Surface analysis and fingerprint recognition from multi-light imaging collections

Multi-light imaging captures a scene from a fixed viewpoint through multiple photographs, each of which are illuminated from a different direction. Every image reveals information about the surface, with the intensity reflected from each point being measured for all lighting directions. The images captured are known as multi-light image collections (MLICs), for which a variety of techniques have been developed over recent decades to acquire information from the images. These techniques include shape from shading, photometric stereo and reflectance transformation imaging (RTI). Pixel coordinates from one image in a MLIC will correspond to exactly the same position on the surface across all images in the MLIC since the camera does not move. We assess the relevant literature to the methods presented in this thesis in chapter 1 and describe different types of reflections and surface types, as well as explaining the multi-light imaging process. In chapter 2 we present a novel automated RTI method which requires no calibration equipment (i.e. shiny reference spheres or 3D printed structures as other methods require) and automatically computes the lighting direction and compensates for non-uniform illumination. Then in chapter 3 we describe our novel MLIC method termed Remote Extraction of Latent Fingerprints (RELF) which segments each multi-light imaging photograph into superpixels (small groups of pixels) and uses a neural network classifier to determine whether or not the superpixel contains fingerprint. The RELF algorithm then mosaics these superpixels which are classified as fingerprint together in order to obtain a complete latent print image, entirely contactlessly. In chapter 4 we detail our work with the Metropolitan Police Service (MPS) UK, who described to us with their needs and requirements which helped us to create a prototype RELF imaging device which is now being tested by MPS officers who are validating the quality of the latent prints extracted using our technique. In chapter 5 we then further developed our multi-light imaging latent fingerprint technique to extract latent prints from curved surfaces and automatically correct for surface curvature distortions. We have a patent pending for this method

Optical Methods in Sensing and Imaging for Medical and Biological Applications

The recent advances in optical sources and detectors have opened up new opportunities for sensing and imaging techniques which can be successfully used in biomedical and healthcare applications. This book, entitled ‘Optical Methods in Sensing and Imaging for Medical and Biological Applications’, focuses on various aspects of the research and development related to these areas. The book will be a valuable source of information presenting the recent advances in optical methods and novel techniques, as well as their applications in the fields of biomedicine and healthcare, to anyone interested in this subject

FTIR difference and resonance raman spectroscopy of rhodopsins with applications to optogenetics

Thesis (Ph. D.)--Boston UniversityThe major aim of this thesis is to investigate the molecular basis for the function of several types of rhodopsins with special emphasis on their application to the new field of optogenetics. Rhodopsins are transmembrane biophotonic proteins with 7 a-helices and a retinal chromophore. Studies included Archaerhodopsin 3 (AR3), a light driven proton pump similar to the extensively studied bacteriorhodopsin (BR); channelrhodopsins 1 and 2, light-activated ion channels; sensory rhodopsin II (SRII), a light-sensing protein that modulates phototaxis used in archaebacteria; and squid rhodopsins (sRho), the major photopigment in squid vision and a model for human melanopsin, which controls circadian rythms. The primary techniques used in these studies were FTIR difference spectroscopy and resonance Raman spectroscopy. These techniques, in combination with site directed mutagenesis and other biochemical methodologies produced new knowledge regarding the structural changes of the retinal chromophore, the location and function of internal water molecules as well as specific amino acids and peptide backbone. Specialized techniques were developed that allowed rhodopsins to be studied in intact membrane environments and in some cases in vivo measurements were made on rhodopsin heterologously expressed in E. coli thus allowing the effects of interacting proteins and membrane potential to be investigated. Evidence was found that the local environment of one or more internal water molecules in SRII is altered by interaction with its cognate transducer, Htrii, and is also affected by the local lipid environment. In the case of AR3, many of the broad IR continuum absorption changes below 3000 cm-1, assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR, were found to be very similar to BR. Bands assigned to water molecules near the Schiff base postulated to be involved in proton transport were, however, shifted or absent. Structural changes of internal water molecules and possible bands associated with the interaction with ,8-arrestins were also detected in photoactivated squid rhodopsin when transformed to the acid Meta intermediate. Near-IR confocal resonance Raman measurements were performed both on AR3 reconstituted into E. coli polar lipids and in vivo in E. coli expressing AR3 in the absence and presence of a negative transmembrane potential. On the basis of these measurements, a model is proposed which provides a possible explanation for the observed fluorescence dependence of AR3 and other microbial rhodopsins on transmembrane potential

