Assist Prof. Dr. Özlem Birgül (Vice Director)

Assist. Prof. Dr. Özlem BİRGÜL

Ankara University

Institute of Nuclear Sciences

Tandoğan Merkez Kampüsü, 06100 Ankara

T 0 312 212 85 77 / 2733 F 0 312 215 33 07

ozlem.birgul@ankara.edu.tr

 

Academic Background
Year Degree University Department
1995 BSc Middle East Technical University Dept. of Electrical and Electronics Eng.
1997 MSc Middle East Technical University Dept. of Electrical and Electronics Eng.
2002 PhD Middle East Technical University Dept. of Electrical and Electronics Eng.
2004 Postdoctoral University of California, Irvine Radiological Sciences        Center for Functional Onco-Imaging

Research Topics

inverse problems

numerical methods (finite element method, boundary element method)

magnetic resonance – electrical impedance tomography

near infrared imaging

three dimensional reconstruction

feature extraction

Positions

1994 – 1995     Student Assistant, Başkent University , Vocational School of Biomedical Equipments

1995 – 2001     Teaching/research Assistant, Middle East Technical University, Dept. of Electrical and Electronics Eng.

2001 – 2004     Assistant Specialist, UCI Radiological Sciences, Center for Functional Onco-Imaging

2004 – 2007     Assistant Researcher, UCI Radiological Sciences, Center for Functional Onco-Imaging

2008 – 2009     Senior Researcher, TÜBİTAK UZAY Artificial Intelligence, Speech Processing, Pattern Recognition and Remote Sensing Group

2009 – 2011     Department Head, TÜBİTAK UZAY, Dept. of Data Processing and Application Software Development

Project Manager, TÜBİTAK UZAY, Development Of High Capacity And High Speed Computerized Ballistic Image Analysis And Recognition System For Cartridge Cases And Bullets – BALİSTİKA 2010

2009 – 2011     Ankara University, Institute of Nuclear Sciences, Part-time instructor

2011 –              Ankara University, Institute of Nuclear Sciences,        Assist. Prof. Dr.

2012 –              Ankara University, Institute of Nuclear Sciences,        Vice Director

Academic Activities

2004-   NIH, Center for Scientific Review, panel reviewer

2005 –  Reviewer for Institute of Physics (IOP) journals (Physics in Medicine and Biology, Physiological Measurement, Inverse Problems, Measurement Science and Technology)

2008-   Reviewer for TÜBİTAK Turkish Journal of ELEKTRİK

Projects

Project Title : Development Of High Capacity And High Speed Computerized Ballistic Image Analysis And Recognition System For Cartridge Cases And Bullets – BALİSTİKA 2010
Position Project Manager
Agency : TÜBİTAK KAMAG
Project ID : 107G194
Duration/Budget : 08/2008 – 04/2012 (8,505,811 TL)
Project Title  : Comparison of the Specificity of Magnetic Resonance-Electrical ImpedanceTomography and Dynamic Contrast-Enhanced MRI in Breast Cancer
Position Project Manager
Agency   : Army Medical Research and Development Command
Project ID :W81XWH-04-1-0446
Duration/Budget  :05/2004 – 04/2007 ($557,639)
Project Title : 3D Tomographic Bioluminescence System for Noninvasive Assessment of Molecular Mechanisms Underlying Metastatic Progression in Mice
Position Researcher
Agency : Army Medical Research and Development Command
Project ID : BC031786
Duration/Budget : 06/2004 – 05/2007 ($288,722)
Project Title : Combined Imaging Modalities for Breast Cancer
Position Researcher
Agency : California Breast Cancer Research Program
Project ID : 12IB-0095
Duration/Budget : 07/2006 – 06/2008 ($150,000)
Project Title : Combined MR-Diffuse Optics for Functional Imaging
Position Researcher
Agency : PHS/NIH National Cancer Institute
Project ID : P30 CA-104548
Duration/Budget : 04/2004 – 03/2008 ($1,815,280)
Project Title : Electrical Impedance Tomography of Breast Cancer
Position : Researcher
Agency : Army Medical Research and Development Command
Project ID : DAMD17-02-0326
Duration/Budget : 05/2002 – 05/2004 ($299.881)

 Publications

1.       Ider Y Z, Birgül Ö, Oran O F, Arikan O, Hamamura M J, Muftuler L T, “Fourier transform magnetic resonance current density imaging (FT-MRCDI) from one component of magnetic flux density,” Physics in Medicine and Biology, vol. 55, pp. 3177-3199, 2010.

