera, computer processing of the image for uniformity, improved resolution, dynamic studies, radioactive tracers, compartment analysis for single pool, interchanging system and multiple pools, gamma and beta counters, radioimmuno assaying, clinical dosimetry, pocket dosimeters, thermoluminescent dosimetry, proportional counters, Geiger counters.

BM 632 Sensory Systems (3+0+0) 3 ECTS 8
(Duyu Sistemleri)
Basic psychophysics, anatomy and physiology of sense organs, neural pathways andinformation processing, skin and peripheral afferent fibery, somatosensory cortex, cortical maps, tactile psychophysics, cochlea and auditory nerve fibers, central auditory nuclei, auditory cortex, auditory psychophysics, retina, ganglion cells and LGN, primary visual cortex, spatiotemporal receptive fields, higher visual areas, visual psychophysics, laboratory techniques in sensory research.

BM 633 Dynamics of Neural Systems (3+0+0) 3 ECTS 8
(Sinir Sistemlerinin Dinamiği)
Introduction to neuroscience. Nonlinear dynamics and bifurcations. Computation by excitatory and inhibitory networks. Nonlinear oscillations. Dynamics of action potentials. Examples of chaotic regimes in neurons. Synaptic coupling and synchronicity in neural networks. Central pattern generation and traveling waves in locomotion. Lyapunov functions and dynamic temporal memories. Space-time model for dendritic computation.

BM 641 Magnetic Resonance Imaging Principles (3+0+0) 3 ECTS 8
(Manyetik Rezonans Görüntüleme Prensipleri)
Fundamental principles of magnetic resonance imaging (MRI). MRI methods and techniques; flow and flow-related MRI, diffusion and perfusion imaging. MRI angiography; chemical shift and spectroscopic MRI. Instrumentation, quality assurance and safety issues. Term project.

BM 681-689 Special Studies (3+0+0) 3 ECTS 8
(Özel Çalışmalar)
Studies of advanced topics in the specialization areas of Biomedical Engineering.

BM 690 Master's Thesis in Biomedical Engineering ECTS 60
(Biyomedikal Mühendisliği Yüksek Lisans Tezi)
Investigation in depth of a special topic related with the student's major area of study and research in Biomedical Engineering, with the aim of original contribution to the subject. Preparation and defense of an M.S. thesis.

BM 691-698 Special Topics (3+0+0) 3 ECTS 8
(Özel Konular)
In depth study of a special topic in the field of Biomedical Engineering.

BM 699 Guided Research (2+0+4) 4 ECTS 12
(Yönlendirilmiş Araştırmalar)
Research in the field of Biomedical Engineering, by arrangement with members of the faculty; guidance of doctoral students towards the preparation and presentation of a research proposal.

BM 700 Graduate Seminar (0+1+0) 0 ECTS 1
(Lisansüstü Seminer)
Seminars offered by faculty, guest speakers and graduate students designed to widen students' perspectives on specific topics of interest and to expand their range of scientific research techniques and publication ethics.

BM 790 Doctoral Dissertation in Biomedical Engineering ECTS 120
(Biyomedikal Mühendisliği Doktora Tezi)
Original research on the theoretical and/or application aspects of a special topic related with the student's major area of specialization in Biomedical Engineering. Preparation and defense of a Ph.D. dissertation.

UNDERGRADUATE COURSES OFFERED BY THE INSTITUTE

BM 402 Engineering in Medicine (3+0+0) 3 ECTS 5
(Tıpta Mühendislik)
The human body as a machine; physiological principles, modeling, neural networks; diagnostic techniques and related instrumentation; high technology in patient care and therapy. Computers in medicine; signal and image processing, picture archiving, telemedicine; biomaterials and prostheses; principles of clinical engineering and safety considerations; technology management in hospitals.
Prerequisite: Technical elective for engineering and science undergraduate students only.