Biometric Systems

Biometric authentication has been widely used for access control and security systems over the past few years. The purpose of this book is to provide the readers with life cycle of different biometric authentication systems from their design and development to qualification and final application. The major systems discussed in this book include fingerprint identification, face recognition, iris segmentation and classification, signature verification and other miscellaneous systems which describe management policies of biometrics, reliability measures, pressure based typing and signature verification, bio-chemical systems and behavioral characteristics. In summary, this book provides the students and the researchers with different approaches to develop biometric authentication systems and at the same time includes state-of-the-art approaches in their design and development. The approaches have been thoroughly tested on standard databases and in real world applications

Vibrational Imaging at the Nanoscale: Surpassing the Diffraction Limit Using Tip-Enhanced Raman Spectroscopy

A deep understanding of the chemical composition of surfaces, interfaces or nanoscale structure with a high spatial resolution is an important goal in nanoscience and nanotechnology. Structural information can be collected using a variety of high spatial resolution techniques such as atomic force microscopy (AFM), scanning tunneling microscopy (STM), scanning electron microscopy (SEM), or transmission electron microscopy (TEM). Nevertheless, these methods do not offer molecular information such as vibrational spectroscopy techniques that allow one to collect molecular or lattice vibrations yielding to a precise picture of the molecular interactions in bulk materials as well as in surfaces and interfaces. Unfortunately optical spectroscopy techniques are limited in terms of spatial resolution and sensitivity due to the poor signal/noise ratio of the localized measurement. Surface- and tip-enhanced Raman spectroscopy (SERS and TERS) are advanced spectroscopic techniques, which are becoming widely used and show a great potential for the structural characterisation of biological systems. Surface-enhanced spectroscopy (SERS) was developed to improve the sensitivity of the chemical measurements by using rough silver or gold surfaces. The challenge of the simultaneous improvement of the spatial resolution and sensitivity was addressed by combining high resolution optical microscopy with the high sensitivity of surface-enhanced spectroscopy and was termed tip-enhanced Raman spectroscopy (TERS). In this thesis, gap-mode TERS is developed for the study of a variety of materials. TERS is used in conjunction with gold nanoplates to serve as an ultraflat substrate that can possibly be functionalized. TERS investigation of monolayers adsorbed onto gold nanoplates such as alkoxy substituted azobenzene thiol and 4-nitrothiophenol is conducted. The monolayer is probed with a silver coated AFM tip in order to obtain the largest electromagnetic field enhancement and the effect of the excitation (linearly or radially polarized) is conducted. TERS is also used to probe graphene flakes and differentiate the edges of a few-layer graphene flakes with a spatial resolution better than 20 nm. Last, TERS was used to investigate single DNA molecules deposited onto gold nanoplates. The DNA, cDNA and pure plasmid were investigated with TERS probing the distribution of nucleobases at a specific location with a spatial resolution which was, in the best conditions below 10 nm

Imaging heritage and other metal surfaces with X-ray excited optical microscopy

Heritage tourism represents a significant source of income for the European Union. Metals are vital to this, but corrode and degrade over time unless curative actions are taken. Conservators require non-destructive analysis techniques and specific instrumentations for the study and analysis of ancient objects that comprise our tangible cultural heritage. XEOM 1, a novel X-ray-excited optical microscopy system, is presented as a new addition to the conservator’s toolbox. XEOM 1 allows non-destructive chemical imaging of heritage metal surfaces (approximately top 200 nm) in air and controlled atmosphere. XEOM exploits the effect in which X-ray absorption results in the emission of electromagnetic radiation in the visible and near-visible bands, a phenomenon known as X-ray-excited optical luminescence (XEOL). The work presented in the thesis comprises ground work for imaging of copper and copper corrosion products on assessment samples of varying patination; a multimethod analysis of heritage artefacts retrieved from King Henry VIII's flagship: the 'Mary Rose' and the study for an alternative excitation source for use of XEOM 1 outside the synchrotron. The research and development of X-ray-excited optical microscopy was supplemented with the research regarding the copper corrosion of frameless coppr and copper- gold intrauterine devices (IUDs)

