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A STUDY OF SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY AND PHOTOACOUSTIC MICROSCOPY FOR BIOMETRIC AND BIOMEDICAL APPLICATIONS by Mengyang Liu A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Master of Science in Electrical and Computer Engineering Spring 2011 Copyright 2011 Mengyang Liu All Rights Reserved A STUDY OF SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY AND PHOTOACOUSTIC MICROSCOPY WITH BIOMETRIC AND BIOMEDICAL APPLICATIONS by Mengyang Liu Approved: __________________________________________________________ Takashi Buma, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Kenneth E. Barner, Ph.D. Chair of the Department of Electrical and Computer Engineering Approved: __________________________________________________________ Michael J. Chajes, Ph.D. Dean of the College of Engineering Approved: __________________________________________________________ Charles G. Riordan, Ph.D. Vice Provost for Graduate and Professional Education ACKNOWLEDGMENTS Here I want to thank for Dr. Buma‟s three years‟ training for me. Without his patient and detailed guidance and supervision I would not be able to do the work shown in this thesis. His working attitudes set up a model for me to follow as an engineer. His training makes me get closer, if any, to the requirements of being a competent researcher. Also I want to thank my parents, Liangchao‟s, Jian Gao‟s and Zhengyu Cao‟s families for backing me up in my years as a graduate student here. It is their help that makes my life easier and drives me back to the focus when my life is disturbed. My colleagues Ya Shu and Xinqing Guo shared a lot of happy moments with me in the small office. Foods in their places are always so good. I am so going to miss them after I leave the U.S. Special thanks are given to the President Yifang Wei and the two VicePresidents Ding Li and Xinquan Zhang of our co-ed fraternity along with my friends Jian Bai, Jiayin Wang, Jamall Willams, Duo Shen, Dr. Amardeep Dhanju, Dr. Xiaoxuan Meng and Erica Dang who are with me through all these years. iii TABLE OF CONTENTS LIST OF TABLES ......................................................................................................... vi LIST OF FIGURES ...................................................................................................... vii ABSTRACT .................................................................................................................. xi 1. INTRODUCTION ...................................................................................................... 1 1.1 Theory of Optical Coherence Tomography ............................................... 2 1.1.1 1.1.2 1.1.3 1.2 Spectral Domain Optical Coherence Tomography ........................ 3 Detection and Reconstruction Derived from Michelson Interferometer ................................................................................ 4 Resolution of SD-OCT System ..................................................... 6 Theory of Photoacoustic Microscopy ........................................................ 7 1.2.1 1.2.2 Optical Resolution Photoacoustic Microscopy ........................... 11 Spectroscopic Photoacoustic Microscopy ................................... 12 2. ECCRINE GLAND MAPPING USING SD-OCT ................................................... 13 2.1 OCT in Biometrics Using Human Fingertips .......................................... 13 2.1.1 2.1.2 2.2 Human Sample Selection and Experiments ................................ 14 Dummy Fingertip Preparation ..................................................... 14 SD-OCT System ...................................................................................... 16 2.2.1 2.2.2 2.2.3 2.2.4 Setup and Parameters .................................................................. 16 System Synchronization and Data Acquisition ........................... 17 Spectrometer Calibration ............................................................. 19 Post Processing ............................................................................ 23 2.2.4.1 2.2.4.2 B-Mode Image Reconstruction ..................................... 23 Fingertip Touchless Scan and Triple Layer Information Retrieval ................................................... 25 iv 2.3 2.4 Experiment Results .................................................................................. 26 Conclusion and Future Work................................................................... 31 3. PHOTOACOUSTIC MICROSCOPY ...................................................................... 33 3.1 PAM and SD-OCT in Osteoarthritis Studies........................................... 33 3.1.1 3.1.2 3.1.3 3.1.4 3.1.5 3.2 Spectroscopic PAM Using a Supercontinuum Source ............................ 43 3.2.1 3.2.2 3.2.3 3.3 Optical Imaging for OA ............................................................... 35 India Ink Staining ........................................................................ 37 Collagenase Treatment for the Sample........................................ 38 Results and Discussion ................................................................ 38 Conclusions ................................................................................. 42 From OR-PAM to Spectroscopic PAM....................................... 43 Materials and Methods ................................................................ 44 Results and Discussion ................................................................ 47 Wavelength Agile Spectroscopic PAM ................................................... 49 3.3.1 3.3.2 3.3.3 3.3.4 Tunable Wavelength Filter .......................................................... 49 Data Acquisition and System Synchronization ........................... 50 Results and Discussion ................................................................ 51 Conclusions ................................................................................. 53 4. FUTURE WORK ..................................................................................................... 54 4.1 4.2 Spectrophotometry for Mixed Dye Solutions .......................................... 54 Stokes Source OR-PAM with Fast Raster Scanning ............................... 58 BIBLIOGRPAHY ......................................................................................................... 61 APPENDIX: HUMAN RESEARCH APPROVAL FORM AND HUMAN SUBJECT CONSENT FORMS ....................................................................... 66 v LIST OF TABLES Table 2.1 Repeatability of Eccrine Glands in Different Subjects Tested in Different Days ......................................................................................... 30 vi LIST OF FIGURES Figure 1.1 Typical configuration of an SD-OCT system ........................................... 3 Figure 1.2 Schematic of a Michelson Interferometer ................................................ 5 Figure 1.3 Schematic of a Confocal Dark Field PAM System .................................. 8 Figure 1.4 Schematic of an OR-PAM system. a, condencer lens; b, pinhole; c, microscope objective; d, ultrasonic transducer; e, correcting lens; f, isosceles prisms; g, acoustic lens; h, silicon oil [5] .................... 12 Figure 2.1 Photograph of a; live finger; b, plastic mold made from that live finger; c, the transparent dummy finger; d, the scattering dummy finger. ..................................................................................................... 15 Figure 2.2 Schematic of the SD-OCT System ......................................................... 16 Figure 2.3 The function generator is used for the Servo Driver and the CCD camera. The triangular waveform is used to control the GM; the Sync channel of the function generator is used as the camera‟s frame trigger. .......................................................................................... 18 Figure 2.4 Schematic of the Spectrometer ............................................................... 19 Figure 2.5 Interference fringe recorded by the uncalibrated spectrometer .............. 22 Figure 2.6 The power spectra of the signals. a, before calibration; b, after calibration ............................................................................................... 23 Figure 2.7 B-Mode image of a fingertip .................................................................. 24 Figure 2.8 B-Mode image showing the surface layer (surface fingerprint) and papillary layer (internal fingerprint). The torturous ducts in between these two layers are eccrine glands. Integration between the surface and papillary layers gives the eccrine gland map, which is the same as pore distribution – a Level 3 fingerprint identification feature............................................................................... 26 vii Figure 2.9 Upper left: B-Mode image (x-z plane) of a live fingertip showing the stratum corneum, eccrine glands and the papillary layer; lower left: B-Mode image of the artificial fingertip shows no internal banding structure and no eccrine gland ducts. The two B-Mode images are displayed over 0.6 × 3.9 mm field of view and 30 dB dynamic range in gray scale. Upper right: 3D display of the digitally straightened live finger; lower right: volumetric display of the fake finger whose surface resembles with that of the real fingertip. The two volumetric images are shown over a 4.6 × 4.0 × 0.5 mm region......................................................................................... 27 Figure 2.10 (a)-(c) the top, eccrine gland and papillary layers of the thumb; (d)-(f) the three layers extracted at the same positions or ranges as those in (a)-(c) for the dummy of the thumb; (g)-(i) the top, eccrine gland and papillary layers of the index finger; (j)-(l) the three layers extracted at the same positions or ranges as those in (g)-(i) for the dummy of the index finger; (m)-(o) the top, eccrine gland and papillary layers of the middle finger; (p)-(r) the three layers extracted at the same positions or ranges as those in (m)-(o) for the dummy of the middle finger. ...................................................... 29 Figure 2.11 a, topography of the surface fingerprint; b, topography of the internal fingerprint; c, triple-layer display of the volumetric fingertip image; d, reconstructed 3D surface without digital straightening shows the feature of touchless scan. ................................. 32 Figure 3.1 Schematic of the OR-PAM system for cartilage imaging ...................... 