<p>Basement membrane (BM) is the thin, dense, highly cross-linked form of extracellular matrix that underlies all epithelia and endothelia, as well as surrounds muscle, nerve and fat. These sheet-like networks function as physiological barriers to maintain tissue homeostasis. During normal developmental processes and immune surveillance, cells invade through BM to establish tissues and fight infection. Similarly, metastatic cancer cells are thought to co-opt normal programs for BM transmigration as they spread from primary tumors and colonize distant tissues. The difficulty of visualizing cell-BM interactions during invasion in vivo has left the cellular and molecular mechanisms used to breach BM undefined. Specialized F-actin-rich matrix-degrading membrane protrusions, termed invadosomes, have been described in cultured invasive cell lines for more 30 years. Invadosomes are hypothesized to mediate BM penetration during cancer metastasis. Despite promising advances in intravital imaging technologies, however, invadosomes have yet to be observed in cells transmigrating BM in vivo, leaving their physiological relevance unclear. Anchor cell invasion in C. elegans is a simple in vivo model of cell invasion that allows for combined visual and genetic analysis of BM transmigration. In this dissertation I develop high-resolution time-lapse imaging approaches to understand the dynamic interactions that occur at the AC-BM interface during invasion. Through the course of this work we identify an integrin-based mechanism that polarizes the AC towards the BM. We further discover protrusive F-actin-based invadosome structures that mediate BM breach during anchor cell (AC) invasion. We find that in most cases only one or two invadosomes penetrate the BM and then transform into an invasive protrusion that guides the AC through a single BM gap. Using genetics and quantitative single-cell image analysis we characterize several molecular regulators of invadosome formation in vivo. Our findings establish an essential role for invadosomes during BM transmigration in vivo, and support the idea that these structures are a core, conserved element of a normal invasive cellular strategy activated during cancer metastasis.</p> / Dissertation

In biology, many different kinds of microscopy are used to study cells. There are many different kinds of transmission microscopy, where light is passed through the cells, that can be used without staining or other treatments that can harm the cells. There is also fluorescence microscopy, where fluorescent proteins or dyes are placed in the cells or in parts of the cells, so that they emit light of a specific wavelength when they are illuminated with light of a different wavelength. Many fluorescence microscopes can take images on many different depths in a sample and thereby build a three-dimensional image of the sample. Fluorescence microscopy can also be used to study particles, for example viruses, inside cells. Modern microscopes often have digital cameras or other equipment to take images or record time-lapse video. When biologists perform experiments on cells, they often record image sequences or sequences of three-dimensional volumes to see how the cells behave when they are subjected to different drugs, culture substrates, or other external factors. Previously, the analysis of recorded data has often been done manually, but that is very time-consuming and the results often become subjective and hard to reproduce. Therefore there is a great need for technology for automated analysis of image sequences with cells and particles inside cells. Such technology is needed especially in biological research and drug development. But the technology could also be used clinically, for example to tailor a cancer treatment to an individual patient by evaluating different treatments on cells from a biopsy. This thesis presents algorithms to find cells and particles in images, and to calculate tracks that show how they have moved during an experiment. We have developed a complete system that can find and track cells in all commonly used imaging modalities. We selected and extended a number of existing segmentation algorithms, and thereby created a complete tool to find cell outlines. To link the segmented objects into tracks, we developed a new track linking algorithm. The algorithm adds tracks one by one using dynamic programming, and has many advantages over prior algorithms. Among other things, it is fast, it calculates tracks which are optimal for the entire image sequence, and it can handle situations where multiple cells have been segmented incorrectly as one object. To make it possible to use information about the velocities of the objects in the linking, we developed a method where the positions of the objects are preprocessed using a filter before the linking is performed. This is important for tracking of some particles inside cells and for tracking of cell nuclei in some embryos.       