Academic literature on the topic 'Time-lapse video analysis'

Abstract STUDY QUESTION Is it possible to develop an automated annotation tool for human embryo development in time-lapse devices based on image analysis? SUMMARY ANSWER We developed and validated an automated software for the annotation of human embryo morphokinetic parameters, having a good concordance with expert manual annotation on 701 time-lapse videos. WHAT IS KNOWN ALREADY Morphokinetic parameters obtained with time-lapse devices are increasingly used for the assessment of human embryo quality. However, their annotation is time-consuming and can be slightly operator-dependent, highlighting the need to develop fully automated approaches. STUDY DESIGN, SIZE, DURATION This monocentric study was conducted on 701 videos originating from 584 couples undergoing IVF with embryo culture in a time-lapse device. The only selection criterion was that the duration of the video must be over 60 h. PARTICIPANTS/MATERIALS, SETTING, METHODS An automated morphokinetic annotation tool was developed based on gray level coefficient of variation and detection of the thickness of the zona pellucida. The detection of cellular events obtained with the automated tool was compared with those obtained manually by trained experts in clinical settings. MAIN RESULTS AND THE ROLE OF CHANCE Although some differences were found when embryos were considered individually, we found an overall concordance between automated and manual annotation of human embryo morphokinetics from fertilization to expanded blastocyst stage (r2 = 0.92). LIMITATIONS, REASONS FOR CAUTION These results should undergo multicentric external evaluation in order to test the overall performance of the annotation tool. Getting access to the export of 3D videos would enhance the quality of the correlation with the same algorithm and its extension to the 3D regions of interest. A technical limitation of our work lies within the duration of the video. The more embryo stages the video contains, the more information the script has to identify them correctly. WIDER IMPLICATIONS OF THE FINDINGS Our system paves the way for high-throughput analysis of multicentric morphokinetic databases, providing new insights into the clinical value of morphokinetics as a predictor of embryo quality and implantation. STUDY FUNDING/COMPETING INTEREST(S) This study was partly funded by Finox-Gedeon Richter Forward Grant 2016 and NeXT (ANR-16-IDEX-0007). We have no conflict of interests to declare. TRIAL REGISTRATION NUMBER N/A

Saccharomyces cerevisiae cnm67Δ cells lack the spindle pole body (SPB) outer plaque, the main attachment site for astral (cytoplasmic) microtubules, leading to frequent nuclear segregation failure. We monitored dynamics of green fluorescent protein–labeled nuclei and microtubules over several cell cycles. Early nuclear migration steps such as nuclear positioning and spindle orientation were slightly affected, but late phases such as rapid oscillations and insertion of the anaphase nucleus into the bud neck were mostly absent. Analyzes of microtubule dynamics revealed normal behavior of the nuclear spindle but frequent detachment of astral microtubules after SPB separation. Concomitantly, Spc72 protein, the cytoplasmic anchor for the γ-tubulin complex, was partially lost from the SPB region with dynamics similar to those observed for microtubules. We postulate that in cnm67Δ cells Spc72–γ-tubulin complex-capped astral microtubules are released from the half-bridge upon SPB separation but fail to be anchored to the cytoplasmic side of the SPB because of the absence of an outer plaque. However, successful nuclear segregation in cnm67Δ cells can still be achieved by elongation forces of spindles that were correctly oriented before astral microtubule detachment by action of Kip3/Kar3 motors. Interestingly, the first nuclear segregation in newborn diploid cells never fails, even though astral microtubule detachment occurs.

We have analysed the behaviour of cultured epidermal keratinocytes using time-lapse video recordings. We have found evidence for heterogeneity in the behaviour of the cells. Some lines underwent extensive self-renewal, thus expanding the population, while others produced daughter cells that migrated suprabasally and are presumed to have undergone terminal differentiation. We also present kinetic data on the cell cycle times, mitotic durations and post-mitotic residence times. The latter is the time between a cell's birth and eventual suprabasal migration. The data suggest that the ‘decision’ to migrate is in some way ‘programmed’ but that the actual migration is a stochastic process. Time-lapse analysis is a very powerful technique for lineage and cell kinetic analysis.