36 Figure 3.2 a, photo showing the treated cartilage submerged in PBS solution; b, SD-OCT image of the untreated cartilage showing an intact region; c, PAM image of the same region as in B; d, SD-OCT image for the untreated cartilage showing a small cleft in the surface; e, PAM image reveals the depth and shape of the fissure in d; f, SD-OCT image showing the 13-hour treated CIA cartilage, note that the smooth gradual change in depth as in b & c is now replaced by a ~10 µm bright surface layer and dark region beneath; g, the PAM image for the same region as shown in f. ............. 40 Figure 3.3 3D volumetric display using SD-OCT showing the isosurfaces with 71, 77 and 83 dB intensity. Isocaps are added and isonormals calculated. ............................................................................................... 41 viii Figure 3.4 3D volumetric display using PAM showing the isosurfaces with 23, -20 and -17 dB intensity. Isocaps are added and isonormals calculated. ............................................................................................... 42 Figure 3.5 a, Q-switched microchip Nd:YAG laser emits 1064 nm pulses coupled into and progagate through 7 m PCF (λzdw = 1040 nm) to generate a supercontinuum. The PCX collimates the microchip laser output. An asperic lens (AL) focuses the 1064 nm pulses into the PCF. A microscope objective (MO) collimates the supercontinuum output; b, The spectrum of the supercontinuum measured by an optical spectrum analyzer; c, A photo showing the dispersed supercontinuum on a piece of white paper. ............................ 45 Figure 3.6 Prism-based monochromator, where a concave mirror collimates the dispersed light. .................................................................................. 46 Figure 3.7 Schematic of the OR-PAM system featuring a 25 MHz transducer....... 47 Figure 3.8 Multi-wavelength images of black, blue, green and red ink spots (left to right). All images displayed over a 1.8 × 5.4 mm range in 40 dB scale. The spectrally processed image clearly identifies the four ink regions. ..................................................................................... 48 Figure 3.9 The automatic tunable wavelength filter. One end of the lever is fastened on top of the wave driver. The other end of the lever is connected to the mask, with a tapered slit going in the diagonal direction. A supercontinuum spectrum is drawn over the mask to demonstrate the mechanism of how bandwidth selection is performed. .............................................................................................. 50 Figure 3.10 Ink spot images for four ink spots (red, green, blue black from left to right). Sequential bandwidths see 20 nm increments in their central wavelength. Images are displayed over 8.4 × 1 mm region in 10 dB range gray scale. ...................................................................... 52 Figure 3.11 The fiber phantom taken at 570 nm and 690 nm with the spectrally processed image in RGB display. .......................................... 53 Figure 4.1 The Spectrophotometry System with a Separate Display of the Cuvette ................................................................................................... 56 ix Figure 4.2 Extinction coefficients calculated from the spectrophotometry data for mixtures made of red and blue food dyes with different ratios. ...................................................................................................... 57 Figure 4.3 USAF resolution target imaged by Stokes source OR-PAM system. All elements in Group 4, 5, 6 and 7 are in the scanning range. From the vertical bars we can see that the interdigitating error has not been fully removed. ........................................................... 59 x ABSTRACT Optical coherence tomography (OCT) has been widely used in biomedical imaging ever since its introduction. However, the application of OCT for biometrics is relatively new. This thesis demonstrates the feasibility of applying a spectral domain optical coherence tomography (SD-OCT) system to fingertip biometric information retrieval. The results show that SD-OCT is capable of retrieving Level 3 fingertip information. Combined with traditional Level 1 and 2 fingerprint information, which can also be easily acquired by SD-OCT, the proposed application shows potential for ultra-secure scenarios. Photoacoustic microscopy (PAM) is another imaging modality gaining considerable interest in the past decade. Different than OCT, it employs ultrasound detection for optically induced thermal expansion in tissue. Bovine articulate cartilage samples are imaged with a single wavelength PAM system using India ink as a contrast agent. The same samples were also imaged with SD-OCT. Image analysis shows that PAM produces excellent contrast between intact and fibrillated regions in cartilage while SD-OCT visualizes topological changes with fine spatial resolution. A spectroscopic PAM system is also developed using a tunable source based on supercontinuum generation in a photonic crystal fiber. Imaging experiments of tissue phantoms demonstrate the ability to differentiate various chromophores with unique absorption characteristics. Another spectroscopic PAM system is currently being developed, where the tunable source is based on stimulated Raman scattering. This xi new system is being studied and some preliminary results are given to demonstrate its advantages over the supercontinuum approach. xii Chapter 1 INTRODUCTION Optical imaging, with its strengths in fast acquisition, nonionizing radiation within human tissue and other functional properties, has been heavily studied in the past few decades and continuously applied clinically. Among them, optical coherence tomography (OCT) and photoacoustic microscopy (PAM) are two relatively novel imaging modalities with more and more applications in both clinics and research. OCT is analogous to conventional B Mode ultrasound imaging in principle and in the sense of its non-invasive, high resolution, cross-sectional imaging features. The difference lies in the use of a broadband light source and the detection of the backscattered light instead of ultrasound pulses which dramatically boosts the spatial resolution of OCT to be in the range of 1 ~ 10 µm that is about 100 times better than the conventional ultrasound imaging [1, 2]. The evolvement of this modality sees a great leap from time domain optical coherence tomography (TD-OCT) to spectral domain optical coherence (SD-OCT) in the sense that the time needed for imaging is greatly reduced [3]. Other sub-modalities of OCT such as full field OCT (FF-OCT), polarization sensitive OCT (PS-OCT), Doppler OCT, Spectroscopic OCT etc. are developed henceforth for different applications and bearing with them unique advantages. PAM is based on the photoacoustic effect, namely: an object is irradiated by a short-pulsed laser beam; the deposition of the laser pulse energy into the object is 1 partially converted into heat; the heat will cause thermoelastic expansion of the object; this thermoelastic expansion will induce the propagation of a ultrasound wave, which is referred to as the photoacoustic wave [1]. This photoacoustic wave can be easily detected using commercially available ultrasound transducers. A raster scan of the photoacoustic wave generated in the object will generate a 3D image with unprecedented contrast and good spatial resolution for the microstructures, hence the name photoacoustic microscopy. In order to improve the resolution of PAM beyond the limitation set by the focal spot size of the transducer which is determined by the frequency response of the transducer without having to trade it off with the increased tissue absorption when higher ultrasound frequency is involved [4], optical resolution PAM (OR-PAM) is proposed and developed, whose transverse spatial resolution is determined by the focal spot size of the illuminating laser beam [5, 6]. Dual wavelengths [7, 8] and multi-wavelengths [9] laser beam as the excitation sources for PAM have demonstrated the feasibility of spectroscopic PAM. This thesis deals with a SD-OCT system which is applied in both biometric research and biomedical imaging along with several PAM systems used for phantom and cartilage imaging. 1.1 Theory of Optical Coherence Tomography The basics of OCT employ a Michelson Interferometer. A broadband light source illuminate the interferometer, then the light is split in two: one serves as a reference beam while the other one serves as the sample illumination beam. The reflected beams from both arms are combined at the beam splitter and sent to a photodiode for detection. The interference fringes can be observed when the optical pathlengths in the sample arm and the reference arm match. In a TD-OCT system, 2 depth information is acquired by scanning the mirror in the reference arm and the axial resolution determined by the coherence length of the light source being used. Due to the limitation for mechanically scanning the mirror and the depth samples needed for a typical A-line of OCT, TD-OCT is excessively slow in many practical applications [10, 11]. Therefore, SD-OCT is developed with faster acquisition rate, which is introduced below. 1.1.1 Figure 1.1 Spectral Domain Optical Coherence Tomography Typical configuration of an SD-OCT system The spectrometer in the sample arm detects the spectral fringes in the interferometer output, which is inversely proportional to the sample depth. An A-line in the sample can be simply reconstructed by taking a Fourier transform of a calibrated and back ground subtracted spectrum fringe. The acquisition speed, instead of being limited by the mechanical scanning of the reference mirror in TD-OCT, is limited by the frame rate of the spectrometer in 3 SD-OCT. With current commercially available charge-coupled device (CCD) cameras, the line scan rate can easily reach tens of kHz [11]. In Fig. 1.1, the broadband laser is used as the light source for the Michelson interferometer. A 50:50 fiber coupler is generally used to split the light into the reference arm and the sample arm. Before the static silver mirror in the reference arm from which the light will be reflected, a neutral density (ND) filter may be used to adjust the light intensity detected by the CCD camera in case it cannot fall into a proper range without the ND filter. A galvanometer controlled scanning mirror is applied in the sample arm for one dimensional scanning necessary to form a B-Scan image. The spectrometer of the SD-OCT system is composed of a diffraction grating, an achromatic doublet and a CCD camera. The CCD camera will capture the interference fringes, converting them to digital form and sending them to a PC with a data acquisition (DAQ) board for data acquisition. The spectrometer calibration from linear wavelength space to linear k space and the image reconstruction are performed by specific software programs after data acquisition. 