Face recognition by means of advanced contributions in machine learning

Face recognition (FR) has been extensively studied, due to both scientific fundamental challenges and current and potential applications where human identification is needed. FR systems have the benefits of their non intrusiveness, low cost of equipments and no useragreement requirements when doing acquisition, among the most important ones. Nevertheless, despite the progress made in last years and the different solutions proposed, FR performance is not yet satisfactory when more demanding conditions are required (different viewpoints, blocked effects, illumination changes, strong lighting states, etc). Particularly, the effect of such non-controlled lighting conditions on face images leads to one of the strongest distortions in facial appearance. This dissertation addresses the problem of FR when dealing with less constrained illumination situations. In order to approach the problem, a new multi-session and multi-spectral face database has been acquired in visible, Near-infrared (NIR) and Thermal infrared (TIR) spectra, under different lighting conditions. A theoretical analysis using information theory to demonstrate the complementarities between different spectral bands have been firstly carried out. The optimal exploitation of the information provided by the set of multispectral images has been subsequently addressed by using multimodal matching score fusion techniques that efficiently synthesize complementary meaningful information among different spectra. Due to peculiarities in thermal images, a specific face segmentation algorithm has been required and developed. In the final proposed system, the Discrete Cosine Transform as dimensionality reduction tool and a fractional distance for matching were used, so that the cost in processing time and memory was significantly reduced. Prior to this classification task, a selection of the relevant frequency bands is proposed in order to optimize the overall system, based on identifying and maximizing independence relations by means of discriminability criteria. The system has been extensively evaluated on the multispectral face database specifically performed for our purpose. On this regard, a new visualization procedure has been suggested in order to combine different bands for establishing valid comparisons and giving statistical information about the significance of the results. This experimental framework has more easily enabled the improvement of robustness against training and testing illumination mismatch. Additionally, focusing problem in thermal spectrum has been also addressed, firstly, for the more general case of the thermal images (or thermograms), and then for the case of facialthermograms from both theoretical and practical point of view. In order to analyze the quality of such facial thermograms degraded by blurring, an appropriate algorithm has been successfully developed. Experimental results strongly support the proposed multispectral facial image fusion, achieving very high performance in several conditions. These results represent a new advance in providing a robust matching across changes in illumination, further inspiring highly accurate FR approaches in practical scenarios.El reconeixement facial (FR) ha estat àmpliament estudiat, degut tant als reptes fonamentals científics que suposa com a les aplicacions actuals i futures on requereix la identificació de les persones. Els sistemes de reconeixement facial tenen els avantatges de ser no intrusius,presentar un baix cost dels equips d’adquisició i no la no necessitat d’autorització per part de l’individu a l’hora de realitzar l'adquisició, entre les més importants. De totes maneres i malgrat els avenços aconseguits en els darrers anys i les diferents solucions proposades, el rendiment del FR encara no resulta satisfactori quan es requereixen condicions més exigents (diferents punts de vista, efectes de bloqueig, canvis en la il·luminació, condicions de llum extremes, etc.). Concretament, l'efecte d'aquestes variacions no controlades en les condicions d'il·luminació sobre les imatges facials condueix a una de les distorsions més accentuades sobre l'aparença facial. Aquesta tesi aborda el problema del FR en condicions d'il·luminació menys restringides. Per tal d'abordar el problema, hem adquirit una nova base de dades de cara multisessió i multiespectral en l'espectre infraroig visible, infraroig proper (NIR) i tèrmic (TIR), sota diferents condicions d'il·luminació. En primer lloc s'ha dut a terme una anàlisi teòrica utilitzant la teoria de la informació per demostrar la complementarietat entre les diferents bandes espectrals objecte d’estudi. L'òptim aprofitament de la informació proporcionada pel conjunt d'imatges multiespectrals s'ha abordat posteriorment mitjançant l'ús de tècniques de fusió de puntuació multimodals, capaces de sintetitzar de manera eficient el conjunt d’informació significativa complementària entre els diferents espectres. A causa de les característiques particulars de les imatges tèrmiques, s’ha requerit del desenvolupament d’un algorisme específic per la segmentació de les mateixes. En el sistema proposat final, s’ha utilitzat com a eina de reducció de la dimensionalitat de les imatges, la Transformada del Cosinus Discreta i una distància fraccional per realitzar les tasques de classificació de manera que el cost en temps de processament i de memòria es va reduir de forma significa. Prèviament a aquesta tasca de classificació, es proposa una selecció de les bandes de freqüències més rellevants, basat en la identificació i la maximització de les relacions d'independència per mitjà de criteris discriminabilitat, per tal d'optimitzar el conjunt del sistema. El sistema ha estat àmpliament avaluat sobre la base de dades de cara multiespectral, desenvolupada pel nostre propòsit. En aquest sentit s'ha suggerit l’ús d’un nou procediment de visualització per combinar diferents bandes per poder establir comparacions vàlides i donar informació estadística sobre el significat dels resultats. Aquest marc experimental ha permès més fàcilment la millora de la robustesa quan les condicions d’il·luminació eren diferents entre els processos d’entrament i test. De forma complementària, s’ha tractat la problemàtica de l’enfocament de les imatges en l'espectre tèrmic, en primer lloc, pel cas general de les imatges tèrmiques (o termogrames) i posteriorment pel cas concret dels termogrames facials, des dels punt de vista tant teòric com pràctic. En aquest sentit i per tal d'analitzar la qualitat d’aquests termogrames facials degradats per efectes de desenfocament, s'ha desenvolupat un últim algorisme. Els resultats experimentals recolzen fermament que la fusió d'imatges facials multiespectrals proposada assoleix un rendiment molt alt en diverses condicions d’il·luminació. Aquests resultats representen un nou avenç en l’aportació de solucions robustes quan es contemplen canvis en la il·luminació, i esperen poder inspirar a futures implementacions de sistemes de reconeixement facial precisos en escenaris no controlats.Postprint (published version