We describe the application of a novel image processing method, which allows quantitative analysis of cell and tissue movement in a series of digitized video images. The result is a vector velocity field showing average direction and velocity of movement for every pixel in the frame. We apply this method to the analysis of cell movement during different stages of the Dictyostelium developmental cycle. We analysed time-lapse video recordings of cell movement in single cells, mounds and slugs. The program can correctly assess the speed and direction of movement of either unlabelled or labelled cells in a time series of video images depending on the illumination conditions. Our analysis of cell movement during multicellular development shows that the entire morphogenesis of Dictyostelium is characterized by rotational cell movement. The analysis of cell and tissue movement by the velocity field method should be applicable to the analysis of morphogenetic processes in other systems such as gastrulation and neurulation in vertebrate embryos.

Despite extensive international acceptance of the critical role of mammalian post-dispersal seed predation in many plant communities, in New Zealand we have limited knowledge of these predators’ influence on plant recruitment in our forests. The principle objective of my thesis was to determine the importance of exotic mammals as post-dispersal seed predators in a New Zealand conifer-broadleaf forest remnant. To address this goal, I used a series of field-based experiments where the actions of different post-dispersal seed predators were separated by wire-mesh exclosures. My study was conducted at Mount Peel Forest Park Scenic Reserve, South Canterbury, New Zealand. Being a human modified conifer forest currently dominated by broadleaf species, it is typical of forest remnants in New Zealand. This presented an opportunity to study a wide range of both potential post-dispersal seed predators and broadleaf tree species. My findings indicate that exotic mammals are not only post-dispersal seed predators at Peel Forest, but are responsible for the majority of post-dispersal predation events observed. Ship rats (Rattus rattus) were the dominant post-dispersal seed predators, while brushtail possums (Trichosurus vulpecula), house mice (Mus musculus) and native invertebrates were also important post-dispersal seed predators for several tree species. Through use of time-lapse video and cafeteria experiments I found that exotic mammalian seed predators, when compared to native invertebrate seed predators, preyed upon larger-seeded plant species and were responsible for considerable seed losses of several tree species. However, exotic mammalian seed predators do share several foraging characteristics with native invertebrate seed predators, as predators foraged in similar habitats and responded in a similar way to changes in seed density. In investigating if post-dispersal seed predation by mammals had a flow-on effect to plant recruitment, I observed natural seedling densities at Peel Forest were significantly higher in the absence of mammalian seed predators, but I found no evidence that the presence of mammals significantly altered the overall species richness. At the community level, I did not find an interaction between habitat and exotic mammals, however I present evidence that for individual plant species a significant mammal : habitat interaction occurred. Consequently, even though my cafeteria experiment implied there was no significant difference in the overall amount of seed preyed upon within different habitats, the less favourable microsite conditions for germination under an intact continuous canopy allows mammals to exacerbate habitat-related patterns of seed mortality and have a noticeable effect on seedling establishment. In an effort to validate the use of manipulative experiments to predict the long-term effect of post-dispersal seed predation on plant dynamics, I attempted to link results of my cafeteria experiment with observed seedling abundance at Peel Forest. Seven tree species were used in this comparison and a strong correlation was observed. This result shows that the level of post-dispersal seed predation determined in the cafeteria experiment provided a good predictor of the effect of mammalian post-dispersal seed predation on seedling establishment. To fully gauge the impact of mammalian post-dispersal seed predators on seedling establishment, the relationship between these seed predators and the type of recruitment limitation experienced by a plant species was also investigated. By using a combination of seed addition, plot manipulations and seed predator exclusion I was able to investigate this relationship. I found evidence that seed limitation at Peel Forest is positively correlated with seed size, and that while mammalian post-dispersal seed predators can further reduce plant recruitment of plant species experiencing seed limitation, the influence of mammals in determining plant recruitment was limited for plant species experiencing microsite limitation. My study has proven that exotic mammals are now the dominant post-dispersal seed predators at Peel Forest, the amount of seed preyed upon varies among plant species, and post-dispersal seed predation by mammalian species can lead to differences in seedling richness and abundance. I proved that the influence of exotic mammals on seedling establishment is also linked to habitat structure and recruitment limitations. When combined these observations suggest that exotic mammalian post-dispersal seed predators may play an important role in determining landscape abundance and distribution of plants at Peel Forest.