We have developed an open source software which contains all tools that are necessary to analyze image sequences with cells or particles. It has tools for segmentation and tracking of objects, optimization of settings, manual correction, and analysis of outlines and tracks. We developed the software together with biologists who used it in their research. The software has already been used for data analysis in a number of biology publications. Our system has also achieved outstanding performance in three international objective comparisons of systems for tracking of cells. / Inom biologi används många olika typer av mikroskopi för att studera celler. Det finns många typer av genomlysningsmikroskopi, där ljus passerar genom cellerna, som kan användas utan färgning eller andra åtgärder som riskerar att skada cellerna. Det finns också fluorescensmikroskopi där fluorescerande proteiner eller färger förs in i cellerna eller i delar av cellerna, så att de emitterar ljus av en viss våglängd då de belyses med ljus av en annan våglängd. Många fluorescensmikroskop kan ta bilder på flera olika djup i ett prov och på så sätt bygga upp en tre-dimensionell bild av provet. Fluorescensmikroskopi kan även användas för att studera partiklar, som exempelvis virus, inuti celler. Moderna mikroskop har ofta digitala kameror eller liknande utrustning för att ta bilder och spela in bildsekvenser. När biologer gör experiment på celler spelar de ofta in bildsekvenser eller sekvenser av tre-dimensionella volymer för att se hur cellerna beter sig när de utsätts för olika läkemedel, odlingssubstrat, eller andra yttre faktorer. Tidigare har analysen av inspelad data ofta gjorts manuellt, men detta är mycket tidskrävande och resultaten blir ofta subjektiva och svåra att reproducera. Därför finns det ett stort behov av teknik för automatiserad analys av bildsekvenser med celler och partiklar inuti celler. Sådan teknik behövs framförallt inom biologisk forskning och utveckling av läkemedel. Men tekniken skulle också kunna användas kliniskt, exempelvis för att skräddarsy en cancerbehandling till en enskild patient genom att utvärdera olika behandlingar på celler från en biopsi. I denna avhandling presenteras algoritmer för att hitta celler och partiklar i bilder, och för att beräkna trajektorier som visar hur de har förflyttat sig under ett experiment. Vi har utvecklat ett komplett system som kan hitta och följa celler i alla vanligt förekommande typer av mikroskopi. Vi valde ut och vidareutvecklade ett antal existerande segmenteringsalgoritmer, och skapade på så sätt ett heltäckande verktyg för att hitta cellkonturer. För att länka ihop de segmenterade objekten till trajektorier utvecklade vi en ny länkningsalgoritm. Algoritmen lägger till trajektorier en och en med hjälp av dynamisk programmering, och har många fördelar jämfört med tidigare algoritmer. Bland annat är den snabb, den beräknar trajektorier som är optimala över hela bildsekvensen, och den kan hantera fall då flera celler felaktigt segmenterats som ett objekt. För att kunna använda information om objektens hastighet vid länkningen utvecklade vi en metod där objektens positioner förbehandlas med hjälp av ett filter innan länkningen utförs. Detta är betydelsefullt för följning av vissa partiklar inuti celler och för följning av cellkärnor i vissa embryon. Vi har utvecklat en mjukvara med öppen källkod, som innehåller alla verktyg som krävs för att analysera bildsekvenser med celler eller partiklar. Den har verktyg för segmentering och följning av objekt, optimering av inställningar, manuell korrektion, och analys av konturer och trajektorier. Vi utvecklade mjukvaran i samarbete med biologer som använde den i sin forskning. Mjukvaran har redan använts för dataanalys i ett antal biologiska publikationer. Vårt system har även uppnått enastående resultat i tre internationella objektiva jämförelser av system för följning av celler. / <p>QC 20161125</p>

Birds are a key environmental asset and this is recognised through comprehensive legislation and policy ensuring their protection and conservation. Many species are active at night and surveys are required to understand the implications of proposed developments such as towers and reduce possible conflicts with these structures. Night vision devices are commonly used in nocturnal surveys, either to scope an area for bird numbers and activity, or in remotely sensing an area to determine potential risk. This thesis explores some practical and theoretical approaches that can improve the accuracy, confidence and efficiency of nocturnal bird surveillance. As image intensifiers and thermal imagers have operational differences, each device has associated strengths and limitations. Empirical work established that image intensifiers are best used for species identification of birds against the ground or vegetation. Thermal imagers perform best in detection tasks and monitoring bird airspace usage. The typically used approach of viewing bird survey video from remote sensing in its entirety is a slow, inaccurate and inefficient approach. Accuracy can be significantly improved by viewing the survey video at half the playback speed. Motion detection efficiency and accuracy can be greatly improved through the use of adaptive background subtraction and cumulative image differencing. An experienced ornithologist uses bird flight style and wing oscillations to identify bird species. Changes in wing oscillations can be represented in a single inter-frame similarity matrix through area-based differencing. Bird species classification can then be automated using singular value decomposition to reduce the matrices to one-dimensional vectors for training a feed-forward neural network.

