The main purpose of the project was to create an initial lab set-up for a dig-ital in-line holographic microscope and a reconstruction algorithm. Different parameters including: light source, pin-hole size and distances pinhole-object and object-camera had to be optimized. The lab set-up is to be developed further by a master student at the University of Nairobi and then be used for malaria detection in blood samples. To acquire good enough resolution for malaria detection it has been found necessary to purchase a gray scale camera with smaller pixel size. Two dierent approaches, in this report called the on-sensor approach and the object-magnication approach, were investigated. A reconstruction algorithm anda phase recovery algorithm was implemented as well as a super resolution algorithm to improve resolution of the holograms. The on-sensor approach proved easier and cheaper to use with approximately the same results as the object-magnication method. Necessary further research and development of experimental set-up was thoroughly discussed. / Projketet har gått ut på att bygga en billigare och enklare metod för att identifiera malaria i blodprover. Malaria är ett stort problem i en mängd områden i världen. Flera av dessa är fattiga och kan i nuläget inte tillhandahålla den här tjänsten till sin befolkning. Förutom att dyr apparatur krävs måste även utbildad personal lägga ner mycket tid för att kolla en stor mängd blodprover för att statistiskt säkerställa om en person har malaria eller inte. Vårt mål var att bygga en labbuppställning för "Digital in line holographic microscopy" och en rekonstruktionsalgoritm som en masterstudent vid Nairobi universitet ska fortsätta utveckla. Vi kom också fram till vilken upplösning som krävdes för att kunna urskilja malaria i blodproverna. Digital in line holographic microscopy går till så att man har en ljuskälla som riktas genom ett pinnhål, ljuset som går genom pinnhålet ljuser upp det prov, blodproverna i vårt fall, man vill undersöka och det resulterande ljuset fångas på en kamera. Med kunskap om fourieroptik går det att rekonstruera den digitala bilden man fångat på kameran, innan rekonstruktion är den ett hologram vilken är svårtydd. Labbuppställningen byggdes delvis med en 3D printer. För att förbättra resultaten implementerades flera algoritmer vilka lade ihop en mängd förskjutna bilder till en bättre bild, så kallad super resolution. Vi lyckades inte komma till den upplösning som krävdes för att urskilja malaria men gjorde en grundlig förstudie och en utförlig beskrivning av det arbete som väntar den student som fortsätter med projektet. Framför allt beskrevs värden på parametrar och vilken typ av kamera som ska användas för att optimera uppställningen.

Dans cette thèse, l'holographie numérique dans l'axe (DIH) est la principale méthode optique utilisée pour analyser des inclusions dans une gouttelette. L'holographie numérique dans l'axe est utilisée pour caractériser des inclusions du point de vue de leur taille, leur position 3D et leur trajectoire à l'intérieur de la gouttelette. Comme les particules sont situées à l'intérieur d'une gouttelette, le front d'onde incident sur l'inclusion est modifié avant qu'il l'illumine. Le défi de ce travail est double : premièrement de prendre en compte la forme de la gouttelette dans le modèle d'holographie et deuxièmement d'étendre l'analyse aux inclusions transparentes (type objet de phase). Pour décrire l'hologramme enregistré par le capteur CCD, l'intégrale d'Huygens-Fresnel et le formalisme des matrices ABCD ont été utilisés. Dans ce modèle, nous introduisons les polynômes de Zernike pour décrire la fonction de transmission d'une particule. Pour l'analyse des hologrammes, l'outil mathématique de la transformation de Fourier fractionnaire 2D (2D-FRFT) est utilisé pour restituer l'image des inclusions et dans ce cas une mesure la taille de l'inclusion et de sa position 3D sont réalisées. Les trajectoires des inclusions dans la goutte est possible avec un long temps de pose de l'obturateur du capteur CCD. Nous avons également proposé un nouveau modèle pour décrire des objets de phases quelconque et des particules opaques. Pour ce nouveau modèle, les mêmes procédés ont été utilisés. Dans le cas d'inclusions filiformes à l'intérieur d'une géométrie cylindrique comme un canal, une méthode de simulation d'imagerie interférométrique multi-coeurs est proposée. Dans ce cas, une somme de distributions de Dirac, localisées le long d'une droite, introduite dans l'intégrale de Fresnel généralisée (c'est-à-dire le formalisme des matrices ABCD et l'intégrale de Fresnel) permet d'obtenir un bon degré de similitude entre l'expérience et la simulation. / In this thesis, the digital in-line holography (DIH) is the main optical method used to analyze inclusions in a droplet. The digital in-line holography is used to characterize the inclusions in terms of of their size, their 3D position, and their