Le cortex cérébral primate a subi des modifications majeures pendant l'évolution qui ont permis le développement de fonctions cognitives supérieures. Un accroissement massif a eu lieu avec l'extension spécifique des couches supragranulaires et une forte expansion tangentielle. Le cortex primate ne possède pas uniquement davantage de neurones, comparé au rongeur, mais aussi des différences qualitatives. Ceci suggère des différences qualitatives pendant le développement du cortex.Une zone proliférative corticale supplémentaire a été identifiée chez le singe macaque: la zone subventriculaire externe (OSVZ) supposée être impliquée dans l'expansion du cortex primate. Mais les propriétés des précurseurs de l'OSVZ restent mal connues. Des techniques de microscopie en temps réel et d'immunofluorescence ont permis de réaliser une description exhaustive des précurseurs de l'OSVZ et de leurs propriétés chez le singe macaque.Nos résultats mettent en évidence des différences primates/rongeurs majeures. Les observations en temps réel révèlent des capacités prolifératives bien plus importantes des précurseurs. Les précurseurs primates de l'OSVZ présentent des taux de prolifération variables pendant la corticogenèse liés à la cinétique du cycle cellulaire. Nos enregistrements ont permis la génération d'une grande base de données de propriétés et lignages de précurseurs et la mise en évidence d’une diversité morphologique inattendue. 5 types ont été identifiés. Impliqués dans des lignages complexes, chaque type a la capacité de s'auto-renouveler et de générer directement des neurones. Parallèlement, nous avons développé une méthode de classification non supervisée des précurseurs corticaux. Cette technique a identifié les mêmes 5 types de précurseurs.Les résultats de cette thèse apportent de nouveaux éléments dans la compréhension des spécificités de la corticogenèse primate qui contribuent à l'expansion corticale et au développement de capacités cognitives supérieures
The primate cerebral cortex underwent major modifications during evolution that enabled the development of high cognitive functions. A massive enlargement occurred with the specific expansion of the supra granular layers and the apparition of new frontal areas. Not only quantitative differences are found compared to the rodent but also qualitative differences. This points to potential qualitative differences in primate cortical development. An extra proliferating zone had already been identified during macaque corticogenesis: the outer subventricular zone (OSVZ). This zone is assumed to play a key role in the expansion of the primate cortex but the cellular and functional properties of OSVZ precursors remain elusive. We used quantitative long-term time-lapse video-microscopy (TLV) and immunofluorescence in and ex vivo to perform a detailed and exhaustive description of OSVZ precursor types and proliferative abilities at different stages of macaque cortical development. Our results highlight major rodent/primate differences. TLV observations revealed a much higher proliferative potential of OSVZ compared to the rodent SVZ. We report variable rates of proliferation linked to cell-cycle duration in a stage-specific manner. TLV recordings allowed the formation of a large database of primate precursor properties and lineages. This dataset unravelled an unexpectedly high diversity of OSVZ precursor morphologies. Five precursor types were identified. Involved in complex lineages, each precursor type can self-renew and directly generate neurons. In a parallel approach, we developed an unbiased clustering tool to automatically classify cortical precursors. This technique returned the same five precursor types as the morphological categorization. The results of this PhD thesis provide new insights into primate specificities during corticogenesis that contribute to cortical expansion and to the development of higher cognitive abilities

