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Relevant bibliographies by topics / Embryo segmentation

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Academic literature on the topic 'Embryo segmentation'

Author: Grafiati

Published: 4 May 2024

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Journal articles on the topic "Embryo segmentation"

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Sheeba, Caroline J. "Mechanisms of vertebrate embryo segmentation." Seminars in Cell & Developmental Biology 49 (January 2016): 57–58. http://dx.doi.org/10.1016/j.semcdb.2016.01.041.

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Kornberg, Thomas B., and Tetsuya Tabata. "Segmentation of the Drosophila embryo." Current Opinion in Genetics & Development 3, no. 4 (January 1993): 585–93. http://dx.doi.org/10.1016/0959-437x(93)90094-6.

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Borman, W. H., and D. E. Yorde. "Analysis of chick somite myogenesis by in situ confocal microscopy of desmin expression." Journal of Histochemistry & Cytochemistry 42, no. 2 (February 1994): 265–72. http://dx.doi.org/10.1177/42.2.8288867.

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We explored the relationship in chick embryos between somitogenesis and the onset of somite myogenesis by immunodetection of the muscle-specific intermediate filament protein desmin. Early somite desmin expression was detected by whole-mount in situ confocal microscopy. No detectable somite desmin was observed in embryos of 15 somites (Stage 12) or younger. In embryos having between 16 and 26 somites (Stages 12-15), desmin could be detected in somites positioned increasingly more caudal in the embryo. Finally, in embryos of 27 somites (Stage 16) and older, somite desmin expression was consistently present in all but the caudal-most six somites. Although the rate of somite formation is fairly constant, the rate of observed somite desmin expression progressing caudally in the embryo is greater initially than the rate of segmentation. After an embryo has formed about 27 somites, the rate of desmin appearance parallels the rate of segmentation at a distance of about six somites. This result suggests that very early somite myogenesis is not linked to somitogenesis.

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Osborne, H. B., C. Gautier-Courteille, A. Graindorge, C. Barreau, Y. Audic, R. Thuret, N. Pollet, and L. Paillard. "Post-transcriptional regulation in Xenopus embryos: role and targets of EDEN-BP." Biochemical Society Transactions 33, no. 6 (October 26, 2005): 1541–43. http://dx.doi.org/10.1042/bst0331541.

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EDEN (embryo deadenylation element)-dependent deadenylation is a regulatory process that was initially identified in Xenopus laevis early embryos and was subsequently shown to exist in Drosophila oocytes. Recent data showed that this regulatory process is required for somitic segmentation in Xenopus. Inactivation of EDEN-BP (EDEN-binding protein) causes severe segmentation defects, and the expression of segmentation markers in the Notch signalling pathway is disrupted. We showed that the mRNA encoding XSu(H) (Xenopus suppressor of hairless), a protein central to the Notch pathway, is regulated by EDEN-BP. Our data also indicate that other segmentation RNAs are targets for EDEN-BP. To identify new EDEN-BP targets, a microarray analysis has been undertaken.

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Sparrow, D. B., W. C. Jen, S. Kotecha, N. Towers, C. Kintner, and T. J. Mohun. "Thylacine 1 is expressed segmentally within the paraxial mesoderm of the Xenopus embryo and interacts with the Notch pathway." Development 125, no. 11 (June 1, 1998): 2041–51. http://dx.doi.org/10.1242/dev.125.11.2041.

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The presomitic mesoderm of vertebrates undergoes a process of segmentation in which cell-cell interactions mediated by the Notch family of receptors and their associated ligands are involved. The vertebrate homologues of Drosophila Δ are expressed in a dynamic, segmental pattern within the presomitic mesoderm, and alterations in the function of these genes leads to a perturbed pattern of somite segmentation. In this study we have characterised Thylacine 1 which encodes a basic helix-loop-helix class transcription activator. Expression of Thylacine is restricted to the presomitic mesoderm, localising to the anterior half of several somitomeres in register with domains of X-Delta-2 expression. Ectopic expression of Thylacine in embryos causes segmentation defects similar to those seen in embryos in which Notch signalling is altered, and these embryos also show severe disruption in the expression patterns of the marker genes X-Delta-2 and X-ESR5 within the presomitic mesoderm. Finally, the expression of Thylacine is altered in embryos when Notch signalling is perturbed. These observations suggest strongly that Thylacine 1 has a role in the segmentation pathway of the Xenopus embryo, by interacting with the Notch signalling pathway.

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Weisblat, David A. "Segmentation and commitment in the leech embryo." Cell 42, no. 3 (October 1985): 701–2. http://dx.doi.org/10.1016/0092-8674(85)90264-8.