trajectories inside the droplet. Since the particles are located within a droplet, the incident wavefront is changed before it illuminates the inclusions. The challenge of this work has two points : first to take into account the shape of the droplet in the holographic model and secondly to extend the analysis to the transparent inclusions (phase object). To describe the hologram recorded by the CCD sensor, the Huygens-Fresnel integral and the ABCD matrix formalism were used. In this model, we introduce the Zernike polynomials to describe the transmission function of a particle. For the analysis of holograms, the2D fractional Fourier transformation (2D-FRFT) is used to reconstruct the image of inclusions and in this case the size and their 3D position of the inclusions are performed.The trajectories of the inclusions in the drop are possible tracked with a long exposure shutter speed of the CCD. We also proposed a new simulation to describe objects of any phases and opaque particles. For this simulation, the same methods of reconstruction were used. In the case of micro-channel inclusions inside a cylindrical geometry such as a pipe, the interferometric imaging of multi-core pipe is proposed. In this case, summation of Dirac delta distribution, located along a line, introduced into the generalized Fresnel integral allows us to get a good agreement between the experiment and the simulation.

<p>A droplet subjected to external aerodynamic disturbances disintegrates into smaller droplets and is known as secondary atomization. Droplet breakup has been studied for low Ohnesorge (<b><i>Oh < </i></b>0.1) numbers and good agreement has been seen amongst researchers. However, when it comes to cases with high the <b><i>Oh</i></b> number, i.e. atomization where the influence of viscosity is significant, very little data is available in the literature and poor agreement is seen amongst researchers. </p> <p> </p> <p>This thesis presents a complete analysis of the modes of deformation and breakup exhibited by a droplet subjected to continuous air flow. New modes of breakup have been introduced and an intermediate case with no droplet fragmentation has been discovered. Further, results are presented for droplet size-velocity distributions. In addition, Digital in-line holography (DIH) was utilized to quantify the size-velocity pdfs using a hybrid algorithm. Finally, particle image velocimetry (PIV) was employed to characterize the air flow in the unique cases where drops exhibited no breakup and cases with multiple bag formation. </p> <p> </p> <p>A droplet subjected to external aerodynamic disturbances disintegrates into smaller droplets and is known as secondary atomization. Secondary breakup finds relevance is almost every industry that utilizes sprays for their application. </p> <p> </p>

Biological studies always start from curious observations. This is exemplified by description of cells for the first time by Robert Hooke in 1665, observed using his microscope. Since then the field of microscopy and cell biology grew hand in hand, with one field pushing the growth of the other and vice-versa. From basic description of cells in 1665, with parallel advancements in microscopy, we have travelled a long way to understand sub-cellular processes and molecular mechanisms. With each day, our understanding of cells increases and several questions are being posed and answered. Several high-resolution microscopic techniques are being introduced (PALM, STED, STORM, etc.) that push the resolution limit to few tens of nm, taking us to a new era where ‘seeing is believing'. Having said this, it is to be noted that the world of cells is vast, with information spread from nanometers to millimetres, and also over extended time-period, implying that not just one microscopic technique could acquire all the available information. The knowledge in the field of cell biology comes from a combination of imaging and quantifying techniques that complement one another.Majority of modern-day microscopic techniques focuses on increasing resolution which, is achieved at the expense of cost, compactness, simplicity, and field of view. The substantial decrease in the field of observation limits the visibility to a few single cells at best. Therefore, despite our ability to peer through the cells using increasingly powerful optical instruments, fundamental biology questions remain unanswered at mesoscopic scales. A global view of cell population with significant statistics both in terms of space and time is necessary to understand the dynamics of cell biology, taking in to account the heterogeneity of the population and the cell-cell variability. Mesoscopic information is as important as microscopic information. Although the latter gains access to sub-cellular functions, it is the former that leads to high-throughput, label-free measurements. By focussing on simplicity, cost, feasibility, field of view, and time-lapse