1.1.2 Detection and Reconstruction Derived from Michelson Interferometer Denote as the electric field at the laser output, pathlength from the laser output to the beam splitter, the reference arm mirror to the beam splitter, sample arm mirror to the beam splitter and as the optical as the optical pathlength from as the optical pathlength from the as the optical pathlength from the beam splitter to the detector, which is a photodiode detector as shown in Fig. 1.2. The electric field at the detector can be expressed as: 4 1.1 Figure 1.2 Schematic of a Michelson Interferometer The optical intensity incident upon the detector can be expressed by: 1.2 where c is the speed of light and n is the refractive index. Substitute Eq. 1.1 into Eq. 1.2 and simplify the expression we can get: 1.3 where is the intensity of the optical source and the multiplier in the right part of Eq. 1.3 is the desired interference term with ∆z being the pathlength difference between the reference arm and the sample arm. 5 In an SD-OCT system where a broadband laser source is used, we can express as a function of k, so that: 1.4 Since in reality, we do not have a perfect 50:50 beam splitter, also there is no 100% reflection, the actual optical intensity reaching the detector is: 1.5 where and are the reference arm and sample arm reflectivity, respectively, assuming the two reflectivities do not depend on k and omitting the detector responsivity. Typically we have . Use this inequality and take the inverse Fourier transform of Eq. 1.5 we can get: 1.6 Generally the camera will detect the fringe in λ space instead of in k space. A conversion and calibration is introduced in detail in Chapter 2. The reconstruction of an A-line is performed using Eq. 1.6 after background subtraction. Note that the last two terms in Eq. 1.6 indicating one real image and a mirror image. Special care is taken when the actual A-line is displayed. Compiling consecutive A-lines in the same cross section comprises a B-Scan image [12]. 1.1.3 Resolution of SD-OCT System Assuming the light source as a Gaussian beam with as the full width half maximum (FWHM) of the Gaussian spectrum, the depth information 6 of the sample, which is the inverse Fourier transform of the backscattered interference signal in k space, has the following relation: 1.7 The FWHM of can be easily calculated, which is: 1.8 Taking into consideration that and the backscattered light travels back and forth in the sample, we have the expression for the axial resolution as the following: 1.9 Instead of depending on the coherence length of the light source which is the case for the axial resolution, the transverse resolution of an SD-OCT system, using beam focusing theory, is a function of the focused probe beam waist beam waist radius of the probe beam before focusing , the minimum , the focal length of the sample arm lens F and the distance between the beam waist of the unfocused probe beam and the focal plane of the sample plane z, which is generalized in the following expression: 1.10 1.2 Theory of Photoacoustic Microscopy PAM, being a hybrid biomedical imaging modality based on the photoacoustic effect, combines the advantages of optical absorption contrast with 7 ultrasonic spatial resolution for deep imaging in optical diffusive or quasi-diffusive regime. It transcends the current depth limit of high resolution optical imaging modalities while maintaining the depth-to-resolution ratio to be greater than 100 [6]. At the same time, PAM is safe for human subjects and hence suitable for both clinical and basic research purposes. A reflection-mode confocal PAM system such as the one given in Fig. 1.3 consists of dark-field pulsed-laser illumination and high numerical aperture (NA) ultrasound detection [1]. Figure 1.3 Schematic of a Confocal Dark Field PAM System The interference caused by strong photoacoustic signals from superficial structures is minimized by dark-field illumination and a high lateral resolution is 8 provided by using a high NA acoustic lens. High axial resolution of about 15 µm can be achieved using a broadband ultrasonic detection system [13]. After the laser beam is collimated, it is incident upon the axicon lens. The donut shaped laser beam is formed after the axicon lens before it is focused by the focusing lens which is coaxially aligned with the ultrasound transducer. The focused beam hit the sample and following the laser pulse energy deposition, heat conversion, thermoelastic expansion and ultrasonic pulse generation, the ultrasound pulse is detected by the spherical ultrasound transducer. The signal is transmitted to an amplifier, a filter and recorded by DAQ board connected to a computer. The signal recorded as a function of time can be easily converted into an A-line based on the sound velocity in soft tissue which is 1.54 mm/µs. 3D images can be reconstructed by raster scanning of the probe in the horizontal plane of the system [1]. In order to interpret the mechanism of the photoacoustic effect quantitatively, the concept of the thermal relaxation time and the stress relaxation time are given below respectively: 1.11 1.12 where is the thermal diffusivity ( heated region and ); is the characteristic dimension of the is the speed of sound. Suppose the laser pulse width is much shorter than both the thermal relaxation time and the stress relaxation time, the excitation is said to be in both thermal confinement and stress confinement. In this case, the local pressure rise immediately after the laser pulse can be expressed as: 9 1.13 where κ is the isothermal compressibility (~5×10-10 Pa-1 for water or soft tissue); β is the thermal coefficient of volume expansion (K-1); T is the temperature change (K); Cv is the heat capacity at constant volume (J/(kg K)); ρ is the mass density (kg/m3); Ae is the specific optical absorption (J/m3) and ηth is the heat conversion percentage. If we define the dimensionless Grueneisen parameter as: 1.14 and use the empirical formula of Γ in water or diluted aqueous solutions: 1.15 where T0 is in the unit of Celsius degree, Eq. 1.13 can be rewritten as: 1.16 where µa is the optical absorption coefficient and F is the optical fluence (J/cm2). By solving the general photoacoustic equation: 1.17 with r and t denoting the position and time, respectively, we can get to the expression of the response of a small sphere to a finite-duration excitation pulse as: 1.18 where S depicts the excitation pulse. From Eq. 1.18 we can see that the photoacoustic pressure is proportional to the time derivative of the excitation pulse [1]. 10 1.2.1 Optical Resolution Photoacoustic Microscopy Traditional PAM is good enough for many applications with a lateral resolution about several 10s of micrometer, but in the situation when finer resolution is required, such as imaging of capillaries whose diameter is 4~9 µm [14], better resolution is needed. An intuitive choice is to use ultrasound transducers with very high response frequencies, corresponding to smaller focal spot size and better later resolution. But the absorption coefficient α of a material is generally dependent on frequency f with a good model for this dependency given below: 1.19 where a and b are two constants with b slightly greater than 1 in biological tissues [15]. If the lateral resolution is dependent on frequency, we can tell from Eq. 1.19 that the absorption will render the imaging depth of high resolution PAM very shallow. Simple calculation reveals that for a 5 µm lateral resolution, an ultrasound transducer with higher than 300 MHz central frequency is needed, and this high frequency makes the penetration depth only about 100 µm [5]. OR-PAM is developed to overcome the ultrasonically provided lateral resolution issue. In an OR-PAM system given in Fig. 1.4 [5], optical focusing can achieve lateral resolutions of several micrometers. Ultrasonic focusing is achieved by an acoustic lens. Isosceles prisms are used to align the laser beam illumination and ultrasonic detection orthogonally since in this schematic the photoacoustic wave is reflected 90°before it is recorded by the ultrasound transducer. 11 Figure 1.4 Schematic of an OR-PAM system. a, condencer lens; b, pinhole; c, microscope objective; d, ultrasonic transducer; e, correcting lens; f, isosceles prisms; g, acoustic lens; h, silicon oil [5] Raster scanning over the sample and proper data processing can give 3D volumetric images or maximum amplitude projection (MAP) images [5]. 1.2.2 Spectroscopic Photoacoustic Microscopy With the contrast of PAM being produced by the endogenous absorption of absorbers within the tissue, different kinds of absorbers or the same kind of absorbers in different physiological statuses tend to give different photoacoustic responses for a certain frequency of light illumination. Thus in Eq. 1.16 the optical absorption coefficient is a function of wavelength. Therefore, when dual wavelengths or multi-wavelengths are applied for the same sample during a PAM experiment, we can reconstruct from the localized photoacoustic (PA) signal the different components or the ratio of them within the sample [8, 9, 16]. 12 Chapter 2 ECCRINE GLAND MAPPING USING SD-OCT OCT has been widely applied in biomedical studies ever since its introduction in the early 1990s. Its application in biometrics study is relatively new. This chapter mainly demonstrates the possibility of applying SD-OCT in the biometrics along with detailed description of the system and the related software programs. 2.1 OCT in Biometrics Using Human Fingertips Fingerprint identification is the most widely used biometric identification method [17, 18]. But this widely applied method showed its unreliability to counterfeited fingers using materials available in grocery and craft stores [19]. The reason for the unreliability is mainly due to the 2D mechanism of currently commercially available automatic fingerprint identification systems (AFIS) [20]. Considering the fine structure of the integumentary system of finger pads and the mechanism of OCT, it can be applied for authenticating purposes using 3D information of the fingertip. In recent years, efforts have been made using TD-OCT to discriminate artificial fingerprint from genuine fingerprint in the 1310 nm imaging window [18, 21, 22]. The use of the dermoepidermal junction undulation as the new fingerprint pattern retrievable by OCT is proven to provide securer approach to biometric identification [17]. But a potential problem of solely relying on this papillary 13 layer is that as one ages, the dermal papillae tend to flatten and the papillary layer undulation may appear less pronounced [17, 23]. All the aforementioned efforts are not using the Level 3 fingerprint information, which is also easily retrievable by using OCT. Thus, in this thesis an SDOCT system is used to accurately map the distribution of eccrine glands within the fingertip [24]. Combining this Level 3 eccrine gland duct distribution information with the surface and inner fingerprint, a triple-layer biometric identification method is realized. 