2.       Unlu M B, Lin Y, Birgül Ö, Nalcioglu O, and Gulsen G, “Simultaneous In vivo Dynamic MR-DOT for Small Animal Imaging,” Journal of Biomedical Optics, Vol. 13, 060501, 2008.

3.       Chung S H, Cerussi A E, Klifa C, Baek H M, Birgül Ö, Gulsen G, Meritt S I, Hsiang D, Tromberg B J, “In vivo water state measurements in breast cancer using broadband diffuse optical spectroscopy,  Physics in Medicine and Biology, vol. 53, pp. 6713–6727, 2008.

4.       Unlu M B, Birgül Ö, and Gulsen G, “A Simulation study of the variability of indocyanine green kinetics and using structural a priori information in dynamic contrast enhanced diffuse optical tomography (DCE-DOT),” Physics in Medicine and Biology, vol. 53, pp. 3189–3200, 2008.

5.       Birgül Ö, Hamamura M J, Muftuler L T, and Nalcioglu O, “Contrast and spatial resolution in MREIT using low amplitude currents” Physics in Medicine and Biology, vol. 51, pp. 5035–5049, 2006.

6.       Gulsen G, Birgül Ö, Unlu M B, Shafiiha R, and Nalcioglu O, “Combined Diffuse Optical Tomography (DOT) and MRI System for Cancer Imaging in Small Animals, ” Technology in Cancer Research and Treatment, vol. 5, no. 4, pp. 351-363, 2006.

7.       Muftuler L T, Hamamura M J, Birgül Ö, and Nalcioglu O, “In vivo MRI Electrical Impedance Tomography (MREIT) of tumors” Technology in Cancer Research and Treatment, vol. 5, no. 4, pp. 381-387, 2006.

8.       Unlu M B, Birgül Ö, Shafiiha R, Gulsen G, and Nalcioglu O, “Diffuse Optical Tomographic Reconstruction using Multi-frequency Data” Journal of Biomedical Optics, vol. 11, 2006.

9.       Hamamura M J, Muftuler L T, Birgül Ö, and Nalcioglu O, “Measurement of ion diffusion using magnetic resonance electrical impedance tomography,Physics in Medicine and Biology, Vol.51, No.11, pp.2753-2762, 2006.

10.    Gulsen G, Xiong B, Birgül Ö, and Nalcioglu O “Design and Implementation of a Multi-Frequency Diffuse Optical Tomography (MF-DOT) System”, Journal of Biomedical Optics, 11(1), Jan/Feb 2006.

11.    Muftuler T, Hamamura M, Birgül Ö, and Nalcioglu O, “Resolution and Contrast in Magnetic Resonance Electrical Impedance Tomography (MREIT) and Its Application to Cancer Imaging, ” Technology in Cancer Research and Treatment, vol. 3, no. 6, pp. 599-609, 2004.

12.    Birgül Ö, Eyuboglu B M, and Ider Y Z, “Experimental results for 2D magnetic resonance electrical impedance tomography (MR-EIT) using magnetic flux density in one direction,” Physics in Medicine and Biology, Vol.48, No.21, pp. 3485-3504, 2003.

13.    Birgül Ö, Eyuboglu B M, and Ider Y Z, “Current Constrained Voltage Scaled Reconstruction (CCVSR) Algorithm for MR-EIT and Its Performance for Different Probing Currents,” Physics in Medicine and Biology, Vol.48, No.5, pp.653-671, 2003.

14.    Ider Y Z and Birgül Ö, “Use of Magnetic Field Generated by the Internal Distribution of Injected Currents for Electrical Impedance Tomography (MR-EIT),” Elektrik, Turkish Journal of Electrical Engineering and Computer Sciences, 6, no 3, 215-225, 1998.

15.    Ider Y Z, Eyuboglu B M, Kuzuoglu M, Leblebicioglu K, Baysal U, Caglar B K, and Birgül Ö, “A Method for Comparative Evaluation of EIT Algorithms Using a Standard Data Set,” Physiological Measurement suppl. A vol.16, pp. 227-236, 1995.

 Thesis

1.       Birgül Ö, “Development of Different Reconstruction Algorithms for MR-EIT and Experimental Realization,” Middle East Technical University, Dept. of Electrical and Electronics Eng., PhD Thesis, 2002.

(this theis recieved M.K. Parlar Thesis of the Year Award)

2.       Birgül Ö, “Electrical Impedance Tomography Using Magnetic Fields Generated by Injected Currents,” Middle East Technical University, Dept. of Electrical and Electronics Eng., MSc Thesis, 1997.