La formation d'un organe repose sur la coordination spatio-temporelle du positionnement et de la différenciation de progéniteurs. La finalité de ces évènements permet la constitution structurelle de l'organe et la production de la diversité cellulaire nécessaire pour assurer ses fonctions. L'épithélium olfactif de l'embryon de poisson-zèbre est issu de la migration de progéniteurs qui vont générer entre autres les neurones olfactifs. Au cours de ma thèse je me suis intéressé aux bases génétiques et moléculaires de la coordination de la morphogenèse et de la neurogenèse de cet épithélium tout en étudiant l'origine de la diversité des types cellulaires olfactifs. L'imagerie en temps réel m'a permis de caractériser la migration de ces progéniteurs en générant une carte morphométrique de leur déplacement. Mon travail de thèse révèle que le proneural Neurog1 régule directement l'expression de cxcr4b, un récepteur au chimiokine, dans les progéniteurs olfactifs assurant leur positionnement. Ainsi, Neurog1 coordonnerait la position et l'identité des progéniteurs olfactifs via ses cibles transcriptionnelles. Au sein de l'épithélium olfactif dans l'embryon, deux populations cellulaires (neurones à GnRH et neurones à microvillosités) ont été décrites comme provenant des crêtes neurales céphaliques (CNC). J'ai pu montrer que l'expression de marqueurs spécifiques de ces populations n'est pas affectée dans un contexte d'absence de différenciation des CNCs (sox10-/-) suggérant que ces types cellulaires ne dérivent pas de ce territoire. Afin d'identifier leur territoire d'origine, j'ai développé une méthode d'imagerie en temps réel, le backtracking, qui m'a permis de déterminer que la région de la placode olfactive, et non les crêtes neurales, génère ces deux types cellulaires. Ainsi j'ai pu définir la source de ces deux populations neuronales tout en minimisant la contribution des crêtes neurales. En conclusion mes résultats suggèrent que la diversité des neurones olfactifs serait produite localement et ceci conjointement à la morphogenèse de l'épithélium. / The correct development of sensory organs relies on the coordination between changes in progenitor positioning over time and the differentiation/specification of different neural subtypes. The outcome of this coordination is proper organ shape and cell diversity, which are required for functionality. The zebrafish embryonic olfactory epithelium arises from progenitor migration and differentiation. During my PhD, I studied the genetic and molecular basis of morphogenesis in this tissue, and how this is coordinated with neurogenesis, as well as revisiting the origin of olfactory cell type diversity.First, I generated a morphometric map of olfactory progenitors through the characterization of their migration in live embryos. Next, I showed that the proneural transcription factor Neurog1 directly regulates cxcr4b expression, a chemokine receptor that has already been shown to govern olfactory progenitor positioning. Thus, Neurog1 orchestrates olfactory progenitor position and the generation of olfactory neurons via distinct transcriptional targets. Secondly, I addressed the origin of olfactory neuron diversity. Within the embryonic olfactory epithelium, two cell populations (GnRH neurons and microvillous neurons) have been described as cephalic neural crest (CNC) derivatives. I found, however, that the expression of specific markers of both populations is unaffected in a genetic context blocking CNC differentiation. To revisit the lineage assignment of these cell types, I developed a backtracking approach through time-lapse live imaging. I found that both populations are derived from classical olfactory placode progenitor and not the CNC. In conclusion, my results indicate that heterogeneity of olfactory cell-types is locally generated, and concomitant with morphogenesis of the placode.