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Davidson, Duncan. "Segmentation in frogs." Development 104, Supplement (October 1, 1988): 221–29. http://dx.doi.org/10.1242/dev.104.supplement.221.

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This paper reviews evidence relating to the question, at what stage in the development of the frog embryo are segment boundaries specified? Current evidence leads to the hypothesis that a spatiotemporal series of cell states leading to segmentation is continuously initiated at a position 200 to 300 μm from the posterior end of the presomitic mesoderm, about nine somite intervals before the formation of a definitive somite. The evidence suggests, though by no means proves, that segment boundaries are specified close to this time. This hypothesis relies critically on evidence concerning the effects of disruptive agents, the extent of cell mixing prior to the early gastrula stage, fate-map data, and a comparison with development in the mouse where a similar fate map can be related to morphological evidence of somitomeric segmentation. Evidence regarding the organization of the posterior, undifferentiated zone of the mesoderm in the frog embryo indicates that the cells are not proliferating rapidly, but are undergoing cell movements and rearrangements associated with caudal extension. The speculation that the segment pattern derives from inductive interactions in this region is discussed.

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Zhang, Kun, Hongbin Zhang, Huiyu Zhou, Danny Crookes, Ling Li, Yeqin Shao, and Dong Liu. "Zebrafish Embryo Vessel Segmentation Using a Novel Dual ResUNet Model." Computational Intelligence and Neuroscience 2019 (February 3, 2019): 1–14. http://dx.doi.org/10.1155/2019/8214975.

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Zebrafish embryo fluorescent vessel analysis, which aims to automatically investigate the pathogenesis of diseases, has attracted much attention in medical imaging. Zebrafish vessel segmentation is a fairly challenging task, which requires distinguishing foreground and background vessels from the 3D projection images. Recently, there has been a trend to introduce domain knowledge to deep learning algorithms for handling complex environment segmentation problems with accurate achievements. In this paper, a novel dual deep learning framework called Dual ResUNet is developed to conduct zebrafish embryo fluorescent vessel segmentation. To avoid the loss of spatial and identity information, the U-Net model is extended to a dual model with a new residual unit. To achieve stable and robust segmentation performance, our proposed approach merges domain knowledge with a novel contour term and shape constraint. We compare our method qualitatively and quantitatively with several standard segmentation models. Our experimental results show that the proposed method achieves better results than the state-of-art segmentation methods. By investigating the quality of the vessel segmentation, we come to the conclusion that our Dual ResUNet model can learn the characteristic features in those cases where fluorescent protein is deficient or blood vessels are overlapped and achieves robust performance in complicated environments.

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Maia-Fernandes, Ana Cristina, Ana Martins-Jesus, Nísia Borralho-Martins, Tomás Pais-de-Azevedo, Ramiro Magno, Isabel Duarte, and Raquel P. Andrade. "Spatio-temporal dynamics of early somite segmentation in the chicken embryo." PLOS ONE 19, no. 4 (April 18, 2024): e0297853. http://dx.doi.org/10.1371/journal.pone.0297853.

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During vertebrate embryo development, the body is progressively segmented along the anterior-posterior (A-P) axis early in development. The rate of somite formation is controlled by the somitogenesis embryo clock (EC), which was first described as gene expression oscillations of hairy1 (hes4) in the presomitic mesoderm of chick embryos with 15–20 somites. Here, the EC displays the same periodicity as somite formation, 90 min, whereas the posterior-most somites (44–52) only arise every 150 minutes, matched by a corresponding slower pace of the EC. Evidence suggests that the rostral-most somites are formed faster, however, their periodicity and the EC expression dynamics in these early stages are unknown. In this study, we used time-lapse imaging of chicken embryos from primitive streak to somitogenesis stages with high temporal resolution (3-minute intervals). We measured the length between the anterior-most and the last formed somitic clefts in each captured frame and developed a simple algorithm to automatically infer both the length and time of formation of each somite. We found that the occipital somites (up to somite 5) form at an average rate of 75 minutes, while somites 6 onwards are formed approximately every 90 minutes. We also assessed the expression dynamics of hairy1 using half-embryo explants cultured for different periods of time. This showed that EC hairy1 expression is highly dynamic prior to somitogenesis and assumes a clear oscillatory behaviour as the first somites are formed. Importantly, using ex ovo culture and live-imaging techniques, we showed that the hairy1 expression pattern recapitulates with the formation of each new pair of somites, indicating that somite segmentation is coupled with EC oscillations since the onset of somitogenesis.

