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Descripción
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| Gene expression atlases at the cellular level are a fundamental resource to quantify and understand embryogenesis multiscale processes in time and space.The automated reconstruction of prototypic atlases from multiple fluorescent in situ hybridization and nuclear counterstaining observed in 3D requires the development of dedicated computational strategies. Match-IT is an original tool requiring minimal human supervision to gather in a reference specimen, with resolution at the cellular level, gene expression patterns observed at various developmental stages from multiple fluorescent staining in different individuals with phenotypic variability. This framework was used to build a gene expression atlas for the zebrafish early embryogenesis from 51 different specimens, about 200,000 cell nuclei, 96 gene expression patterns for 9 different genes and 6 time cohorts spanning from 4 to 6.3 hpf (hours post fertilization). An interactive visualization application, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Automatic methods and tools are also proposed here to allow the assessment of gene expression at the single cell level and the automated identification, visualization and analysis of co-expression patterns and synexpression groups with their dynamics through developmental stages in a vertebrate early embryo. | |
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Internacional
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JCR del ISI
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Título de la revista
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Nature Methods |
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ISSN
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1548-7091 |
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Factor de impacto JCR
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19,276 |
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Información de impacto
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Datos JCR del año 2011 |
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DOI
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