The CO2SINK (and CO2MAN) project is the first onshore CO2 storage project in Europe. The research site is located near the town of Ketzin, close to Potsdam in Germany. Injection started in June 2008, with a planned injection target of 100,000 tonnes of CO2. In February 2011, around 45, 000 tons of CO2 had been injected into the saline aquifer at an approximate depth of 630 m. This thesis focuses on time-lapse analysis of borehole seismic data, surface seismic data and reservoir characterization at the Ketzin site. Baseline Moving Source Profiling (MSP) data were acquired in the borehole Ketzin 202/2007 (OW2), along seven lines in 2007. The zero-offset Vertical Seismic Profile (VSP) data were acquired in the same borehole. The main objective of the VSP and MSP survey was to generate high-resolution seismic images around the borehole. After modeling and data processing, the sandy layers within the Stuttgart Formation can potentially be imaged in the VSP and MSP data whereas reflections from these layers are not as clearly observed in the 3D surface seismic data. 2D and pseudo-3D time-lapse seismic surveys were conducted at the Ketzin site. Interpretation of 2D baseline and repeat stacks shows that no CO2 leakage related time lapse signature is observable where the 2D lines allow monitoring of the reservoir. This is consistent with the time-lapse results of the 3D surveys showing an increase in reflection amplitude just centered around the injection well. The results from the pseudo-3D surveys are also consistent with the 3D seismic time-lapse studies and show that the sparse pseudo-3D geometry can be used to qualitatively map the CO2 in the reservoir with significantly less effect than the full 3D surveying. The 2nd pseudo-3D repeat survey indicates preferential migration of the CO2 to the west. There are no indications of migration into the caprock on either of the repeat surveys. Amplitude Versus Offset (AVO) analysis was performed on both 2D and 3D repeat surveys. A Class 3 AVO anomaly is clearly observed on the 3D repeat data and matches the synthetic modeling well. No AVO anomaly was observed on the 2D repeat data, which was anticipated, but the result shows signs of a pressure response at the reservoir level in the data. Reflection coefficients were calculated using surface seismic data (3D and pseudo-3D) at the site. Pre-injection calculations agree well with calculations from logging data. Post-injection calculations are in general agreement with the seismic modeling, but generally show higher amplitudes than those expected. The full 3D data show a better image of the reflection coefficients before and after injection than the pseudo-3D data and can potentially be used to make quantitative calculations of CO2 volumes. The pseudo-3D data only provide qualitative information.

Die vorliegende Arbeit beschäftigt sich mit der Bestimmung von räumlich und zeitlich hochaufgelösten Bewegungsvektorfeldern von Gletschern aus monokularen Bildsequenzen. Diese stellen eine wertvolle Grundlage für glaziologische Analysen des Bewegungsverhaltens von Gletschern dar. Im Rahmen der Arbeit wurden Bildsequenzmessungen an fünf schnellfließenden Gletschern im Bereich der Diskobucht in Westgrönland durchgeführt. Insbesondere erfolgte die Aufnahme von Bildsequenzen und multi-temporalen Laserscannerdaten am Jakobshavn Isbræ, einem der schnellsten und produktivsten Gletscher Grönlands. Diese Messungen bilden die Datengrundlage der Arbeit. Es werden Messkonzepte zur Aufnahme der entsprechenden Bildsequenzen und multi-temporalen Laserscans bereitgestellt sowie Methoden entwickelt, um die Auswertung dieser Daten nach dem Prinzip der monoskopischen Bildsequenzanalyse zu ermöglichen. Die Bildsequenzen und multi-temporalen Laserscans werden von einem festen Standpunkt aus aufgenommen. Die Ableitung von Bewegungsvektorfeldern erfolgt dann durch eine automatische Zuordnung von Grauwertmustern in den Bildsequenzen bzw. durch die Zuordnung von 3D-Punktmustern in den multi-temporalen Laserscannerdaten. Bestehende Punktzuordnungsmethoden werden einerseits an die besonderen Eigenschaften der Gletscherdaten angepasst, andererseits werden geeignete Methoden zur Lösung von Detailproblemen neu entwickelt. Die Methodik der Bildsequenzanalyse wird dabei vor allem hinsichtlich ihrer Robustheit – beispielsweise gegenüber durch Schattenwurf verursachten Störungen im Bild – optimiert und es