2.1.1 Human Sample Selection and Experiments I myself and two other fellow research assistants are enrolled in this study. Every enrollee signed the consent form for this project and an IRB review approved this study under expedited review category. Experiment data are safely saved and enrollees are referred to as Subject # 1, 2 and 3 to protect privacy. To achieve statistically convincing results and to show repeatability, experiments were performed in different days for the same finger of the same subject. Also multiple fingers of the same subject were compared to test the applicability of this method on different fingers of the same subject. 2.1.2 Dummy Fingertip Preparation Spoofing proof of this proposed method can only be tested when fake fingers are used. Plastic (Friendly Plastic, AMACO/Brent Ceramic & Craft Materials) is used for making the mold of dummy fingertips. When making the mold, the plastic is firstly heated till it is transparent and soft. The live finger is pushed firmly into the 14 plastic for several minutes when the temperature of the plastic dropped to about 60°C. The live finger is then carefully dispatched from the plastic to form the mold. Polydimethylsiloxane (PDMS) (Sylgard 184, Dow Corning corp.) is used for making the transparent fake finger while a mixture of PDMS with titanium oxide (Sigma Aldrich) with a 100:1 mass ratio is used for making scattering fake fingers. When the mold is cooled down to room temperature, PDMS or PDMS/ TiO2 mixture is poured into the mold. Dummy fingers are peeled off carefully from the mold about one day later after they are solidified. Fig. 2.1 shows the photographs of a live finger, the plastic mold, the transparent dummy and the scattering dummy, respectively. Figure 2.1 Photograph of a; live finger; b, plastic mold made from that live finger; c, the transparent dummy finger; d, the scattering dummy finger. The live fingers and their corresponding dummy fingers are imaged for the same registered region to compare the difference. For more accurate results, only the scattering dummy fingers are used in the actual comparison. 15 2.2 SD-OCT System 2.2.1 Setup and Parameters The home-built fiber-optic SD-OCT system is sketched in Fig. 2.2. The Ti:Sapphire oscillator (KM Labs) emits 60 nm bandwidth pulses with center wavelength at 830 nm. Measured at the sample arm cube entrance, the average power is 14 mW. A 12 bit 2048 pixel line scan camera (CL2014-SM2, Atmel) is used for the home-made spectrometer with 29 kHz line scan rate and 30 µs integration time. Figure 2.2 Schematic of the SD-OCT System The x-axis scanning range determined by the galvanometer scanning mirror (GM) is 6.6 mm in this experiment and the depth range was calculated to be 3.4 mm although the effective depth range is within 2 mm. Each B-Mode (x-z plane) frame consists of 2048 A-lines. The y-axis scanning is achieved by using a stepper 16 motor (T-LA13A, Zaber Technologies). This stepper motor translates the sample arm cube in 20 µm increments over a 4.04 mm range, corresponding to 202 frames for each individual data set. The axial resolution of the system is experimentally tested by the 6 dB points to be 7.0 µm and the lateral resolution about 10 µm. 2.2.2 System Synchronization and Data Acquisition The acquisition is through National Instrument Image Acquisition (NIIMAQ) Board (PCI-1426), which serves as the interface between the PC and the camera. The camera is connected with PCI-1426 by the Camera Link cable, which has two MDR 26-pin connectors that can provide reliable high-frequency transfer rates. The CCD camera is set in free run mode in each cross sectional frame acquisition. The GM (6210H, Cambridge Technology) is controlled by a Servo Driver. The Servo Driver is connected to a function generator (33220A, Agilent) to provide the GM with a certain frequency and amplitude (in degrees). The angle of the GM is directly proportional to the voltage applied on the Servo Driver. The sign of the angle, with respect to the 0 volt position, agrees with the sign of the voltage applied on the Servo Driver. The successfulness of the acquisition depends on the proper synchronization of the components of the SD-OCT system. Namely between the CCD camera frame trigger, the y-axis stepper motor and the GM Servo Driver. The following sequence is used for this system: 1. Initialization of the NI-IMAQ board and the stepper motor; 2. Pose the GM to one end of the range; 3. Same trigger sent for GM Servo Driver and the CCD camera frame grabber; 17 4. One B-Mode image scanned and data stored in PC memory; 5. GM retreats to the starting position; stepper motor moves one increment; data streamed to PC hard drive; 6. Go to step 3 or stop acquisition. Since the angle of the GM is proportional to the voltage applied on the Servo Driver, the function generator sending a triangular waveform is set to work in burst mode with 5 Hz frequency, 7 volts peak-to-peak amplitude and -90°starting phase, which is sketched in Fig. 2.3: Figure 2.3 The function generator is used for the Servo Driver and the CCD camera. The triangular waveform is used to control the GM; the Sync channel of the function generator is used as the camera’s frame trigger. A LabVIEW project is made for this SD-OCT system. One of the VIs in this project performs the function of acquisition and synchronization. This VI enables the system to work in three modes: 1. Don‟t Save Data: used to test whether every component of this system is working properly. No data is saved. 2. Save Data without Background Subtraction: the program will save data to the specific file name defined by the user. No 18 background subtraction is performed. Data is streamed continuously into one binary file using data streaming technique. 3. Save Data with Background Subtraction: user need to block the sample arm first for this VI to store a background frame. After the background frame is captured, the actual data streamed into the hard drive will have undergone background subtraction already. All synchronization issues are taken care by this VI. Users only need to adjust the control values and select a proper mode for the experiments. 2.2.3 Spectrometer Calibration The schematic of the home-made spectrometer is given in Fig. 2.4: Figure 2.4 Schematic of the Spectrometer 19 For the SD-OCT system, back-reflected light from both the sample arm and the reference arm will be incident upon a spectrometer after they interfere in the optical fiber Michelson interferometer. Based on the mechanism of the spectrometer, we know that the output beam from the interferometer is separated by wavelength . So the distribution of λ on the CCD is according to the grating equation proportional to sinθ instead of a linear distribution. From the theory of SD-OCT we know that for a certain depth in the sample, the signal to be detected is proportional to , which means that we are expecting a signal linearly scaled in the k space. In order to properly process the data and perform the inverse Fourier transform for the acquired signal, it is necessary for us to use an algorithm to convert the signal from wavelength scale to linear k space. A wavelength independent method is used for this conversion [25]. A gold mirror is placed in the sample arm at the focal plane of the objective focusing lens. The reference arm beam pathlength is adjusted so that the zero-pathlength-difference plane coincides with the objective focusing lens's focal plane. Then shorten (lengthen) the reference arm beam pathlength to manually set the pathlength difference, hence the interferometry pattern on the CCD camera. The GM is temporarily disabled to make sure that the laser beam is exactly incident upon the same point on the gold mirror. The data that we recorded in fact has an ideal sinusoidal pattern taken the frequency as the horizontal axis, but because this signal is recorded in the λ space, the data will look like a nonlinear quasi-sinusoidal pattern. In order to convert the signal, we can first detect the phase of the signal. To do the phase detection, we first perform fast Fourier transform (FFT) to the original data. In order to get the complex form of the data, we only keep the positive frequency 20 part. But by doing this we will lose half of the samples when the spectrum is transformed back by inverse Fourier transform, thus zero-padding is used in frequency domain to compensate for the loss of samples. When the frequency signal is transformed back, we get the complex form of the original signal. The phase information is included in the angle of the complex signal. Now, we use the array of phase values as the x-axis; use the index of the pixel as the y-axis; we can perform a polynomial curve fitting and get the equation of n(Φ), where n is the pixel index number and Φ is phase. Divide Φ into equal distances according to the total index number, then we can find the indices (now expressed as decimals) that correspond to equal phase increment. That is to say: using the angle information, firstly we get , where i is the index number and get the inverse function of ( . Then via polynomial curve fitting we , which is . Let have a unit increment ), we will be able to get a new set of ''index'' (we can call it to distinguish it from the integer index in order ), which is actually decimals and correspond to equal phase increment. Save the new index set get directly is . In the future, after the data acquisition, what we . Via interpolation, we can easily get . Save the array which is in effect a signal expressed in linear k space. This method is free of spectrometer wavelength calibration. It can be applied to whatever wavelength bandwidth being used. The manually set pathlength difference of the Michelson interferometer will not affect the final result of this method, since it only contributes to the first order term of . Both LabVIEW and MATLAB programs were made to perform this spectrometer calibration. Following the calibration results are given by LabVIEW 21 processing and the raw data is used when the pathlength difference is set to be 400 μm. CCD array size is 2048. Fig. 2.5 shows the raw data after averaging: Figure 2.5 Interference fringe recorded by the uncalibrated spectrometer Fig. 2.6 compares the power spectra of the raw data before and after spectrometer calibration: 22 Figure 2.6 The power spectra of the signals. a, before calibration; b, after calibration From Fig. 2.6 it is clearly shown that after this wavelength independent spectrometer calibration the spectrum is much more accurate. 