Automated Low-Cost Malaria Detection System in Thin Blood Slide Images Using Mobile Phones

Malaria, a deadly disease which according to the World Health Organisation (WHO) is responsible for the fatal illness in 200 million people around the world in 2010, is diagnosed using peripheral blood examination. The work undertaken in this research programme aims to develop an automated malaria parasite-detection system, using microscopic-image processing, that can be incorporated onto mobile phones. In this research study, the main objective is to achieve the performance equal to or better than the manual microscopy, which is the gold standard in malaria diagnosis, in order to produce a reliable automated diagnostic platform without expert intervention, for the effective treatment and eradication of the deadly disease. The work contributed to the field of mathematical morphology by proposing a novel method called the Annular Ring Ratio transform for blood component identification. It has also proposed an automated White Blood Cell and Red Blood Cell differentiation algorithm, which when combined with ARR transform method, has wide applications not only for malaria diagnosis but also for many blood related analysis involving microscopic examination. The research has undertaken investigations on infected cell identification which aids in the calculation of parasitemia, the measure of infection. In addition, an automated diagnostic tool to detect the sexual stage (gametocytes) of the species P.falciparum for post-treatment malaria diagnosis was developed. Furthermore, a parallel investigation was carried out on automated malaria diagnosis on fluorescent thin blood films and a WBC and infected cell differentiation algorithm was proposed. Finally, a mobile phone application based on the morphological image processing algorithms proposed in this thesis was developed. A complete malaria diagnostic unit using the mobile phones attached to a portable microscope was set up which has enormous potential not only for malaria diagnosis but also for the blood parasitological field where advancement in medical diagnostics using cellular smart phone technology is widely acknowledged

Raman spectroscopy: techniques and applications in the life sciences

Raman spectroscopy is an increasingly popular technique in many areas including biology and medicine. It is based on Raman scattering, a phenomenon in which incident photons lose or gain energy via interactions with vibrating molecules in a sample. These energy shifts can be used to obtain information regarding molecular composition of the sample with very high accuracy. Applications of Raman spectroscopy in the life sciences have included quantification of biomolecules, hyperspectral molecular imaging of cells and tissue, medical diagnosis, and others. This review briefly presents the physical origin of Raman scattering explaining the key classical and quantum mechanical concepts. Variations of the Raman effect will also be considered, including resonance, coherent, and enhanced Raman scattering. We discuss the molecular origins of prominent bands often found in the Raman spectra of biological samples. Finally, we examine several variations of Raman spectroscopy techniques in practice, looking at their applications, strengths, and challenges. This review is intended to be a starting resource for scientists new to Raman spectroscopy, providing theoretical background and practical examples as the foundation for further study and exploration

Biometric identification with 3D fingerprints acquired through optical coherence tomography