werden Bewegungseffekte in den Bildsequenzen korrigiert, die durch die Eigenbewegung der Kamera verursacht werden. Bei der Entwicklung der Methodik zur Analyse multitemporaler Laserscannerdaten werden vor allem Effekte berücksichtigt, die durch das sequenzielle Aufnahmeprinzip eines Scanners auftreten. Auf Basis der entwickelten und implementierten Methodik erfolgt die Auswertung der aufgenommenen Bildsequenzen und multi-temporalen Laserscans. Das Ergebnis der monoskopischen Bildsequenzauswertung ist ein dichtes Raster an Bewegungskurven für jede Bildsequenz. Die einzelnen Translationen der Bewegungskurven können mit einer Genauigkeit von einigen Zentimetern bis zu einem Dezimeter bestimmt werden. Die Auswertung der Laserscannerdaten liefert räumlich hochaufgelöste digitale Geländemodelle der Gletscheroberfläche sowie ein dichtes Raster von 3D-Bewegungsvektoren, deren Genauigkeit im Dezimeterbereich liegt. Anhand von Beispielen wird gezeigt, dass sich die aus monokularen Bildsequenzen abgeleiteten Bewegungsvektorfelder zur Bestimmung frontnaher Geschwindigkeitsfelder mit hoher räumlicher Auflösung, zur Ableitung der Lage und der Migration der Aufsetzlinie aus gezeiteninduzierten Vertikalbewegungen sowie zur Untersuchung des Geschwindigkeitsverhalten von Gletschern bei Kalbungsereignissen eignen. Aus den Laserscannerdaten können hochaufgelöste digitale Geländemodelle zur Dokumentation von Fronthöhen und Gletscherstrukturen abgeleitet werden, zudem eignen sie sich zur Bestimmung von Geschwindigkeitsfeldern, die eine sehr hohe räumliche Auflösung besitzen. / This research aims to determine the motion vector fields of glaciers with high spatial and temporal resolution. These vector fields can be derived from monocular image sequences and are a valuable data source for glaciological analysis of the motion behaviour of glaciers. Image sequence measurements have been conducted at five fast-flowing glaciers in the Disko Bay region in western Greenland. Especially at the Jakobshavn Isbræ – one of the fastest and most productive glaciers in Greenland – numerous image sequences have been recorded, as well as multi-temporal laser scanner data sets. These measurements provide the basic data sets for this thesis. The measurement concepts for the acquisition of image sequences and multi-temporal laser scans are presented, and procedures for the processing of the recorded data are developed, based on the principle of monoscopic image sequence analysis. Both the image sequences and multi-temporal laser scans are acquired statically. Motion vector fields can be derived by applying automatic co-registration methods on grey value patterns in the image sequences and on 3D point patterns in the laser scanner datasets respectively. Thus, standard matching techniques have been adapted to the special characteristics of the glacier data, and suitable methods that solve detail problems have been developed in addition. The method of the image sequence analysis has been optimised with respect to its robustness against errors caused by moving shadows. Furthermore, motion effects caused by small instabilities in the camera setup have been corrected. Regarding the analysis of multi-temporal laser scanner data, effects that occur because of the sequential acquisition principle of a laser scanner must also be considered. Based on the developed method, the image sequences and multi temporal laser scans have been processed. The result of the monoscopic image sequence analysis is a dense raster of trajectories for each image sequence. Each translation component from these trajectories can be determined with an accuracy of some centimeters up to one decimetre. The processing of the laser scanner data provides digital surface models of the glacier with high spatial resolution, and a dense raster of 3D motion vectors with accuracy in the range of decimetres. Specific examples show that motion vector fields derived from monocular image sequences can be used for the determination of high resolution velocity fields of glaciers, for the determination of the position and migration of the grounding line and for the investigation of a glacier’s motion behaviour during calving events. From the multi-temporal laser scanner data, velocity fields with high spatial resolution can be derived as well as digital surface models from single scans that document glacier front heights and glacier structures.