Invited Talks

1.       Birgül Ö, Hamamura M J, Muftuler L T, and Nalcioglu O, “Magnetic Resonance-Electrical Impedance Tomography in Breast Cancer Imaging,” IEEE, International Symposium on Biomedical Imaging, Arlington VI, 2006.

2.       Gulsen G, Unlu M B, Birgül Ö, Yan H, and Nalcioglu O, “A Multi-Modality System for Dynamic Imaging of Cancer, ” IEEE, International Symposium on Biomedical Imaging, Arlington VI, 2006.

 

Conference Papers 

1.       Sakarya U, Es A E, Leloğlu U M, Tunalı E, Birgül Ö,A Case Study of an Automated Firearms Identification System: BALİSTİKA 2010,” BIT’s 1st Annual World Congress of Forensics (WCF-2010), Dalian, China, October 21-23, 2010.

2.       Öztürk A O, Büyükatalay S, Birgül Ö, “Tek Kamera ve Tek Yapısal Işık Kaynağı Kullanarak Mermi Kovanı Yükseklik Haritasının Oluşturulması”, IEEE 18. Sinyal İşleme ve Uygulamaları Kurultayı, 22-24 Nisan 2010, Diyarbakır, Türkiye

3.       Büyükatalay S, Birgül Ö, Halıcı U, ” Işık Kaynakları Seçiminin ve Yüzey Özelliklerinin Fotometrik Stereo Hatasına Etkisi”, IEEE 18. Sinyal İşleme ve Uygulamaları Kurultayı, 22-24 Nisan 2010, Diyarbakır, Türkiye

4.       Büyükatalay S, Birgül Ö, Halıcı U, “Surface Reconstruction from Multiple Images Filtering Non-Lambert Regions,” IEEE International Conference on Image Processing, Mısır, 7-11 Kasım  2009.

5.       Büyükatalay S, Birgül Ö, Halıcı U, “3B Geriçatım için Gölge ve Parlama Bölgesi Saptamalı Döngülü Fotometrik Stereo,” SİU 2009 IEEE 17. Sinyal İşleme ve İletişim Uygulamaları Kurultayı, Antalya, Nisan 2009.

6.       Öztürk A O, Birgül Ö, Esen E, Sakarya U, “Fotometrik Stereo Yönteminde Fotoğraflardali Gürültülerin Geriçatılmış Kovan Yükseklik Haritasına Etkileri,” SİU 2009 IEEE 17. Sinyal İşleme ve İletişim Uygulamaları Kurultayı, Antalya, Nisan 2009.

7.       İder Y Z, Birgül Ö, Arıkan O, Hamamura M J, Müftüler L T, “Tekrarlamalı FT-MRCI yönteminin 2-Boyutlu Deneysel Fantom Verilerine Uygulanması,” 13. Biyomedikal Mühendisliği Ulusal Toplantısı, Ankara, Mayıs 2008.

8.       Birgül Ö, Muftuler T M Hamamura M J, Nalcioglu O, “3D Magnetic Resonance Electrical Impedance Tomography at 4T using Sensitivity Matrix based Reconstruction,” ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

9.       Birgül Ö, Hamamura M J, Muftuler L T, and Nalcioglu O, “Comparison of Magnetic Resonance Electrical Impedance Tomography at 4T and 7T Field Strengths,” ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

10.    Hamamura M J, Muftuler L T, Birgül Ö, and Nalcioglu O, “Fast Imaging for Magnetic Resonance Electrical Impedance Tomography,” ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

11.    Hamamura M J, Muftuler M J, Birgül Ö, and Nalcioglu O, “Magnetic Resonance Electrical Impedance Tomography Using Biologically Safe Injected Current Levels,” ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

12.    Chen G, Muftuler L T, Birgül Ö, Hamamura M J, and Nalcioglu O, “Mutual Information Based MREIT Reconstruction Using MR Anatomical Data,” ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

13.    Muftuler M J, Birgül Ö, Hamamura M J, and Nalcioglu O, “Effects of Limited Volume Coverage on Accuracy of MR-Electrical Impedance Tomography”, ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

14.    Gulsen G, Unlu M B, Birgül Ö, and Nalcioglu O, “Combined MR and Diffuse Optical Tomography for Dynamic Contrast Enhanced Imaging,” ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

15.    Unlu M B, Gulsen G, Birgül Ö, Su M Y, and Nalcioglu O, “Improvement of the Specificity of DCE-MRI Using a Dynamic Optical Imaging System,” ISMRM 15th Scientific Meeting and Exhibition Germany, May 2007.

16.    Gulsen G, Unlu M B, Birgül Ö, Shafiiha R, and Nalcioglu O, “Simultaneous monitoring of multiple contrast agents using a hybrid MR-DOT system” Proceedings of SPIE (6431-Multi-modal Biomedical Imaging) 20-25 January 2007.

