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3.3 Mueller Matrix Spectro-Polarimeter (MMSP) Characterization of Turbid Media Using Stokes and Mueller-Matrix Polarimetry Manzoor Ahmad A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physics Department of Physics and Applied Mathematics, Pakistan Institute of Engineering and Applied Sciences, Islamabad 45650, Pakistan. 2014 Dedicated to My Parents, Wife and sweet kids Muhammad Hassaan and Muhammad Abdullah, my inspirations ii Declaration I hereby declare that the work contained in this thesis and the intellectual content of this thesis are the product of my own work. This thesis has not been previously published in any form nor does it contain any verbatim of the published resources which could be treated as infringement of the international copyright law. I also declare that I do understand the terms ‘copyright’ and ‘plagiarism’, and that in case of any copyright violation or plagiarism found in this work, I will be held fully responsible of the consequences of any such violation. Signature : _______________________ Name: _____ Manzoor Ahmad___ Date: _______________________ Place: _______________________ iii Certificate This is to certify that the work contained in this thesis entitled: Characterization of turbid media using Stokes and Mueller-matrix polarimetry was carried out by Mr. Manzoor Ahmad, and in my opinion, it is fully adequate, in scope and quality, for the degree of Doctor in Philosophy. Dr Masroor Ikram Dr Shamaraz Firdous Supervisor Co-Supervisor Department of Physics and Applied National Institute of Laser and Mathematics, Pakistan Institute of Optoronics Engineering and Applied Sciences, Islamabad, Pakistan Islamabad, Pakistan Dr Shahid Qamar Head of Department, Department of Physics and Applied Mathematics, Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan iv Acknowledgments First and foremost, I would like to articulate-my-heartedly thanks to Almighty Allah for His blessings in achieving my goals. He has given me the courage, strength and patience during the completion of this research work. Having sincere teachers and cooperative friends during my PhD studies are all the blessings of Allah almighty. Next, I would like to pay deepest gratitude to my supervisor Dr Masroor Ikram whose dedication, enthusiasm, and devotion to work always inspired me. He has been a constant source of motivation and inspiration for me throughout my PhD research. I always found him generous in sharing his knowledge and wisdom. Working with him was a great learning experience. His kind attitude really made the difference. I would also like to thank my co-supervisor Dr Shamaraz Firdous (Principal Scientist at NILOP) for his consistent guidance and support during my research work. I would also like to pay my gratitude to Dr I. Alex Vitkin, who provided me the opportunity to work under his kind supervision at University of Toronto, during my six months research training sponsored by HEC through IRSAP program. He has given me full support in pursuing my scientific interests along with editing of manuscripts, and being so readily available. I am also very grateful to Dr Michael F. G. Wood, Sanaz Alali and Dr Anthony Kim for their cooperation during my research training, I learned much in a very short time. I am also very grateful to Dr. Malik Sajjad Mehmood, Dr. Ahmat Khurshid, and Dr. Saeed Ehsan for their advice, guidance, and invaluable comments during my PhD. I would also appreciate my friends, particularly, Dr. Anwar Hussain, Dr. Hafeezullah, Mr. Banat Gul Mr. Tahir, Mr. Ihtisham, Mr. Fazal Badshah, Mr. Zia-ur-Rahman, Mr. Attaullah Shah, Mr. Safdar Ali, Mr. Sohail, Mr. Zaheer Uddin, Mr. Rasid, Mr. Iftikhar, Mr. Abdul Basit and Mr. Atta-ur-Rahman for their cooperative and encouraging behavior during my stay at PIEAS. Most importantly, I am thankful to my parents, brother Zahoor Ahmad and sisters for their unconditional support and unmatchable love throughout my educational career which made all this possible. At the same time I proudly appreciate the extremely supporting role of my uncle Noor Zaman, and cousin Noor Rahman, they put me in pursuing educational career and supported throughout my studies. I am also thankful v to Mr. Khalil, Atiq, Habib, Ismail, Aftab, Safdar Ali and Munir for their support and motivation throughout my educational career The constant support that I received from wife since my very first day in the PIEAS is priceless. Without her support, hard work and dedication I could not have been able to complete this research. She through her patience, love and tolerance has motivated me at each step and turn of my research work. She in true meaning deserves a sweet and special ‘Thank You’!. Furthermore, I would also thank my in-laws for their unconditional support during my studies Finally, I would like to thank Higher Education Commission of Pakistan, for their financial support under the Indigenous 5000 PhD scholarship and International research support initiative program (IRSIP). vi List of Publications Publications from thesis 1. M. Ahmad, S. Alali, A. Kim, M. F. G. Wood, M. Ikram and I. A. Vitkin “Do different turbid media with matched bulk optical properties also exhibit similar polarization properties?”, Biomedical Optics Express 2 (12), 3248-3258 (2011). 