Hydrocarbon deposits in the form of petroleum, natural gas, and natural gas hydrates occur offshore worldwide. Electromagnetic methods that measure the electrical resistivity of sediments can be used to map, assess, and monitor these resistive targets. In particular, quantitative assessment of hydrate content in marine deposits, which form within the upper few hundred meters of seafloor, is greatly facilitated by complementing conventional seismic methods with EM data. The North-East Pacific Time-series Undersea Network Experiment (NEPTUNE) is an underwater marine observatory that provides power and network connection to a host of instruments installed on the seafloor on the Cascadia Margin offshore Vancouver Island. The observatory’s aim is to provide a platform for very long-term studies in which access to data is available on a continuous basis. For this thesis project, a transient dipole-dipole time-domain EM system was constructed and deployed on the NEPTUNE network with the goal of long-term monitoring of a well-studied hydrate deposit in the area. The instrument includes a source transmitter of electrical current and individual receivers to measure small electric field variations. The instrument is powered by the NEPTUNE observatory and data can be collected remotely by connecting to the instrument through the web. Data collected so far from the instrument are consistent with a resistive structure. The best fitting model from 1D inversion is a 36 ± 3 m thick layer of 5.3 ± 0.3 Ωm resistivity, overlaying a less resistive 0.7 ± 0.1 Ωm halfspace. Average hydrate concentration, deduced with the aid of ODP-889 well-log derived Archie’s parameters, is approximately 72% of pore space in the resistive layer, consistent with the very high concentration of gas hydrates (~80%) recovered from seafloor cores. The weekly collection of data from the instrument shows that the resistive structure has changed little since monitoring began in October of 2010.

Hydrocarbon deposits in the form of petroleum, natural gas, and natural gas hydrates occur offshore worldwide. Electromagnetic methods that measure the electrical resistivity of sediments can be used to map, assess, and monitor these resistive targets. In particular, quantitative assessment of hydrate content in marine deposits, which form within the upper few hundred meters of seafloor, is greatly facilitated by complementing conventional seismic methods with EM data. The North-East Pacific Time-series Undersea Network Experiment (NEPTUNE) is an underwater marine observatory that provides power and network connection to a host of instruments installed on the seafloor on the Cascadia Margin offshore Vancouver Island. The observatory’s aim is to provide a platform for very long-term studies in which access to data is available on a continuous basis. For this thesis project, a transient dipole-dipole time-domain EM system was constructed and deployed on the NEPTUNE network with the goal of long-term monitoring of a well-studied hydrate deposit in the area. The instrument includes a source transmitter of electrical current and individual receivers to measure small electric field variations. The instrument is powered by the NEPTUNE observatory and data can be collected remotely by connecting to the instrument through the web. Data collected so far from the instrument are consistent with a resistive structure. The best fitting model from 1D inversion is a 36 ± 3 m thick layer of 5.3 ± 0.3 Ωm resistivity, overlaying a less resistive 0.7 ± 0.1 Ωm halfspace. Average hydrate concentration, deduced with the aid of ODP-889 well-log derived Archie’s parameters, is approximately 72% of pore space in the resistive layer, consistent with the very high concentration of gas hydrates (~80%) recovered from seafloor cores. The weekly collection of data from the instrument shows that the resistive structure has changed little since monitoring began in October of 2010.