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Resende, Tatiana P., Raquel P. Andrade, and Isabel Palmeirim. "Timing Embryo Segmentation: Dynamics and Regulatory Mechanisms of the Vertebrate Segmentation Clock." BioMed Research International 2014 (2014): 1–12. http://dx.doi.org/10.1155/2014/718683.

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All vertebrate species present a segmented body, easily observed in the vertebrate column and its associated components, which provides a high degree of motility to the adult body and efficient protection of the internal organs. The sequential formation of the segmented precursors of the vertebral column during embryonic development, the somites, is governed by an oscillating genetic network, the somitogenesis molecular clock. Herein, we provide an overview of the molecular clock operating during somite formation and its underlying molecular regulatory mechanisms. Human congenital vertebral malformations have been associated with perturbations in these oscillatory mechanisms. Thus, a better comprehension of the molecular mechanisms regulating somite formation is required in order to fully understand the origin of human skeletal malformations.

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Dissertations / Theses on the topic "Embryo segmentation"

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Jaques, Karen F. "Segmentation and axonal guidance in the vertebrate embryo." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386159.

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Lim, Tit Meng. "Segmentation in the nervous system of the chick embryo." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329053.

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Vermeren, Matthieu M. "Molecular basis of peripheral nerve segmentation in the chick embryo." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621857.

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Shah, Sheetal Mansukhlal. "Genetic and molecular studies of segmentation and axon guidance in Drosophila." Thesis, University College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312177.

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Rajasekaran, Bhavna. "Analysis of Movement of Cellular Oscillators in the Pre-somitic Mesoderm of the Zebrafish Embryo." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-110304.

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During vertebrate embryo development, the body axis is subdivided into repeated structures, called somites. Somites bud off from an un-segmented tissue called the pre-somitic mesoderm (PSM) in a sequential and periodic manner, tightly controlled by an in built molecular clock, called the "segmentation clock". According to current understanding, the clock is comprised of: (i) an autonomous cellular oscillator consisting of an intracellular negative feedback loop of Her genes within the PSM cells, (ii) Delta-ligand and Notch-receptor coupling that facilitates synchronization of oscillators among the PSM cells, (iii) Tissue level waves of gene expression that emerge in the posterior PSM and move coherently towards anterior, leading to global arrest of oscillations in the form of somites. However, the movement of cellular oscillators within the PSM before the formation of somitic furrows, a prominent feature of the tissue as observed through this work has not been experimentally considered as a constituent of the segmentation clock so far. Our work aims to incorporate movement of cellular oscillators in the framework of the segmentation clock. It is well known from theoretical studies that the characteristics of relative motion of oscillators affect their synchronization properties and the patterns of oscillations they form. Particularly, theoretical studies by Uriu et al., PNAS (2010) suggest that cell movements promotes synchronization of genetic oscillations. Here, we established experimental techniques and image analysis tools to attain quantitative insight on (i) diffusion co-efficient of cellular oscillators, (ii) dynamics of a population of oscillators, within the PSM aiming towards concomitant understanding of the relationship between movement and synchronization of cellular oscillators. In order to quantitatively relate cellular oscillators and their motion within the PSM, I established imaging techniques that enabled visualization of fluorescenctly labeled nuclei as readouts of cell positions in live embryo, and developed dedicated segmentation algorithm and implemented tracking protocol to obtain nuclei positions over time in 3D space. Furthermore, I provide benchmarking techniques in the form of artificial data that validate segmentation algorithm efficacy and, for the first time proposed the use of transgenic embryo chimeras to validate segmentation algorithm performance within the context of in vivo live imaging of embryonic tissues. Preliminary analysis of our data suggests that there is relatively high cell mixing in the posterior PSM, within the same spatial zone where synchronous oscillations emerge at maximum speed. Also, there are indications of gradient of cell mixing along the anterior-posterior axis of the embryo. By sampling single cell tracks with the help of nuclei markers, we have also been able to follow in vivo protein oscillations at single cell resolution that would allow quantitative characterization of coherence among a population of cellular oscillators over time. Our image analysis work flow allows testing of mutant embryos and perturbation of synchrony dynamics to understand the cause-effect relationship between movement and synchronization properties at cellular resolution. Essentially, through this work, we hope to bridge the time scales of events and cellular level dynamics that leads to highly coordinated tissue level patterns and thereby further our understanding of the segmentation clock mechanism.

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Genest, Diane. "Imaging of the fish embryo model and applications to toxicology." Thesis, Paris Est, 2019. http://www.theses.fr/2019PESC2008/document.