2.2.4 Post Processing 2.2.4.1 B-Mode Image Reconstruction Both LabVIEW VIs and MATLAB programs are prepared for the post processing of the SD-OCT data to reconstruct B-Mode images. The program generally deals with background subtraction first, then the predetermined “new” index value for the spectrometer calibration is applied to the data through interpolation to get the λ- to k-space conversion done. FFT is used to generate the B-Mode image and the image may undergo 2D interpolation, A-line compression to enhance image quality. A Ronchi Pattern (Edmund Optics) is imaged in order to experimentally determine the lateral scanning range. The axial range and axial increment between consecutive indices in the reconstructed B-Mode images are acquired by placing a mirror in the 23 sample arm and manually adjust the height of this mirror to a set of predetermined values. The reconstruction programs compensate for the increments in both dimensions in the B-Mode image automatically when interpolations with different orders are used. Fig. 2.7 shows a test image using my left hand index fingertip. Contrast improvement is accomplished both by properly selecting the dynamic range of the gray scale display and by A-line compression – in this figure it is by grouping every four neighboring A-lines and averaging them, which also suppresses the random noise in the reconstructed image. Figure 2.7 B-Mode image of a fingertip 24 2.2.4.2 Fingertip Touchless Scan and Triple Layer Information Retrieval A special holder is designed to secure the subjects‟ fingers during scanning. The movement of the finger scanned in free space is reduced by using this holder. The frame rate is set to 1 Hz which is experimentally determined to be a suitable value considering the line scan rate of the CCD camera and the subject movement during scan. As is shown in Fig. 2.7, the fingertip is scanned in air; therefore the natural curvature is preserved. Though this touchless scan has potential for even finer details which can be used for biometric purposes, in order to effectively retrieve the surface fingerprint, eccrine gland duct map and the internal fingerprint, every B-Mode image is digitally straightened to make the ridge-ravine undulating on a horizontal line. This digital straightening is performed in the following manner: Find and save the vertical indices of the maximum values in the BMode images. This corresponds to the stratum corneum position of the epidermis of the fingertip. Perform 3rd order polynomial fitting for the indices, basically serving as a low pass filter. Save the vertical indices of the fitted curve. Using the indices acquired in step 2 in the original B-Mode image. Select a certain depth range above the “new” indices and another certain depth range below the “new” indices. The selected region, after realignment, is a digitally straightened BMode image with fingerprint fringe undulation in a fixed horizontal value. After the overall curvature of the stratum corneum is shifted in every BMode image, these shifted cross sectional images are combined into one 3D matrix, containing the volumetric information of the fingertip. Integration over the top 32.5 µm of the volumetric matrix gives the surface fingerprint. Integration over the 166.7 µm range from 100 µm under the stratum corneum surface gives the eccrine gland 25 layer. Finally, integration over the 149.2 µm range from 290 µm under the stratum corneum surface gives the internal fingerprint pattern. Because the laser pulse intensity incident on the sample in the same cross section may not be the same due to the focusing lens used in the sample arm cube, a background x-y plane is generated to normalize the eccrine gland layer display. 2.3 Experiment Results Fig. 2.8 gives a B-Mode fingertip cross section image showing the tortuous eccrine gland ducts distributed in the epidermis. The bright surface layer is the stratum corneum and the internal ridge-furrow undulation is the dermoepidermal junction, which is taken as the internal fingerprint pattern. Figure 2.8 B-Mode image showing the surface layer (surface fingerprint) and papillary layer (internal fingerprint). The torturous ducts in between these two layers are eccrine glands. Integration between the surface and papillary layers gives the eccrine gland map, which is the same as pore distribution – a Level 3 fingerprint identification feature. To compare the differences between a dummy finger and its live counterpart, both B-Mode images and their 3D rendering are given in Fig. 2.9. Note that the 3D volumetric display is after the digital straightening. 26 Figure 2.9 Upper left: B-Mode image (x-z plane) of a live fingertip showing the stratum corneum, eccrine glands and the papillary layer; lower left: B-Mode image of the artificial fingertip shows no internal banding structure and no eccrine gland ducts. The two B-Mode images are displayed over 0.6 × 3.9 mm field of view and 30 dB dynamic range in gray scale. Upper right: 3D display of the digitally straightened live finger; lower right: volumetric display of the fake finger whose surface resembles with that of the real fingertip. The two volumetric images are shown over a 4.6 × 4.0 × 0.5 mm region. Clearly indicated by Fig. 2.9, the lack of internal structure in the dummy finger makes SD-OCT based fingertip biometric system spoofing proof, although the top surfaces of the two volumes appear similar, which contributes to the susceptibility to artificial fingers of current AFIS. Another observation by comparing the two cross sectional images is that we can see the natural curvature of the live finger and the dummy finger is different. This attributes to the touchless feature of the SD-OCT system. And the preservation of the fine natural curvature can be utilized as another extra level of information in touchless AFIS. 27 Eccrine gland duct distribution maps along with the surface and internal fingerprints for three different fingertips of one subject are given in Fig. 2.10. The dummy fingertips and their corresponding images are also shown for comparison. Three fingers – thumb, index finger and middle finger – of a male left hand are taken as the samples along with their scattering dummies. Figs. (a)-(c), (g)-(i), (m)-(o) are live thumb, forefinger and middle finger images, respectively; Figs. (d)-(f), (j)-(l), (p)(r) are the layers extracted at corresponding depths in the dummies for the thumb, the forefinger and the middle finger. Surface and papillary layer images are displayed in a 30 dB dynamic range gray scale and the eccrine gland distribution is shown in 1.7 dB reverse gray scale. Although the actual scanning range is larger than what is displayed in Fig. 2.10, a 4 × 4 mm area is used for all the images in Fig. 2.10 in order to be in agreement with palmar sweat index (PSI) [26, 27] and for better registration between real and fake fingerprints. From the left column we can find that the dummy fingers bear a close resemblance to the real fingers in surface fingerprint pattern. The comparison given by the middle column and the right column demonstrates the feasibility and robustness of this approach to tell dummy fingertips from the real ones. Another observation is that in this specific subject, different fingertips all give an eccrine gland duct density of higher than 640/cm2. This density gives sufficient information within a fairly small region for identification purposes. 28 Figure 2.10 (a)-(c) the top, eccrine gland and papillary layers of the thumb; (d)(f) the three layers extracted at the same positions or ranges as those in (a)-(c) for the dummy of the thumb; (g)-(i) the top, eccrine gland and papillary layers of the index finger; (j)-(l) the three layers extracted at the same positions or ranges as those in (g)-(i) for the dummy of the index finger; (m)-(o) the top, eccrine gland and papillary layers of the middle finger; (p)-(r) the three layers extracted at the same positions or ranges as those in (m)-(o) for the dummy of the middle finger. 29 It is known that eccrine glands may not be active at all time. Also due to the mechanism of SD-OCT and the composition of the skin tissue surrounding the eccrine gland ducts, an inactive eccrine gland may not be discernable in a reconstructed image [28]. This issue poses potential question to this biometric mapping approach. Therefore the repeatability of eccrine gland maps in different subjects scanned in different days is tested and the results are given in Tab. 2.1: Table 2.1 Subject Scan 1st Round 2nd Round 3rd Round Repeatability of Eccrine Glands in Different Subjects Tested in Different Days Subject 1 Miss New Match ≥157; template 11 3 90.85% 11 2 91.72% Subject 2 Miss New Match 10 2 89.47% Subject 3 Miss New Match 2 ≥114; template 5 1 93.48% 1 96.34% ≥99; template 5 1 93.94% Three rounds of scan are performed on each subject. One of the scans is selected for each subject as the template with which the other two rounds of scan are compared to calculate the match, which is given as: 2.1 The number of eccrine glands used in the template is given in the table for each individual subject. The Miss column gives the number of eccrine glands shown in the template but not appear in the other scan. The New column gives the number of eccrine glands shown in the scan but not appear in the template. From Table 2.1, we 30 can easily conclude that the repeatability of eccrine glands in different subjects is fairly high. This implies that the eccrine gland mapping is a reliable approach for biometric application. 2.4 Conclusion and Future Work Human fingertip eccrine glands can be mapped for biometric identification purpose using SD-OCT. The map, along with the surface and internal fingerprints, which are also retrievable through SD-OCT, shows high repeatability for the same subject and universality for different subjects. The identification based on eccrine gland maps, though similar with poroscopy, should have its own software algorithm, which is one of the future works. Another direction to go which is made possible by SD-OCT based biometric system is the topography and touchless scan. Shown in Fig. 2.11 there are two topography images showing the surface fingertip ridge-furrow structure as well as the internal one. This topography information is useful to enhance the counterspoofing ability. Also, the overall contour of the fingertip, resolved in the lower right image, gives potential for touchless fingerprint identification application. 