L’objectif de la thèse est de développer une méthodologie permettant d’obtenir une interprétation quantitative des données de sismique répétée (sismique 4D). Une étape essentielle consiste à évaluer la répétitivité des données, puis à filtrer les bruits indésirables, qui peuvent masquer ou détériorer la signature 4D. Une méthodologie basée sur des outils géostatistiques a été développée. Deux fenêtres temporelles des cubes sismiques étudiés sont choisies, l’une au-dessus du réservoir - où aucun effet 4D n’est attendu - et l’autre incluant le réservoir. Une analyse statistique et variographique conduite sur ces différentes fenêtres permet de proposer une décomposition des variogrammes en structures communes ou indépendantes, qui sont ensuite interprétées en termes de bruit, de signature géologique ou 4D. Les structures interprétées comme indépendantes de la géologie ou de la production sont ensuite filtrées à l’aide de la technique du krigeage factoriel proposée par Matheron en 1982. La méthodologie a été testée sur deux cas réels. Le premier concerne un champ d’huiles lourdes canadien, sur lequel trois campagnes sismiques ont été enregistrées, avant et pendant la production obtenue à l’aide d’injection de vapeur. Le bruit interprété comme tel sur les 3 campagnes a été filtré à l’aide la méthode décrite plus haut ; une analyse en termes de faciès sismiques non supervisée a ensuite été conduite sur les données brutes et filtrées afin d’évaluer l’intérêt du filtrage. Finalement, une interprétation des décalages en temps observés entre campagnes a été proposée. Le deuxième cas réel concerne un champ turbiditique profond dans l’offshore du Brésil, sur lequel deux campagnes sismiques 3D ont été acquises, avant et après le début de la production obtenue par injection d’eau. Le bruit présent sur les deux campagnes a été filtré à l’aide de la technique du krigeage factoriel, et la qualité de ce filtrage a pu être évaluée par comparaison avec d’autres techniques couramment utilisées / This thesis research aims at investigating seismic interpretation methodologies and techniques that will help on better characterizing time-lapse, or 4D, seismic signatures. These techniques and methodologies are used to evaluate the time-lapse repeatability and then to filter out undesirable artefacts that are non-related to the production, while enhancing the 4D signature. To achieve these goals, a methodology based on geostatistical tools, was developed. Typically, at least two time-interval windows are considered: one above and the other comprising the reservoir of interest. A statistical and variographic analysis, conducted on both windows and on all surveys, leads to an interpretation step where common or independent structures – in the variographic sense- can be pointed out. The structures interpreted as not related to the geology or to the production mechanism are filtered from the data by a multivariate factorial cokriging technique, based on the concept of Kriging Analysis developed by Matheron in 1982. Two real case time-lapse studies were used to test the methodology. The first case is a Canadian onshore heavy oil reservoir submitted to steam injection, where three different time-lapse surveys were shot to monitor the steam-chamber evolution. The noise present in the three surveys was first filtered using the technique described above; next, an unsupervised seismic facies analysis was conducted on both raw and filtered data in order to evaluate the filtering technique, and finally an interpretation, in terms of reservoir properties changes, of the time-shit observed between the campaigns was proposed. In the second case, the seismic data was acquired on a deepwater turbiditic oilfield from Brazil at two different times of reservoir life, before and after production and water injection. The two seismic surveys were filtered using the factorial kriging technique; the quality of the filtering was, in this case, evaluated by comparison with more common techniques

Live cell imaging is the study of living cells using microscope images and is used by biomedical researchers to provide a novel way to analyze biological functions through cell behavior and motion studies. Cell events are seen as morphological changes in image sequences, and their analysis has great potential for the study of normal/abnormal phenotypes and the effectiveness of drugs. While current quantitative cell analysis typically focuses on measuring whole populations of cells, we need to be able to recognize cell events at the single cell level, identify these events automatically, and analyze these events over time. For this reason, we developed and evaluated several novel automatic single cell event detection and analysis methods based on a detailed knowledge of the cell cycle and other cell event characteristics. The first method detects significant events within the temporal sequence using a machine learning method to use features derived from segmented cell images. We used a Neural Network (NN) algorithm to classify cell events to pre-defined categories. The second and third methods apply statistical and econometric techniques originally developed for time-series analysis of financial markets to facilitate the identification of cell entry into mitosis. We developed graph trend analysis and paired graph analysis methods from trend analysis and pairs trading to determine significant data points in cell feature data. The final method determines the position of cells in order to associate daughter cells with their parent cells after mitosis using Kalman filter techniques. By using the Kalman filter approach, we estimated future cell border centroid positions and successfully associated daughter cells with their parent cells after mitosis. In this study, the performance of these novel computer vision algorithms for automatic cell event detection and analysis were evaluated and verified by applying models to different image sequences from the Large Scale Digital Cell Analysis System (LSDCAS). The results show that the approaches developed can yield significant improvements over existing algorithms.