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De nombreuses substances chimiques sont utilisées par l’industrie cosmétique pour entrer dans la composition de formules. En dehors de la nécessité d’évaluer leur efficacité, l’industrie cosmétique se doit surtout d’évaluer la sécurité de leurs substances pour l’humain. L'évaluation toxicologique des substances chimiques est réalisée dans le but de révéler un effet toxique potentiel de la substance testée. Parmi les effets potentiels que l’on souhaite détecter, la toxicité du développement (tératogénicité), c’est-à-dire la capacité d’une substance à provoquer l’apparition d’anomalies lors du développement embryonnaire, est fondamentale. En accord avec les législations internationales qui interdisent à l’industrie cosmétique d’avoir recours à des tests sur animaux de laboratoire pour l’évaluation de leurs substances, l’évaluation toxicologique de ces substances se base sur les résultats de tests in silico, in vitro et de tests faits sur des modèles alternatifs aux animaux de laboratoire. Pour le moment cependant, peu de méthodes alternatives existent et ont été validées pour la toxicologie du développement. Le développement de nouvelles méthodes alternatives est donc requis. D'autre part, en plus de l’évaluation de la sécurité des substances chez l’humain, l’évaluation de la toxicité pour l’environnement est nécessaire. L’usage de la plupart des produits cosmétiques et d’hygiène corporelle conduit, après lavage et rinçage, à un rejet à l’égout et donc dans les cours d’eau. Il en résulte que les environnements aquatiques (eaux de surface et milieux marins côtiers) sont parfois exposés aux substances chimiques incluses dans les formules cosmétiques. Ainsi, l’évaluation toxicologique environnementale des cosmétiques et de leurs ingrédients nécessite de connaître leur toxicité sur des organismes représentatifs de chaînes alimentaires aquatiques. Dans ce contexte, le modèle embryon de poisson présente un double avantage pour l’industrie cosmétique. Ce modèle, jugé par les législations internationales comme étant éthiquement acceptable pour les évaluations toxicologiques réalisées par l’industrie cosmétique, est représentatif des organismes aquatiques. Il est donc pertinent pour évaluer la toxicité environnementale des substances chimiques. D'autre part, ce modèle apparaît prometteur pour évaluer l’effet tératogène de substances chimiques chez l’humain. Pour ces raisons, un test d’analyse de la tératogénicité des substances chimiques est actuellement développé. Ce test se base sur l’analyse d’embryons de medaka (Oryzias Latipes) à 9 jours post fertilisation, après exposition des embryons par balnéation à des substances à concentrations déterminées. L’analyse de paramètres fonctionnels et morphologiques conduit au calcul d’un indice tératogène, qui permet de tirer une conclusion quant à l’effet tératogène de la substance testée. Cet indice est calculé à partir des mesures du taux de mortalité et du taux de malformations chez les embryons. L’objectif de ce projet est d’automatiser le test d’analyse de la tératogénicité, par classification automatique des embryons faite à partir d’image et de vidéo. La première méthode développée concerne la détection des battements cardiaques à partir de séquences vidéos, dans le but de calculer le taux de mortalité. Nous nous sommes ensuite concentrés sur deux types de malformations courantes qui sont les malformations axiales, et l'absence de vessie natatoire, en utilisant une méthode d'apprentissage automatique. Cette analyse doit être complétée par l'analyse d'autres malformations et conduire à un calcul du taux de malformations et de l’indice tératogène pour la substance testée
Numerous chemicals are used as ingredients by the cosmetics industry and are included in cosmetics formula. Aside from the assessment of their efficacy, the cosmetics industry especially needs to assess the safety of their chemicals for human. Toxicological screening of chemicals is performed with the aim of revealing the potential toxic effect of the tested chemical. Among the potential effects we want to detect, the developmental toxicity of the chemical (teratogenicity), meaning its capability of provoking abnormalities during the embryonic development, is crucial. With respect to the international regulations that forbid the use of animal testing for the safety assessment of cosmetics, the toxicological assessment of chemicals must base on an ensemble of in silico assays, in vitro assays and alternative models based assays. For now, a few alternative methods have been validated in the field of developmental toxicology. The development of new alternative methods is thus required. In addition to the safety assessment, the environmental toxicity assessment is also required. The use of most of cosmetics and personal care products leads to their rejection in waterways after washing and rince. This results in the exposition of some aquatic environments (surface waters and coastal marine environments) to chemicals included in cosmetics and personal care products. Thus, the environmental assessment of cosmetics and of their ingredients requires the knowledge of their toxicity on organisms that are representative of aquatic food chains. In this context, the fish embryo model, which is ethically acceptable according to international regulations, presents a dual advantage for the cosmetics industry. Firstly, as a model representative of aquatic organisms, it is accurate for the environmental assessment of chemicals. Secondly, this model is promising for the assessment of the teratogenic effect of chemicals on human. For this reason, a teratogenicity assessment test is developed. This test is based on the analysis of medaka fish embryos (Oryzias Latipes) at 9 days post fertilization, after balneation in a predetermined concentration of the chemical under study. The analysis of functional and morphological parameters allows to calculate a teratogenicity index, that depends on both rates of dead and malformed embryos. This index allows to to draw a conclusion concerning the teratogenic effect of the chemical.The objective of this project is to automate the teratogenicity test, by automated image and video classification. A first method is developed that aims to automatically detect embryo heart beats from acquired video sequences. This method will allow to calculate the proportion of dead embryos. We then focus on the detection of two common malformations: axial malformations and absence of a swim bladder, based on a machine learning classification. This analysis must be completed by the detection of other malformations so that we can measure the rate of malformed embryos and thus, calculate the teratogenicity index of the tested chemical