Nous présentons dans la première partie du document une étude portant sur l'imagerie de temps de vie de fluorescence sur structures dynamiques dans le domaine de fréquence (FD FLIM). Une mesure en FD FLIM est définie par une série d'images présentant une variation d'intensité sinusoïdale. La variation d'un temps de vie se traduit par une variation dans la phase de la sinusoïde décrite par l'intensité. Notre étude comporte deux contributions principales: une modélisation du processus de formation de l'image et du bruit inhérent au système d'acquisition (capteur ICCD) ; une méthode robuste d'estimation du temps vie sur des structures mobiles et des vésicules intracellulaires. Nous présentons ensuite une étude en microscopie de fluorescence portant sur la quantification du transport hétérogène dans un environnement intracellulaire dense. Les transitions entre la diffusion Brownienne dans le cytoplasme et les transports actifs supportés par le cytosquelette sont en effet des scénarios très couramment observés dans des cellules vivantes. Nous montrons que les algorithmes classiques de suivi d'objets nécessaires dans ce contexte, ne sont pas conçus pour détecter les transitions entre ces deux types de mouvement. Nous proposons donc un nouvel algorithme, inspiré de l'algorithme u-track [Jaqaman et al., 2008], qui s'appuie sur plusieurs filtrages de Kalman adaptés à différents types de transport (Brownien, Dirigé ...), indépendamment pour chaque objet suivi. Nous illustrons sur séquences simulées et expérimentales (vimentine, virus) l'aptitude de notre algorithme à détecter des mouvements dirigés rares
We propose in this manuscript a study of the instrumentation required for the quantification in frequency domain fluorescence lifetime imaging microscopy (FD FLIM). A FD FLIM measurement is defined as a series of images with sinusoidal intensity variations. The fluorescence lifetime is defined as the nanosecond-scale delay between excitation and emission of fluorescence. We propose two main contributions in the area: a modeling of the image process and noise introduced by the acquisition system (ICCD sensor); a robust statistical method for lifetime estimation on moving structures and intracellular vesicles. The second part presents a contribution to the tracking of multiple particles presenting heterogeneous transports in dense conditions. We focus here on the switching between confined diffusion in the cytosol and motor-mediated active transport in random directions. We show that current multiple model filtering and gating strategies fail at estimating unpredictable transitions between Brownian and directed displacements. We propose a new algorithm, based on the u-track algorithm [Jaqaman et al., 2008], based on a set of Kalman filters adapted to several motion types, for each tracked object. The algorithm has been evaluated on simulated and real data (vimentin, virus) data. We show that our method outperforms competing methods in the targeted scenario, but also on more homogeneous types of dynamics challenged by density

Vascular endothelial cells are known to respond to fluid shear stress. To gain insights into the mechanism of flow response by these cells, various types of in vitro devices in which endothelial cells can be cultured under flowing culture medium have been designed. Using such a device, one can apply known levels of (usually laminar) fluid shear stress to cultured endothelial cells. We have made two types of devices: a viscometer-based cone-and-plate flow apparatus and a parallel plate chamber. The cone-and-plate apparatus is used to do biochemical analyses of flow effects on cells while the parallel plate chamber is used to observe dynamic behavior of endothelial cells under flow. We were able to maintain confluent endothelial cell cultures under flow for over a week in the parallel plate flow apparatus. Using this chamber and high resolution time-lapse video microscopy, we studied morphological changes of endothelial cells exposed to different levels of fluid shear stress. We found that endothelial cells in a confluent monolayer exhibited three types of fluid shear stress level-dependent morphological and motile responses within a narrow fluid shear stress range between 0.1–10 dyn/cm2. Endothelial cells cultured under no flow exhibited variable shapes and no preferred orientation of their long cell axes and showed a jiggling motion. When exposed to fluid shear stress levels of below 0.5 dyn/cm2, endothelial cell morphology and motility were not affected. However, when fluid shear stress levels were increased to 2–4 dyn/cm2, they became polygonal and showed increased random-walk activity. Fluid shear stress over 6 dyn/cm2 caused endothelial cells to initially become polygonal and increase their random-walk activity, but they soon became elongated and aligned in the direction of flow. As the cells elongated and aligned, they migrated in the direction of flow. The average velocity of this directed cell migration was less than that of cells moving randomly under the same flow condition at earlier times. These observations indicate that endothelial cells are able to detect and respond to a surprisingly small change in fluid shear stress. It is possible that endothelial cell physiology in vivo is also regulated by small changes in fluid shear stress and that a fluid shear stress change of a few dynes per cm2 within a certain region of an artery could trigger atherogenesis in that particular location.