in-incubator imaging, we developed ‘Lensfree Video Microscope' based on digital in-line holography that is capable of providing a new perspective to cell culture monitoring by being able to capture the kinetics of thousands of cells simultaneously. In this thesis, we present our lensfree video microscope and its applications in in-vitro cell culture monitoring and quantification.We validated the system by performing more than 20,000 hours of real-time imaging, in diverse conditions (e.g.: 37°C, 4°C, 0% O2, etc.) observing varied cell types and culture conditions (e.g.: primary cells, human stem cells, fibroblasts, endothelial cells, epithelial cells, 2D/3D cell culture, etc.). This permitted us to develop label-free cell based assays to study the major cellular events – cell adhesion and spreading, cell division, cell division orientation, cell migration, cell differentiation, network formation, and cell death. The results that we obtained respect the heterogeneity of the population, cell to cell variability (a raising concern in the biological community) and the massiveness of the population, whilst adhering to the standard cell culture practices - a rare combination that is seldom attained by existing real-time monitoring methods.We believe that our microscope and associated metrics would complement existing techniques by bridging the gap between mesoscopic and microscopic information. / Biological studies always start from curious observations. This is exemplified by description of cells for the first time by Robert Hooke in 1665, observed using his microscope. Since then the field of microscopy and cell biology grew hand in hand, with one field pushing the growth of the other and vice-versa. From basic description of cells in 1665, with parallel advancements in microscopy, we have travelled a long way to understand sub-cellular processes and molecular mechanisms. With each day, our understanding of cells increases and several questions are being posed and answered. Several high-resolution microscopic techniques are being introduced (PALM, STED, STORM, etc.) that push the resolution limit to few tens of nm, taking us to a new era where ‘seeing is believing'. Having said this, it is to be noted that the world of cells is vast, with information spread from nanometers to millimetres, and also over extended time-period, implying that not just one microscopic technique could acquire all the available information. The knowledge in the field of cell biology comes from a combination of imaging and quantifying techniques that complement one another.Majority of modern-day microscopic techniques focuses on increasing resolution which, is achieved at the expense of cost, compactness, simplicity, and field of view. The substantial decrease in the field of observation limits the visibility to a few single cells at best. Therefore, despite our ability to peer through the cells using increasingly powerful optical instruments, fundamental biology questions remain unanswered at mesoscopic scales. A global view of cell population with significant statistics both in terms of space and time is necessary to understand the dynamics of cell biology, taking in to account the heterogeneity of the population and the cell-cell variability. Mesoscopic information is as important as microscopic information. Although the latter gains access to sub-cellular functions, it is the former that leads to high-throughput, label-free measurements. By focussing on simplicity, cost, feasibility, field of view, and time-lapse in-incubator imaging, we developed ‘Lensfree Video Microscope' based on digital in-line holography that is capable of providing a new perspective to cell culture monitoring by being able to capture the kinetics of thousands of cells simultaneously. In this thesis, we present our lensfree video microscope and its applications in in-vitro cell culture monitoring and quantification.We validated the system by performing more than 20,000 hours of real-time imaging, in diverse conditions (e.g.: 37°C, 4°C, 0% O2, etc.) observing varied cell types and culture conditions (e.g.: primary cells, human stem cells, fibroblasts, endothelial cells, epithelial cells, 2D/3D cell culture, etc.). This permitted us to develop label-free cell based assays to study the major cellular events – cell adhesion and spreading, cell division, cell division orientation, cell migration, cell differentiation, network formation, and cell death. The results that we obtained respect the heterogeneity of the population, cell to cell variability (a raising concern in the biological community) and the massiveness of the population, whilst adhering to the standard cell culture practices - a rare combination that is seldom attained by existing real-time monitoring methods.We believe that our microscope and associated metrics would complement existing techniques by bridging the gap between mesoscopic and microscopic information.