17.    Birgül Ö, Muftuler L T, Hamamura M J, and Nalcioglu O, “Reconstruction of Irregular Conductivity Distributions using MREIT at Low Current Levels,” ISMRM 14th Scientific Meeting and Exhibition Seattle, Washington, May 2006.

18.    Hamamura M J, Muftuler L T, Birgül Ö, and Nalcioglu O, “Dynamic Magnetic Resonance Electrical Impedance Tomography Using Sub-Milliamp Injected Currents,” ISMRM 14th Scientific Meeting and Exhibition Seattle, Washington, May 2006.

19.    Hamamura M J, Muftuler L T, Birgül Ö, and Nalcioglu O, “Electrode Misalignment Correction Algorithms In Magnetic Resonance Electrical Impedance Tomography,” ISMRM 14th Scientific Meeting and Exhibition Seattle, Washington, May 2006.

20.    Hamamura M J, Muftuler L T, Birgül Ö, and Nalcioglu O, “Multiple Current Injection Schemes In Magnetic Resonance Electrical Impedance Tomography,” ISMRM 14th Scientific Meeting and Exhibition Seattle, Washington, May 2006.

21.    Muftuler L T, Hamamura M J, Birgül Ö, and Nalcioglu O, “In Vivo MRI Based Electrical Impedance Tomography of Malignant Tumors,” ISMRM 14th Scientific Meeting and Exhibition Seattle, Washington, May 2006.

22.    Shafiiha R, Unlu M B, Gulsen G, Birgül Ö, Hamamura M, Chu Y, and Nalcioglu O, “Improving the accuracy of the chromophore reconstruction in diffuse optical tomography by using structural and functional-priors from MRI,” ISMRM 14th Scientific Meeting and Exhibition Seattle, Washington, May 2006.

23.    Birgül Ö, Unlu M B, Shafiiha R, Gulsen G, and Nalcioglu O, “Selection of Optimal Modulation Frequencies in Multi-Frequency DOT,” OSA Biomedical Optics Topical Meeting, 2006.

24.    Birgül Ö, Gulsen G, Shafiiha R, Unlu M B, and Nalcioglu O, “In vivo Small Animal Imaging using Combined MR-DOT System,” OSA Biomedical Optics Topical Meeting, 2006.

25.    Gulsen G, Unlu M B, Birgül Ö, Yan H, and Nalcioglu O, “A Dual Modality System for Dynamic Contrast Enhanced Imaging,” OSA Biomedical Optics Topical Meeting, 2006.

26.    Birgül Ö, Muftuler L T, Hamamura M, and Nalcioglu O, “Iterated Sensitivity Algorithm for Magnetic Resonance Electrical Impedance Tomography,” Era of Hope DOD Breast Cancer Research Program Meeting, Philadelphia PA, June 8-11, 2005.

27.    Unlu M B, Birgül Ö, and Gulsen G, “3D Bioluminescence Tomography for Animal Imaging,”Era of Hope DOD Breast Cancer Research Program Meeting, Philadelphia PA, June 8-11, 2005.

28.    Muftuler L T, Hamamura M, Birgül Ö, and Nalcioglu O, “MRI Based Electrical Impedance Imaging of Tumors,” Era of Hope DOD Breast Cancer Research Program Meeting, Philadelphia PA, June 8-11, 2005.

29.    Gulsen G, Birgül Ö, Shafiiha R, Unlu M B, and Nalcioglu O, “Design and implementation of a multi-frequency diffuse optical tomography system (MF-DOT) system compatible with MRI,” Network for Translational Research Optical Imaging (NTROI) Retreat, Newport Beach, CA., June 3-5 2005.

30.    Unlu M B, Birgül Ö, and Gulsen G, “Bioluminescence tomography with a-priori information,” Network for Translational Research Optical Imaging (NTROI) Retreat, Newport Beach, CA, June 3-5 2005.

31.    Muftuler L T, Hamamura M, Birgül Ö, and Nalcioglu O, “MRI Based Electrical Impedance Imaging of Tumors with Iterated Sensitivity Reconstruction using Regularization,” ISMRM 13th Scientific Meeting, Miami, FL, May 2005.

32.    Hamamura M, Muftuler T, Birgül Ö, and Nalcioglu O, “Tracking of Sodium Changes Using MR-EIT,” ISMRM 13th Scientific Meeting, Miami, FL, May 2005.

33.    Gulsen G, Birgül Ö, Xiong B, and Nalcioglu O, “Multi-frequency DOT and MR Imager for Small Animal Imaging,” Photonics West, San Jose, CA, January 2005.