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Schaeffer, Julia. "The molecular regulation of spinal nerve outgrowth." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/271632.

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During amniote embryogenesis, the segmented pattern characteristic of the vertebral column appears early during development through the sequential formation of multipotent structures called somites. Somites differentiate subsequently into dermomyotome (giving rise later to skin and skeletal muscles) and sclerotome (giving rise to vertebral bone structures and cartilage). In addition, sclerotomes subdivide following their rostro-caudal intrasegmental boundary into an axon growth-permissive region (anterior half) and an axon growth-repulsive region (posterior half). This binary system instructs motor and sensory axon navigation, as well as neural crest cell migration, to ensure that the peripheral nervous system develops without obstruction by the future cartilage and bones of the vertebral column. Repellent cues are expressed in posterior half-sclerotomes in order to exclude navigating axons from “no-go” areas and restrict their growth to specific exit points of the future vertebral column. Interestingly, similar repellent cues (e.g. Eph/Ephrins) are expressed in the adult central nervous system (CNS) and have been shown to control connectivity and plasticity throughout life. Following brain or spinal cord injury, these repellent molecules are upregulated by reactive astrocytes accumulating at the lesion site, and may impede axon regeneration in this region. In this dissertation, I am presenting the results of a differential gene expression analysis of anterior and posterior half-sclerotomes, based on RNA-sequencing data and using the chick embryo as a model organism. This study led to the identification of molecules, previously uncharacterized in this system, that may play a role in adhesive and mechanical properties of somites and in axon guidance and fasciculation. I focused on the functional analysis of one molecule of the posterior half-sclerotome, the extracellular matrix protein Fibulin-2. To look at its role in the segmentation of spinal axons, I used ectopic misexpression in a subset of segments based on somite electroporation. The width of spinal nerve bundle growth was restricted by Fibulin-2 overexpression in posterior and anterior half-sclerotomes, suggesting a role in sharpening/controlling the path of spinal axon growth. In addition, I showed that this could occur via an interaction with the axon growth repellent Semaphorin 3A. Then I looked at the expression of Fibulin-2 in two models of CNS injury: mouse cerebral cortical stab injury and rat dorsal crush spinal cord injury. In both cases, I observed an increase in Fibulin-2 protein level compared to control. I also used primary cultures of rat cortical astrocytes to show that the expression of Fibulin-2 after inflammatory cytokine-induced activation is increased. Finally, I studied a candidate axon growth repellent previously identified in the laboratory. I explored the hypothesis that this repellent molecule is an O-glycosylated, spliced variant form of a known protein. To characterize this repellent molecule, I used RNA-sequencing data from chick embryonic somites and 2D gel electrophoresis of an astrocytic cell line protein extract. Together, these results suggested that the developing vertebral column and the adult CNS share molecular features to control axon growth and plasticity. This type of study could lead to the characterization of molecular systems that regulate axon growth, and to the identification of novel therapeutic targets in brain or spinal cord injury.

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Janštová, Michaela. "Segmentace měkkých tkání v obličejové části myších embryí v mikrotomografických datech." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2019. http://www.nusl.cz/ntk/nusl-400988.

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This diploma thesis deals with a segmentation of soft tissues in facial part of mouse embryos in Matlab. Segmentation of soft tissues of mouse embryos was not fully automated and every case needs a specific solution. Solving parts of this issues can provide valuable data for evolutionary biologists. Issues about staining and segmentation techniques are described. On the basis of accessible literature otsu thresholding, region growing, k-means clustering and segmentation with atlas were tested. In the end of this paper are those methods tested and evaluated on 3D microtomography data.