Orientador : Prof. Dr. Luciano SilvaCoorientador : Profª. Olga Regina Pereira BellonTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 28/06/2016Inclui referências : f. 75-82Área de concentraçãoResumo: Um método para se obter impressões digitais 3D da derme e da epiderme a partir de imagens em alta resolução adquiridas utilizando Tomografia de Coerência Ótica (OCT) é proposto neste trabalho. Este método, resolve limitações das técnicas de reconstrução 3D de impressões digitais que empregam múltiplas câmeras/triangulação ou iluminação estruturada, tais como variações de resolução do centro para as bordas das impressões digitais 3D causadas por erros de reconstrução, sensibilidade a baixa iluminação e contraste insuficiente. Uma técnica de busca e identificação baseados em padrões inovativos, os "mapas KH " (usados para a segmentação de regiões de superfície em imagens de intensidade e de profundidade), extraídos computando as curvaturas Gaussiana (K) e média (H) de uma região de interesse na vizinhança das minúcias (denominada nuvem de minúcia), é apresentada. Grandes bases de mapas KH, uma para cada nuvem de minúcia identificada, podem ser construídos com essa técnica. A estratégia de busca e identificação, em duas etapas, baseia-se primeiro em padrões locais de gradientes (LGP) dos mapas KH, para reduzir o espaço de busca dentro da base, seguidos de uma comparação que utiliza uma medida de similaridade, a correlação cruzada normalizada dos padrões pré-selecionados com o LGP com os que se quer identificar. A acuracidade do método e sua compatibilidade com os métodos correntes, comparável ou superior à dos métodos 2D, é verificada através da identificação biométrica de impressões digitais 3D utilizando duas bases de imagens, uma adquirida através da tecnologia OCT e a outra gentilmente cedida pela Universidade Politécnica de Hong Kong. A base de imagens OCT, a primeira adquirida com essa tecnologia, é composta de imagens coletadas de onze voluntários em duas sessões de escaneamento e contém imagens de dedos de pessoas com diferentes idades, gênero e etnias e contém casos de cicatrizes, calos e alterações, tais como abrasão e arranhões. Uma base de impressões digitais 2D, obtida dos mesmos voluntários através de um leitor regular de impressões digitais, foi adquirida para permitir uma comparação da técnica proposta com os métodos de identificação tradicionais. A aplicabilidade do método proposto à identificação de impressões digitais alteradas, deterioradas acidentalmente ou intencionalmente, é investigada. Nesses casos, a impressão digital 3D extraída da derme e compatível com a da epiderme é empregada. A identificação destas impressões 3D alteradas é testada utilizando a base de imagens adquiridas com OCT. A acuracidade da técnica é comparada com a obtida utilizando os métodos tradicionais 2D usando os gráficos de taxas de Falsa Aceitação e Falsa Rejeição (FAXxFRR) e de Características Cumulativas de Identificação (CMC). Impressões digitais 2D, extraídas a partir das impressões digitais 3D simulando o rolamento do dedo durante a aquisição (rolamento virtual), foram geradas e sua compatibilidade com as bases de imagens 2D foi testada. Um conjunto de medidas de avaliação de qualidade foram aplicados às bases de imagens de impressões digitais 3D e sua correspondência aos escores de identificação foi analisada para determinar aqueles que podem contribuir para melhorar a acuracidade da identificação. Palavras-chave: Impressões digitais 3D. Identificação Biométrica. Tomografia de Coerência Ótica.Abstract: A method to obtain epidermal and dermal 3D fingerprints from high-resolution images acquired using Optical Coherence Tomography (OCT) is proposed. This method addresses limitations of current 3D reconstruction techniques that employ multiple cameras/triangulation or structured illumination such as depth and resolution variations from the center to the borders of the fingerprint caused by reconstruction errors, sensitivity to low illumination and poor contrast. The availability of these 3D fingerprints allowed the creation of new matching methods that benefit from the rich information available in 3D. A 3D fingerprint matching technique based on novel patterns, the KH maps (used to surface region segmentation in range and intensity images), extracted by computing the Gaussian and mean curvatures (SILVA; BELLON; GOTARDO, 2001) from a region of interest around the minutiae, named minutiae clouds is presented. Large databases of KH maps, one for each identified minutiae cloud can be built. The matching strategy, a two-step approach, relies on local gradient patterns (LGP) of the KH maps to narrow the search space, followed by a similarity matching, the normalized cross correlation of patterns being matched. The accuracy and matching compatibility, comparable or improved in relation to the 2D matching methods, is verified through matching 3D fingerprints from two databases one acquired using OCT and a public database gently made available by the Hong Kong Polytechnic University. The OCT database, the first 3D database acquired using Optical Coherence Tomography, to our knowledge, is made of images collected from eleven volunteers in two scanning sessions and contains images of people of different ages, genders and ethnicities and also cases of scars, calluses and alterations as abrasion and scratches. A 2D fingerprint database, scanned from the same volunteers using a regular fingerprint reader was also obtained for comparison with traditional matching methods. We investigate the applicability of our method to the identification of altered fingerprints, damaged unintentionally or accidentally. In these cases, the 3D dermal fingerprint, compatible with the epidermis fingerprint, is employed. Matching with 3D dermal and epidermal fingerprints is tested in the OCT database. Matching accuracy is compared with the obtained using traditional matching 2D methods by using False Acceptance and False rejection rate (FARxFRR) and Cumulative Matching Characteristics (CMC) graphs. Unwrapped fingerprints, 2D fingerprints extracted from 3D fingerprints by virtual unrolling were generated and tested for compatibility with 2D databases. A set of quality evaluation measures were employed to the 3D fingerprint databases and their correspondence to the matching scores was analyzed to identify those that can contribute to improve the matching accuracy. Key-words: 3D Fingerprints. Biometric identification. Optical Coherence Tomography