34.    Gulsen G, Birgül Ö, and Nalcioglu O, “A hybrid DOT and MR Imager for Small Animal Imaging,” 4th Inter-Institute Workshop on Optical Diagnostic Imaging from Bench to Bedside at the National Institute of Health, Washington, 20-22 September 2004.

35.    Gulsen G, Birgül Ö, and Nalcioglu O, “Combined CT and 3D Bioluminescence Tomography System,” Network for Translational Research Imaging (NTROI) Retreat, Newport Beach, CA, June 2004.

36.    Birgül Ö, Muftuler L T, Hamamura M J, and Nalcioglu O, “MR-EIT of Malignant Tumors in Rats,” ISMRM 11th Scientific Meeting, 2003.

37.    Hamamura M J, Muftuler L T, Birgül Ö, and Nalcioglu O, “Assessment of the Efficacy of Electrical Impedance Imaging Using MRI,” ISMRM 11th Scientific Meeting, 2003.

38.    Birgül Ö, Eyuboglu B M and Ider Y Z, “Magnetic resonance – electrical impedance tomography (MR-EIT) using magnetic flux density in one direction and experimental realization,” Proceedings of the Fourth Engineering Network Meeting on Biomedical Applications of EIT, Manchester – U.K., pp.52, 2003.

39.    Gulsen G, Birgül Ö, and Nalcioglu O, “Hybrid DOT and MRI System”, Proceedings of SPIE, vol. 4955, pp 246-252, 2003.

40.    Birgül Ö, Ozbek O, Eyuboglu M, and Ider Y Z, “Magnetic Resonance-Conductivity Imaging using 0.15 Tesla MRI Scanner,” IEEE EMBS 23rd Annual Conference, Istanbul, 2001.

41.    Ozbek O, Birgül Ö, Eyuboglu M, and Ider Y Z, “Imaging Current Density Using 0.15T MRI System,” IEEE EMBS 23rd Annual Conference, Istanbul, 2001.

42.    Birgül Ö, Eyuboglu M, and Ider Y Z, “A New Technique for High Resolution Absolute Conductivity Imaging Using Magnetic Resonance-Electrical Impedance Tomography (MR-EIT),” SPIE Medical Imaging Conference, San Diego, 2001.

43.    Birgül Ö, Eyuboglu B M, and Ider Y Z, “Manyetik Rezonans Kullanilarak Yuksek Çozunurluklu Mutlak Empedans Goruntuleme,” ELECO Elektrik-Elektronik-Bilgisayar Muhendisligi Sempozyum ve Fuari, Bursa, November 2000.

44.    Eyuboglu B M, Birgül Ö, and Ider Y Z, “Magnetic Resonance – Electrical Impedance Tomography (MR-EIT), a New Technique for High Resolution Conductivity Imaging,” 2nd EPSRC Engineering Network Meeting: “Biomedical Applications of EIT”, University College, London, April 5-7 2000.

45.    Birgül Ö, Eyuboglu B M, and Ider Y Z, “Magnetic Resonance – Electrical Impedance Tomography (MR-EIT), a New Technique for High Resolution Conductivity Imaging”, Proc. of IEEE Engineering in Medicine and Biology, 21st Annual International Conference, CD-ROM, Atlanta, 1999.

46.    Birgül Ö, Ider Y Z, and Gencer N G, “MRI-EIT icin Duyarlilik Matrisinin Turetilmesi,” TMMOB Elektrik Muhendisleri Odasi Elektrik-Elektronik Bilgisayar Muhendisligi 7. Ulusal Kongresi Bildiri Kitabi, pp. 338-171, Ankara, 1997.

47.    Birgül Ö and Ider Y Z, “Electrical Impedance Tomography using Magnetic Field Generated by Internal Currents.” Proc. of IEEE Engineering in Medicine and Biology, 18th Annual International Conference, CD-ROM, Amsterdam, 1996

48.    Birgül Ö and Ider Y Z, “Use of Magnetic Field Generated by the Internal Distribution of Injected Currents for Electrical Impedance Tomography,” Proc. of IXth International Conference on Electrical Bio-Impedance in conjunction with European Concerted Action on Impedance Tomography, pp 418-414, Heidelberg, September 1995.

49.    Ider Y Z, Muftuler L T, and Birgül Ö, “Use of MRI for Measuring AC Internal Currents of EIT: A feasibility Study,” Proc. of IXth International Conference on Electrical Bio-Impedance in conjunction with European Concerted Action on Impedance Tomography, pp 420-421, Heidelberg, September 1995.