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Kočendová, Kateřina. "Automatické vyhlazení 3D modelů kraniální embryonální myší chrupavky." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2020. http://www.nusl.cz/ntk/nusl-413111.

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The focus of this thesis is the smoothing of manually segmented 3D models of mouse embryo craniofacial cartilege. During the process of manual segmentation, artefacts and other imperfections appear in the final models and need to be repaired. Firstly, manual segmentation is corrected using gradients and thresholding. Subsequent smoothing methods are constructed based on theoretical research. Algorithmizing is executed in the MATLAB environment. All the designed algorithms are then tested on selected models. Statistical evaluation is determined using the Srensen–Dice coefficient, where manually smoothened models cleared of all artefacts are used as the gold standard.

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Nasser, Khalafallah Mahmoud Lamees. "A dictionary-based denoising method toward a robust segmentation of noisy and densely packed nuclei in 3D biological microscopy images." Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS283.pdf.

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Les cellules sont les éléments constitutifs de base de tout organisme vivant. Tous les organismes vivants partagent des processus vitaux tels que croissance, développement, mouvement, nutrition, excrétion, reproduction, respiration et réaction à l’environnement. En biologie cellulaire, comprendre la structure et fonction des cellules est essentielle pour développer et tester de nouveaux médicaments. Par ailleurs, cela aide aussi à l’étude du développement embryonnaire. Enfin, cela permet aux chercheurs de mieux comprendre les effets des mutations et de diverses maladies. La vidéo-microscopie (Time Lapse Fluorescence Microscopie) est l’une des techniques d’imagerie les plus utilisées afin de quantifier diverses caractéristiques des processus cellulaires, à savoir la survie, la prolifération, la migration ou la différenciation cellulaire. En vidéo-microscopie, non seulement les informations spatiales sont disponibles, mais aussi les informations temporelles en réitérant l’acquisition de l’échantillon, et enfin les informations spectrales, ce qui génère des données dites « cinq dimensions » (X, Y, Z + temps + canal). En règle générale, les jeux de données générés consistent en plusieurs (centaines ou milliers) d’images, chacune contenant des centaines ou milliers d’objets à analyser. Pour effectuer une quantification précise et à haut débit des processus cellulaires, les étapes de segmentation et de suivi des noyaux cellulaires doivent être effectuées de manière automatisée. Cependant, la segmentation et le suivi des noyaux sont des tâches difficiles dû notamment au bruit intrinsèque dans les images, à l’inhomogénéité de l’intensité, au changement de forme des noyaux ainsi qu’à un faible contraste des noyaux. Bien que plusieurs approches de segmentation des noyaux aient été rapportées dans la littérature, le fait de traiter le bruit intrinsèque reste la partie la plus difficile de tout algorithme de segmentation. Nous proposons un nouvel algorithme de débruitage 3D, basé sur l’apprentissage d’un dictionnaire non supervisé et une représentation parcimonieuse, qui à la fois améliore la visualisation des noyaux très peu contrastés et bruités, mais aussi détecte simultanément la position de ces noyaux avec précision. De plus, notre méthode possède un nombre limité de paramètres, un seul étant critique, à savoir la taille approximative des objets à traiter. Le cadre de la méthode proposée comprend le débruitage d’images, la détection des noyaux et leur segmentation. Dans l’étape de débruitage, un dictionnaire initial est construit en sélectionnant des régions (patches) aléatoires dans l’image originale, puis une technique itérative est implémentée pour mettre à jour ce dictionnaire afin d’obtenir un dictionnaire dont les éléments mis à jour présentent un meilleur contraste. Ensuite, une carte de détection, basée sur le calcul des coefficients du dictionnaire utilisés pour débruiter l’image, est utilisée pour détecter le centre approximatif des noyaux qui serviront de marqueurs pour la segmentation. Ensuite, une approche basée sur le seuillage est proposée pour obtenir le masque de segmentation des noyaux. Finalement, une approche de segmentation par partage des eaux contrôlée par les marqueurs est utilisée pour obtenir le résultat final de segmentation des noyaux. Nous avons créé des images synthétiques 3D afin d’étudier l’effet des paramètres de notre méthode sur la détection et la segmentation des noyaux, et pour comprendre le mécanisme global de sélection et de réglage de ces paramètres significatifs sur différents jeux de données
Cells are the basic building blocks of all living organisms. All living organisms share life processes such as growth and development, movement, nutrition, excretion, reproduction, respiration and response to the environment. In cell biology research, understanding cells structure and function is essential for developing and testing new drugs. In addition, cell biology research provides a powerful tool to study embryo development. Furthermore, it helps the scientific research community to understand the effects of mutations and various diseases. Time-Lapse Fluorescence Microscopy (TLFM) is one of the most appreciated imaging techniques which can be used in live-cell imaging experiments to quantify various characteristics of cellular processes, i.e., cell survival, proliferation, migration, and differentiation. In TLFM imaging, not only spatial information is acquired, but also temporal information obtained by repeating imaging of a labeled sample at specific time points, as well as spectral information, that produces up to five-dimensional (X, Y, Z + Time + Channel) images. Typically, the generated datasets consist of several (hundreds or thousands) images, each containing hundreds to thousands of objects to be analyzed. To perform high-throughput quantification of cellular processes, nuclei segmentation and tracking should be performed in an automated manner. Nevertheless, nuclei segmentation and tracking are challenging tasks due to embedded noise, intensity inhomogeneity, shape variation as well as a weak boundary of nuclei. Although several nuclei segmentation approaches have been reported in the literature, dealing with embedded noise remains the most challenging part of any segmentation algorithm. We propose a novel 3D denoising algorithm, based on unsupervised dictionary learning and sparse representation, that can both enhance very faint and noisy nuclei, in addition, it simultaneously detects nuclei position accurately. Furthermore, our method is based on a limited number of parameters, with only one being critical, which is the approximate size of the objects of interest. The framework of the proposed method comprises image denoising, nuclei detection, and segmentation. In the denoising step, an initial dictionary is constructed by selecting random patches from the raw image then an iterative technique is implemented to update the dictionary and obtain the final one which is less noisy. Next, a detection map, based on the dictionary coefficients used to denoise the image, is used to detect marker points. Afterward, a thresholding-based approach is proposed to get the segmentation mask. Finally, a marker-controlled watershed approach is used to get the final nuclei segmentation result. We generate 3D synthetic images to study the effect of the few parameters of our method on cell nuclei detection and segmentation, and to understand the overall mechanism for selecting and tuning the significant parameters of the several datasets. These synthetic images have low contrast and low signal to noise ratio. Furthermore, they include touching spheres where these conditions simulate the same characteristics exist in the real datasets. The proposed framework shows that integrating our denoising method along with classical segmentation method works properly in the context of the most challenging cases. To evaluate the performance of the proposed method, two datasets from the cell tracking challenge are extensively tested. Across all datasets, the proposed method achieved very promising results with 96.96% recall for the C.elegans dataset. Besides, in the Drosophila dataset, our method achieved very high recall (99.3%)