31 Figure 2.11 a, topography of the surface fingerprint; b, topography of the internal fingerprint; c, triple-layer display of the volumetric fingertip image; d, reconstructed 3D surface without digital straightening shows the feature of touchless scan. 32 Chapter 3 PHOTOACOUSTIC MICROSCOPY In this chapter, two PAM systems are introduced. The first PAM system is applied to study collagenase-induced-osteoarthritis (CIA) in bovine articulate cartilage samples. Using the SD-OCT system introduced in Chapter 2, images for the same bovine samples are reconstructed and compared. The chemical treatment of the bovine cartilage sample enables a longitudinal study using both PAM and SD-OCT and some useful information about different stages of CIA is extracted from comparing these two modalities‟ images. Another OR-PAM system is used for spectroscopic PAM study. Using a supercontinuum source and a home-mode bandwidth selection mask, fast selection of different bandwidths makes this spectroscopic OR-PAM system suitable for differentiating different kind of absorbers within a sample. Both ink spot and dyed cotton swab phantoms are used to demonstrate this feature and the micrometer level lateral resolution. 3.1 PAM and SD-OCT in Osteoarthritis Studies Osteoarthritis (OA) is a disease characterized by deterioration and localized erosion of articular cartilage, accompanied by bone remodeling and changes of the periarticular tissues, and characterized by a variable rate of progression [29]. There is no complete cure for OA currently, hence the degenerateness of this disease that is symptomatically affecting about 14% of the adult population of the U.S. alone 33 [30]. Thus, non-invasive imaging modalities for OA detection are needed for the monitoring of this disease and are especially useful for early stage prevention of the degeneration of OA. Both SD-OCT and PAM have been applied in imaging cartilage structures. SD-OCT, with its high resolution, gives information of articular cartilage structural changes including cartilage thinning, fissures and fibrillation [30-32]; PAM has been used to the diagnosis of OA by detecting the ultrasound pulses‟ relaxation time changes [33, 34]. Although SD-OCT showed promising images for the changes in OA samples, the lack of contrast in the gray scale intensity images makes this modality hard to be used as easy and decisive criteria for diagnostic purposes. The PAM method, though accurate in the aspect for relying on the relaxation time of the ultrasound pulses within the tissue, neglected the most helpful feature of photoacoustic effect – the absorbing agent as a contrast enhancer [35]. Therefore, a combination of SD-OCT and PAM imaging techniques for the detection of CIA has the potential to give high-resolution structural images with high-contrast. The CIA will cause cartilage fibrillation, erosion of cartilage and eventually the erosion of subchondral bone [36]. For in vitro treatment using collagenase, the destruction of cartilage superficial zone and the reduction of safraninO stainability were observed, indicating breakdown of the cartilage layers [37]. By histology, a digestion of the superficial zone of the murine femoral condyles‟ cartilage after 10 hours of in vitro treatment by collagenase was observed. Though intraarticular injection of collagenase is better in producing OA like changes, in vitro treatment‟s faster speed of digestion [37] makes it preferred in this study. 34 After the collagenase treatment of cartilage, India ink staining is a very useful and efficient way to tell the degradation of the cartilage. The particles of India ink cannot penetrate into the intact cartilage, whose pore size is around 6 nm, but can be entrapped by surface irregularities and fibrillation of the degraded cartilage [38]. Previous studies show that the degree of India ink staining is proportional to the fibrillation, erosion of the cartilage and the subchondral bone [39]. Therefore India ink staining is used to indicate in a macro scale the stages of OA development [39-43]. At the same time, India ink, consisting of both small (0.1 µm diameter) and large (1.0 µm diameter) particles [44], can serve as a good absorber for the PAM mechanism and a scattering enhance agent due to the significant scattering component in its optical attenuation coefficient for SD-OCT scanning. In this section, experiments are performed firstly on an intact region of the bovine osteochondral core cartilage by both SD-OCT and PAM. A fissure, presumably due to the spontaneous OA in the bovine knee joint, which is noticeable by unaided eye, is also scanned by these two imaging modalities after India ink staining. After these scanning, the osteochondral core undergoes 13 hours of in vitro collagenase treatment for CIA. The treated sample is again imaged by the two techniques after India ink staining for an overt fibrillation and subchondral bone exposed region. Pairs of images for both SD-OCT and PAM at the same regions are given to show the structural changes and the distribution of India ink. 3.1.1 Optical Imaging for OA Fig. 3.1 gives the schematic of the PAM system designed for this particular imaging application: 35 Figure 3.1 Schematic of the OR-PAM system for cartilage imaging A Q-switched Nd:YAG microchip laser (NP10820-100, Teem Photonics) produces 0.9 ns duration pulses at 1064 nm with 8 µJ of energy at a 6.6 kHz repetition rate. The frequency of the laser pulse is doubled by a frequency-doubling crystal and then delivered in optical fiber. The final stage 532 nm laser pulse illuminating the sample is measured to be 1 µJ. A double-prism is attached to a 50 MHz flat surface ultrasound transducer (Olympus) to reflect the excitation light to the sample but let through the PA wave. On the laser incident side of the double-prism a plano-convex glass lens is used to compensate for aberration at the light-glass interface while a plano-concave acoustic lens on the PA wave side is used for correcting the aberration for the ultrasound wave. A holder for the osteochondral plug is designed to secure the position of the sample during the hours‟ long scan. The holder is glued to the bottom of a high profile petri dish, which contains 1X phosphate buffered solution (PBS) to preserve the cartilage sample. 36 The petri dish is secured in its position while the probing head performs a raster scan using two orthogonally placed stepper motors (T series, Zaber Technology) over the cartilage surface. PA signals are amplified by a 60 dB amplifier (ultrasound pulser/receiver, 507LPR, Olympus) before digitized by an oscilloscope (WaveJet 324, LeCroy) and recorded by PC. All the system synchronization and data saving functions are realized by LabVIEW programs. The increment of the two stepper motors is set to 10 µm considering the spatial and axial resolution of this system, which are ~30 µm for each. The stepper motor of the SD-OCT system is also set to 10 µm for this specific application in agreement with the settings for the PAM system. In order to improve image SNR in the PAM image, a Butterworth 7th order low pass filter having a cutoff frequency of 70MHz was applied in MATLAB code and a linear interpolation to the factor of 3 was used in both dimensions of the PAM B mode image. The sampling frequency for this PAM scan is 1GHz. 3.1.2 India Ink Staining Commercially available India ink (Higgins Water Proof Ink, Higgins) is purchased for the staining of the cartilage. The detailed procedure is: 1. Move the osteochondral core from 1X PBS solution; 2. Drip the surface of the core with India ink and wait for about half a minute; 3. Rinse with tap water for about 1 minute; 4. Use a Q-tip to brush out the remaining ink on the cartilage surface; 5. Repeat 2-4 for three times; 6. Put the osteochondral core back into sample holder and fill the holder with PBS solution. 37 3.1.3 Collagenase Treatment for the Sample Solution of 150 units/ml bacterial collagenase (Collagenase Type 2, Worthington Biotech) in 50mmol/l Tris-HCl containing 5mmol/l CaCl2 is prepared for the treatment [45] of the osteochondral core. The sample, fastened in the HDPE block is submerged into a beaker of this solution and the beaker is placed on top of a hot plate (Cimarec, Barnstead/Thermdyne) for heating. A magnetic stirrer is placed within the beaker to agitate the solution for better digestion. The temperature of the solution was measured to be 38°C and the pH was maintained within 7.33-7.4 in our home build rocker. The treatment lasts 13 hours. 3.1.4 Results and Discussion Before any results are shown, a well-accepted India ink cartilage staining categorization is given below [40]: Sites at which no distinct markings were seen; Sites showing dark ink markings against a pale grey background, such marking having either approximately parallel alignments or other, more complex, configurations on macroscopic examination; Sites showing confluent or semi-confluent blackening; Sites of full thickness loss of the original cartilage; Experiment results are analyzed per the list above. Fig. 3.2 gives the B-Mode images for both the untreated and post treatment cartilage. In Fig. 3.2 (a) a photo is taken for the osteochondral plug (after collagenase treatment) in the high profile petri dish. A ruler is used to show the dimension. As we can see, the osteochondral plug is held in a holder and India ink is applied to stain the cartilage. Fig. 3.2 (b) and (c) give the SD-OCT image and the 38 PAM image for the intact bovine cartilage, respectively. The two slices are carefully chosen to represent the same registered area in the osteochondral plug. For the intact cartilage, India ink is not able to stain the surface, thus the reconstructed PAM BMode image does not show anything but background noise. In contrast, Fig. 3.2 (b) shows the smooth inner structure of the cartilage. Close to the position where (b) and (c) are taken, there is a cleft in the cartilage which is presumably caused by spontaneous OA. This cleft is taken to be imaged before collagenase treatment and the results are given in Fig. 3.2 (d) and (3) for SD-OCT and PAM, respectively. The cleft measures about 10 µm in dimension, which is too small for current major arthroscopic method to detect. Fig. 3.2 (f) and (g) are the B-Mode images for the treated cartilage (photo given in (a)) using SD-OCT and PAM, respectively. Overt fibrillation is shown in the treated cartilage, this is confirmed by the wide spread entrapment of India ink implied by the PAM image. In (f) we can also see that the inner display of the cartilage in SD-OCT also changes before and after the collagenase treatment. All B-Mode SD-OCT images are shown in 40 dB dynamic range while PAM B-Mode images are given in 19 dB gray scale. 