2. S. Alali, M. Ahmad, A. Kim, N. Vurgun, M. F. G. Wood, I. A. Vitkin “Quantitative correlation of depolarization in biological tissues with their optical properties”, Journal of Biomedical Optics 17(4), 045004 (2012). 3. M. Ahmad, S. Ali, M. S. Mehmood, H. Ali, A. Khurshid, S. Firdous, S. Muhammad and M. Ikram “Ex vivo assessment of carbon tetrachloride (CCl4) induced chronic injury using polarized light spectroscopy”, Applied Spectroscopy 67 (12), 1382-1389 (2013). 4. S. Ali, M. Ahmad, S. Muhammad and M. Ikram “Ex-vivo study for assessment of liver injury induced by carbon tetrachloride by using Mueller matrix analysis” symposium on Biphotonics PIEAS, 19 March, 2013 (Poster Presentation). Other Publications 5. M. S. Mehmood, T. Yasin, M. S. Jahan, B. M. Walters, M. Ahmad & M. Ikram “EPR Study of γ-Irradiated UHMWPE Doped with Vitamin E: Assessment of Thermal Effects on the Organic Radicals During Vitamin E Diffusion”, Appl. Magn. Reson 44, 531–542(2013) 6. M. S. Mehmood, T. Yasin, M. S. Jahan, S. R. Mishra, B. M. Walters, M. Ahmad and M. Ikram “Assessment of residual radicals in ɤ sterilized shelf-aged UHMWPE stabilized with α-tocopherol”, Polym. Degrad. Stabil. , 98 1256e1263 (2013). 7. M. S. Mehmood, B. M. Walters, T. Yasin, M. Ahmad, M. S. Jahan, S. R. Mishra, and M. Ikram “Correlation of residual radical’s with three phase morphology of UHMWPE: Analysis for the dependence on heat involved during vitamin E diffusion”, Eur. Polym. J. 53, 13-21 (2014). vii Abstract In this thesis we present the application of polarized light to characterize porcine liver and phantoms with matched bulk optical properties, correlate the depolarization of tissues with transport albedo and evaluate the severity of liver injury. We have used the Mueller matrix analysis and polar decomposition method for extraction of individual polarization properties in this thesis. We investigated the polarization properties of thick samples (1 cm) of porcine liver, intralipid phantoms and polystyrene micro-spheres phantoms with matched bulk optical properties. Significant depolarization differences between porcine liver and phantoms are observed. Contrary to previously reported results for transmission geometry, our results show the enhanced polarization preservation for porcine liver tissues as compared to fabricated phantoms, particularly in the backscattering detection geometry. Moreover, the intralipid phantoms, polarization behavior is well- approximated with liver tissue as compared to the polystyrene sphere phantoms. Polarized light imaging was employed to investigate the correlation between light depolarization and transport albedo for six different isotropic and anisotropic thick tissues in both transmission and backscattering mode. Total, linear and circular depolarization rates were observed to be dependent on the measured transport albedos, where depolarization increases with transport albedo for all type of tissues independent of detection geometries. Higher depolarization rates were observed for anisotropic tissues as compared to isotropic ones for comparable transport albedos, demonstrating the birefringence-caused depolarization in addition to scattering-caused depolarization. The ex vivo severity assessment of different liver injuries induced by carbon tetra chloride (CCl4) was probed by polarized light in the visible spectral range. Less injured liver samples show higher linear retardance as compared to normal liver tissue, while worse injuries correspond to almost no retardance. Fibrosis is the likely cause at less severe injuries results in higher observed linear retardance whereas more serious injuries destroy any kind of organization and hence yield no retardance. Furthermore, total- linear- and circular-depolarizations were observed to decrease with increased injuries. Most likely causes include change of transport albedo and relative refractive index of extracellular matrix. viii Table of Contents Dedicated to ................................................................................................................. ii Declaration.................................................................................................................. iii Certificate ..................................................................................................................
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