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Books on the topic "Embryo segmentation"

1

Vaage, Sigmund. Segmentation of the Primitive Neural Tube in Chick Embryos: A Morphological, Histochemical and Autoradiographical Investigation. Springer London, Limited, 2013.

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Book chapters on the topic "Embryo segmentation"

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Bagnall, Keith M. "Segmentation and Compartments in the Vertebrate Embryo." In Formation and Differentiation of Early Embryonic Mesoderm, 133–47. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4615-3458-7_12.

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Trainor, Paul A., Miguel Manzanares, and Robb Krumlauf. "Genetic Interactions During Hindbrain Segmentation in the Mouse Embryo." In Results and Problems in Cell Differentiation, 51–89. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-540-48002-0_3.

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3

Bellairs, Ruth. "The Tail Bud and Cessation of Segmentation in the Chick Embryo." In Somites in Developing Embryos, 161–78. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4899-2013-3_13.

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4

Keynes, Roger J., and Claudio D. Stern. "Mesenchymal-Epithelial Interactions during Neural Segmentation in the Chick Embryo." In Mesenchymal-Epithelial Interactions in Neural Development, 309–22. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-71837-3_24.

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5

Bastiaansen, Wietske A. P., Melek Rousian, Régine P. M. Steegers-Theunissen, Wiro J. Niessen, Anton Koning, and Stefan Klein. "Atlas-Based Segmentation of the Human Embryo Using Deep Learning with Minimal Supervision." In Medical Ultrasound, and Preterm, Perinatal and Paediatric Image Analysis, 211–21. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-60334-2_21.

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Osmond, Mark. "The Effects of Retinoic Acid on Early Heart Formation and Segmentation in the Chick Embryo." In Formation and Differentiation of Early Embryonic Mesoderm, 275–300. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4615-3458-7_23.