39 Figure 3.2 a, photo showing the treated cartilage submerged in PBS solution; b, SD-OCT image of the untreated cartilage showing an intact region; c, PAM image of the same region as in B; d, SD-OCT image for the untreated cartilage showing a small cleft in the surface; e, PAM image reveals the depth and shape of the fissure in d; f, SD-OCT image showing the 13-hour treated CIA cartilage, note that the smooth gradual change in depth as in b & c is now replaced by a ~10 µm bright surface layer and dark region beneath; g, the PAM image for the same region as shown in f. 3D display is a built-in feature of both SD-OCT and PAM. By stacking together slices and carefully choosing the viewing perspective, volumetric figures are given in Fig. 3.3 using SD-OCT and in Fig. 3.4 using PAM for the post treatment 40 bovine cartilage showing CIA. Fig. 3.3 and 3.4 cover a region of 4 mm× 0.578 mm × 1 mm and 5 mm × 0.59 mm × 1.54 mm (width × length × depth), respectively. Figure 3.3 3D volumetric display using SD-OCT showing the isosurfaces with 71, 77 and 83 dB intensity. Isocaps are added and isonormals calculated. 41 Figure 3.4 3D volumetric display using PAM showing the isosurfaces with -23, -20 and -17 dB intensity. Isocaps are added and isonormals calculated. From the two volumetric images, manifested surface structure and indepth banding in SD-OCT are observed, which is different than the India ink staining pattern indicated by Fig. 3.4. Thus, combining these two images allows a detailed structural display of the cartilage as well as a depth and lateral distribution information of India ink. 3.1.5 Conclusions SD-OCT shows better than 15μm resolution laterally and axially, enabling the imaging of delicate structural change detection in the bovine femoral condyle articulate cartilage before and after collagenase treatment. PAM shows great contrast 42 between intact and fibrillated region in cartilage. India ink, as an indicator of overall cartilage OA stage, successfully served as the optical absorber, hence contrast enhancer, for the PAM images. The combination of SD-OCT and PAM shows promising future in OA progression detection and monitoring. 3.2 Spectroscopic PAM Using a Supercontinuum Source In the previous section, the wavelength of the illumination source is fixed at 532 nm, thus precludes its use in spectroscopic PAM. In this section, a tunable optical source based on the same microchip laser is developed, generating a supercontinuum spectrum spanning 500 – 1300 nm. The PA detection is achieved using a 25 MHz spherically focused detection transducer. By selecting different wavelength bands from the supercontinuum spectrum and run a raster scan, the PA data produces images that clearly distinguish the different absorbing regions of ink phantoms after a simple discriminant analysis. 3.2.1 From OR-PAM to Spectroscopic PAM From Eq. 1.16 we can tell that low laser pulse energies (e.g. less than 100 nJ) are still sufficient for OR-PAM because the extremely small optical focus produces high enough optical fluence. Therefore, OR-PAM can be used with high repetition rate pulsed lasers to significantly increase image acquisition speed. The Q-switched microchip laser source described in the previous section, however, emits single wavelength pluses, making it not suitable for spectroscopic PAM [46-48]. To deal with this, we propagate the laser pulses through several meters of photonic crystal fiber (PCF) to generate an ultra-broadband spectrum [49, 50]. After the tunable band pass filter, the low pulse energy is still sufficient for OR-PAM. Seven 43 different wavelength bands are used to successfully differentiate ink phantoms with overlapping absorption spectra. 3.2.2 Materials and Methods Fig. 3.5 depicts the system and a photo for the resulting supercontinuum spectrum. In Fig. 3.5 (a) we can see the laser pulses at 1064 nm is coupled into the 7 m long PCF (Crystal Fibre, Inc.) through an aspherical lens (NA = 0.4). The air-silica honeycomb-like microstructure of the PCF provides favorable dispersion properties to boost the nonlinear optical transmission. The input average power is 51 mW and the output power is 2.8 mW for the supercontinuum. After collimated by a 20X microscope objective lens, the beam diameter is measured to be 3 mm. Fig. 3.5 (b) gives the spectrum measured by an optical spectrum analyzer with a useful scanning range from 600 to 1700 nm. The residual power in the pump wavelength is represented by the large spike at 1064 nm. Fig. 3.5 (c) shows the dispersed light on a piece of paper, which confirms that the supercontinuum contains wavelengths near 500 nm, which is beyond the useful scanning range of the optical spectrum analyzer used to give Fig. 3.5 (b). 44 Figure 3.5 a, Q-switched microchip Nd:YAG laser emits 1064 nm pulses coupled into and progagate through 7 m PCF (λzdw = 1040 nm) to generate a supercontinuum. The PCX collimates the microchip laser output. An asperic lens (AL) focuses the 1064 nm pulses into the PCF. A microscope objective (MO) collimates the supercontinuum output; b, The spectrum of the supercontinuum measured by an optical spectrum analyzer; c, A photo showing the dispersed supercontinuum on a piece of white paper. Fig. 3.6 shows the mechanism of wavelength selection. The dispersed light from an equilateral BK-7 prism is collimated by a 75 mm diameter spherical mirror with a focal length of 500 mm. Spectral filtering is performed in the Fourier plane using a manually adjusted slit placed in front of the mirror [51]. The flat mirror has a slight vertical tilt in order to separate the return beam from the incident beam. 45 Seven wavelength bands with 40 nm bandwidth from 575 to 875 nm in 50 nm increment are used for this experiment with 7, 15, 24, 31, 31, 31 and 33 nJ as their pulse energies. Figure 3.6 Prism-based monochromator, where a concave mirror collimates the dispersed light. The schematic of this system is modified from the one given in previous section. As shown in Fig. 3.7, the PA beam splitter transmits the laser beam but reflects the PA signal. The excitation laser pulse is focused with 4X infinity corrected microscope objective (NA = 0.1). The beam splitter is composed by a plane glass wafer surrounded on both sides by water. The upper water section is in contact with a glass PCX lens for aberration reduction. The lower water section is in contact with a 25 MHz spherically focused f/2 transducer (Olympus V324). The bottom of the chamber is sealed by 25 micron thick Mylar membrane. The detection and the raster scanning mechanism are the same with the one described in the previous section. 46 Figure 3.7 Schematic of the OR-PAM system featuring a 25 MHz transducer 3.2.3 Results and Discussion En face imaging of a USAF resolution target (Edmund Optics) was performed on Group 3 elements and the simulated profile assuming a Gaussian-shaped point spread function (PSF) with a FWHM of 18 µm is indicated as the lateral resolution. Four ink spots with black, blue, green and red color are imaged afterwards. MAP images of these spots for all the seven wavelengths are given in Fig. 3.8 over 40 dB dynamic range covering an area of 1.8 × 5.4 mm. The different colored spots clearly exhibit different wavelength behavior. Using a simplified discriminant analysis [9], the classified groups are displayed as red-green-blue (GRB) image. The classification has some error, such as in the blue and green ink regions and for the black ink spot which appeared purple in the reconstructed image. Higher accuracy is achievable with more sophisticated multispectral image analysis and a larger number of wavelength bands. 47 Figure 3.8 Multi-wavelength images of black, blue, green and red ink spots (left to right). All images displayed over a 1.8 × 5.4 mm range in 40 dB scale. The spectrally processed image clearly identifies the four ink regions. In order to demonstrate the system‟s optical resolution, a more realistic phantom made of stained cotton-swab fibers are imaged under 0.4 mm scattering layer consisting of an aqueous suspension of 1 µm diameter polystyrene microspheres at a 0.09% concentration whose extinction coefficient measured by spectrophotometry is 1.9 mm-1 at 675 nm [9]. Though showing great potential of real world application using this spectroscopic OR-PAM system, two issues are present: 1. the bandwidth selection is manually controlled. Each time this experiment is done the cover slit needs to be manually adjusted to select the desired wavelength bandwidth. This makes the experiment very time consuming; 2. the bandwidth is 40 nm, although useful for many 48 spectroscopic applications, is still big for more accurate detection and monitoring. Efforts are made to solve these issues and some results are given in the following sections of this thesis. 3.3 Wavelength Agile Spectroscopic PAM In this section, the system described in section 3.2 has a new automatic wavelength bandwidth selection mechanism enabling fast sweeping through more than 10 bandwidths with 20 nm span. The acquisition is also changed from digital oscilloscope to a DAQ board for fast data transfer and easier system synchronization. These system modifications are introduced in detail in this section and experiment results on ink spots and cotton swabs are given to demonstrate the function of this wavelength agile spectroscopic PAM system. 3.3.1 Tunable Wavelength Filter In Fig. 3.5 (c) we observe that in the supercontinuum spectrum, each wavelength occupies a different lateral position along the focal plane of the mirror. This allows spectral filtering to be achieved by placing an appropriately sized slit. The width of the slit and its projection on the spectrum determines the wavelength range of the filtered light. Fig. 3.9 shows the automatic externally triggered tunable wavelength filter. A voice-coil actuator called the wave driver (SF-9324, Pasco Scientific) drives the leverage system to provide rapid wavelength sweep from 570 to 930 nm within 500 ms. Since the dispersed wavelengths are not evenly distributed along the focal plane of the concave mirror as shown in Fig. 3.6, the slit is tapered to produce an approximately constant spectral bandwidth during the wavelength sweep. The bandwidth for the filtered light is measured to be 20 nm with about 10 nJ pulse energy. 49 Due to the low pulse energy, signal averaging is done during acquisition for better SNR. Immediately behind the slit is a flat mirror to reflect the spectrally filtered light back to the concave mirror as is described in the previous section. This wave driver is controlled by a function generator & amplifier (Frederiksen) which is externally triggered. The amplitude and frequency of the triangular output from the function generator & amplifier is predetermined based on experiment results. Figure 3.9 The automatic tunable wavelength filter. One end of the lever is fastened on top of the wave driver. The other end of the lever is connected to the mask, with a tapered slit going in the diagonal direction. A supercontinuum spectrum is drawn over the mask to demonstrate the mechanism of how bandwidth selection is performed. 