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Meinhardt, Hans. "Models of Segmentation." In Somites in Developing Embryos, 179–89. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4899-2013-3_14.

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Keynes, Roger, Geoffrey Cook, Jamie Davies, Paul Scotting, Wendie Norris, Claudio Stern, and Andrew Lumsden. "Segmentation and Neuronal Development in Vertebrate Embryos." In Brain Repair, 213–24. London: Macmillan Education UK, 1990. http://dx.doi.org/10.1007/978-1-349-11358-3_17.

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Katona, Melinda, Tünde Tőkés, Emília Rita Szabó, Szilvia Brunner, Imre Zoltán Szabó, Róbert Polanek, Katalin Hideghéty, and László G. Nyúl. "Automatic Segmentation and Quantitative Analysis of Irradiated Zebrafish Embryos." In Computational Modeling of Objects Presented in Images. Fundamentals, Methods, and Applications, 95–107. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-20805-9_9.

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Chlyah, H., M. Hsaine, R. Karim, and A. Chlyah. "Improvement of Somatic Embryogenesis in Wheat by Segmentation of Cultured Embryos." In Biotechnology in Agriculture and Forestry, 88–97. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-662-10933-5_5.

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Conference papers on the topic "Embryo segmentation"

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Jamal, Ade, Aditya Pratama Dharmawan, Ali Akbar Septiandri, Pritta Amelia Iffanolida, Oki Riayati, and Budi Wiweko. "Densely U-Net Models for Human Embryo Segmentation." In 2023 4th International Conference on Artificial Intelligence and Data Sciences (AiDAS). IEEE, 2023. http://dx.doi.org/10.1109/aidas60501.2023.10284599.

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Khan, Aisha, Stephen Gould, and Mathieu Salzmann. "Segmentation of developing human embryo in time-lapse microscopy." In 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI 2016). IEEE, 2016. http://dx.doi.org/10.1109/isbi.2016.7493417.

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Zouagui, T., E. Chereul, C. Odet, and M. Janier. "Mouse embryo’s heart segmentation on μMRI acquisitions." In 2007 9th International Symposium on Signal Processing and Its Applications (ISSPA). IEEE, 2007. http://dx.doi.org/10.1109/isspa.2007.4555372.

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Saifullah, Shoffan, and Andiko P. Suryotomo. "Thresholding and Hybrid CLAHE-HE for Chicken Egg Embryo Segmentation." In 2021 International Conference on Communication & Information Technology (ICICT). IEEE, 2021. http://dx.doi.org/10.1109/icict52195.2021.9568444.

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Sidhu, Simarjot S., and James K. Mills. "Automated Blastomere Segmentation for Early-Stage Embryo Using 3D Imaging Techniques." In 2019 IEEE International Conference on Mechatronics and Automation (ICMA). IEEE, 2019. http://dx.doi.org/10.1109/icma.2019.8816615.

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Jen-Wei Kuo, Yao Wang, Orlando Aristizabal, Jeffrey A. Ketterling, and Jonathan Mamou. "Automatic mouse embryo brain ventricle segmentation from 3D 40-MHz ultrasound data." In 2013 IEEE International Ultrasonics Symposium (IUS). IEEE, 2013. http://dx.doi.org/10.1109/ultsym.2013.0454.

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Zanella, Cecilia, Barbara Rizzi, Camilo Melani, Matteo Campana, Paul Bourgine, Karol Mikula, Nadine Peyrieras, and Alessandro Sarti. "Segmentation of Cells from 3-D Confocal Images of Live Zebrafish Embryo." In 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2007. http://dx.doi.org/10.1109/iembs.2007.4353722.

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Zacharia, E., M. Bondesson, A. Riu, N. A. Ducharme, J. Gustafsson, and I. A. Kakadiaris. "Automatic segmentation of time-lapse microscopy images depicting a live Dharma embryo." In 2011 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2011. http://dx.doi.org/10.1109/iembs.2011.6091993.

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Corpuz, Shaun, and Aaron T. Ohta. "Deep Neural Network Segmentation of Embryo Inner Cell Mass and Trophectoderm Epithelium." In 2023 IEEE 16th International Conference on Nano/Molecular Medicine & Engineering (NANOMED). IEEE, 2023. http://dx.doi.org/10.1109/nanomed59780.2023.10404589.

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Kheradmand, S., A. Singh, P. Saeedi, J. Au, and J. Havelock. "Inner cell mass segmentation in human HMC embryo images using fully convolutional network." In 2017 IEEE International Conference on Image Processing (ICIP). IEEE, 2017. http://dx.doi.org/10.1109/icip.2017.8296582.

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