3.3.2 Data Acquisition and System Synchronization The data acquisition is achieved by a PCI DAQ board (NI 5114, National Instruments) in this experiment. The board provides dual channel 250 MS/s sampling rate with 8 bit analog to digital conversion (ADC) and 8 MB on board memory. 50 Trigger is provided externally from the photodiode detecting the 1064 nm laser output but a software acquisition delay is in effect to compensate for the time elapse before the mask moves to such a position that the first desired bandwidth is selected. This delay time is experimentally determined by triggering the acquisition in software and recording a fairly long continuous trace. The whole system works in the following manner: 2D stepper motors position the sample to the proper location; Wave driver moves downward, hence the upward movement of the mask; After waiting for a certain delay time, the acquisition starts on the DAQ board; Number of average for each bandwidth is predetermined experimentally. The averaged data corresponding to all the bandwidths are saved in the on board memory during one upward movement of the mask; One position‟s data is streamed to the hard drive of the PC. The mask moves back to the initial position and the 2D motor moves the sample to the next position for scan. 3.3.3 Results and Discussion MATLAB is used to produce the MAP images for all the bandwidths and the same discriminant analysis is applied to give RGB coloring to the MAP images. Fig. 3.10 shows the 4 ink spot MAP images for all the bandwidths. All images span an 8.4 × 1 mm region and are given in 10 dB dynamic range. From left to right they are red, green, blue and black in color. Compare this with Fig. 3.8 we can see that this system provides similar spectroscopic PAM function as that described in section 3.2 51 but significant speed improvement is realized in this system, potentially enabling functional imaging. Figure 3.10 Ink spot images for four ink spots (red, green, blue black from left to right). Sequential bandwidths see 20 nm increments in their central wavelength. Images are displayed over 8.4 × 1 mm region in 10 dB range gray scale. Cotton swab images are given in Fig. 3.11 along with its spectrally processed RGB display. 52 Figure 3.11 The fiber phantom taken at 570 nm and 690 nm with the spectrally processed image in RGB display. All the three images in Fig. 3.11 are shown in a 0.9 ×0.9 mm range over 20 dB scale. The disappearance of the two parallel diagonal fibers visible in the 570 nm image suggests these threads are stained by red ink. This is confirmed in the RGB image. The remaining threads are identified as stained with either green or blue ink. Only the 570 nm and 690 nm images are used for the RGB image, so there is slight error (blue-green). This should be corrected with a more sophisticated spectral processing algorithm. 3.3.4 Conclusions In this section, a spectroscopic PAM system with rapidly tunable optical source based on a PCF supercontinuum source is demonstrated. The tunable bandpass filter provides rapid access to any desired wavelength band. 53 Chapter 4 FUTURE WORK In sections 3.2 and 3.3, OR-PAM system has been applied on ink spot and cotton swab phantoms and shows promising images successfully differentiating either ink spots or stained cotton swabs with different colors. With this in mind, we need better phantoms for microvasculature PAM imaging and higher pulse energies in each bandwidth for better SNR. Previous studies have shown the potential of using PAM to discover the hemoglobin oxygen saturation (SO2) in the subcutaneous microvasculature of rats in vivo. Their phantom tests using two inks matched the actual values pretty well and the SO2 acquired by PAM agrees with the spectrophotometric measurements with only a 4% systematic difference [8]. Inspired by this research, our future work involves developing a system with high energy multiwavelength pulses for an OR-PAM system to test the ratio of a certain dye component in mixed dye solutions enclosed in thin tubes mimicking human vasculature. Some preliminary results are given in the following sections. 4.1 Spectrophotometry for Mixed Dye Solutions From section 1.2 we know that the absorption coefficient of a sample is directly proportional to the PA signal generated after laser illumination. In the preliminary test, red and blue food dyes (McCormick) are used and mixed with different mass ratios. Eq. 4.1 gives the relationship between PA signal strength and the dye absorption coefficient: 54 4.1 where 1 is the extinction coefficient of the solution at a certain wavelength (cm-1M- ); [red] and [blue] are the concentrations of the dye solutions; PA(λ) is the PA signal detected at a certain wavelength. Denote the extinction coefficient matrix as M, the concentration matrix as C and the photoacoustic signal matrix as PA, using leastsquare-method (LSM), we can then calculate the concentration of the two dyes based on the PA matrix and the predetermined M matrix, which is given in Eq. 4.2: 4.2 Therefore we need accurate measurement of the extinction coefficients to get correct concentration information. A home-made spectrophotometry system is used to test solutions with various red/blue dye ratios. Fig. 4.1 shows the schematic of the spectrophotometry system with multiple views of the home-made cuvette. A halogen bulb is used as the white light source. The white light is focused on the cuvette, and then coupled into another optical fiber directly connected to a spectrometer (SP2-USB, Thorlabs). The data is stored in PC and processed using MATLAB. Cost consideration makes us fabricate cuvettes on our own using glass slides and cover slips (Fisher Scientific). The side view and top view of the home-made cuvette in Fig. 4.1 shows the overall structure. The effective thickness of the cuvette is 0.19 mm in the experiments. Solutions are injected into the gap between the cover slip and the glass slide carefully before spectrophotometry experiment. After a certain solution is measured by this system, 0.9% saline solution is used to wash thoroughly the cuvette 55 followed by pure water wash. The cuvette is kept stable in the system to guarantee the same thickness being used when different solutions are tested. Figure 4.1 The Spectrophotometry System with a Separate Display of the Cuvette The spectrum data are averaged by 100 before recording and the integration time for the spectrometer is 40 ms. An all dark spectrum by blocking the cuvette with opaque cover is recorded along with a reference spectrum by using pure water in the cuvette. The recorded data along with the all dark spectrum and the reference spectrum are used to calculate the transmittance first using the following equation 4.2 where A is the recorded spectrum data. The transmittance is related to the extinction coefficient showing in Eq. 4.3: 56 4.3 where d is the thickness of the cuvette. From Eq. 4.3 we can easily get the expression for the extinction coefficient given below: 4.4 Using the equations above, the extinction coefficient for different mixtures is given in Fig. 4.2 as a function of wavelength: Extinction coefficient V.S. wavelength for different dye mixtures RED BLUE RED:BLUE=1:2 RED:BLUE=2:1 RED:BLUE=1:3 RED:BLUE=3:1 200 180 160 cm-1 140 120 100 80 60 40 20 0 550 Figure 4.2 600 650 700 750 800 /nm 850 900 950 1000 Extinction coefficients calculated from the spectrophotometry data for mixtures made of red and blue food dyes with different ratios. The processing includes a moving average filter for the raw data to smooth the spectra. The extinction coefficients are saved in matrix format as a function of 57 wavelength for future use in the concentration calculation by spectroscopic PA experiment. 4.2 Stokes Source OR-PAM with Fast Raster Scanning Systems described in Chapter 3 suffers from two main problems: the low energy from the laser source available for each bandwidth and the slow speed of scanning which takes hours for finish a fairly small region (< 1 mm2). In order to overcome these two concerns, a Stokes source for the OR-PAM system is developed using stimulated Raman scattering (SRS) in single mode optical fiber [52]. After filters matched with each Stokes line, three wavelengths are picked to image the sample, which are 532 nm (seed light frequency), 546 nm and 560 nm with pulse energies being approximately 60 nJ, 80 nJ and 110 nJ, respectively. When a certain wavelength is selected, fast raster scan is performed using two stepper motors. The x-axis stepper motor moves at a constant speed with maximum acceleration over the full range in x-direction. A laser pulse counter circuit is made to select every 1 in 8 pulses from a photodiode detector and this selected pulse is used to trigger the data acquisition performed by the NI-DAQ board. When each line in the x-direction is finished, the y-axis motor moves a certain distance. Then the xaxis motor moves at the same speed in the backward direction as it was moving in the forward direction. Data is also collected during this backward direction movement. All the scanned records are temporarily stored in the DAQ device on board memory and saved in the hard drive after the whole raster scan is finished. The new Q-switched microchip laser source (Teem Phonics) emits 1064 nm pulses at 7.45 kHz repetition rate with a pulse width of 0.6 ns. All the other hardware instruments are the same with those in section 3.2 and 3.3. The digital 58 counter circuit and the LabVIEW programs are carefully designed to take care of all the synchronization and data saving issues. A MATLAB code is programed to process the data and compensate for the interdigitating error in the reconstructed MAP image caused by the dual direction scan of the x-axis stepper motor. An image reconstructed for the USAF resolution target is shown in Fig. 4.3 with Group 3, 4, 5, 6 elements displayed. Though in this image only Group 5 elements can be well resolved, corresponding to a maximum lateral resolution of 17.5 µm, better alignment of the system and further process to compensate for the interdigitating error should get us better resolution limited by the optical focal spot size, which is calculated to be around 8 µm. Figure 4.3 USAF resolution target imaged by Stokes source OR-PAM system. All elements in Group 4, 5, 6 and 7 are in the scanning range. 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