title: Image processing challenges in the creation of spatiotemporal gene expression atlases of developing embryos.
abstract: To properly understand and model animal embryogenesis it is crucial to obtain detailed measurements, both in time and space, about their gene expression domains and cell dynamics. Such challenge has been confronted in recent years by a surge of atlases which integrate a statistically relevant number of different individuals to get robust, complete information about their spatiotemporal locations of gene patterns. This paper will discuss the fundamental image analysis strategies required to build such models and the most common problems found along the way. We also discuss the main challenges and future goals in the field.
authors.affiliation: Biomedical Image Technologies, Universidad Politécnica de Madrid 28040,Spain. fccastro@die.upm.es
authors.forename: Carlos
authors.initials: C
authors.lastname: Castro
authors.forename: Miguel Ángel
authors.initials: MÁ
authors.lastname: Luengo-Oroz
authors.forename: Louise
authors.initials: L
authors.lastname: Douloquin
authors.forename: Thierry
authors.initials: T
authors.lastname: Savy
authors.forename: Camilo
authors.initials: C
authors.lastname: Melani
authors.forename: Sophie
authors.initials: S
authors.lastname: Desnoulez
authors.forename: Paul
authors.initials: P
authors.lastname: Bourgine
authors.forename: Nadine
authors.initials: N
authors.lastname: Peyriéras
authors.forename: María Jesús
authors.initials: MJ
authors.lastname: Ledesma-Carbayo
authors.forename: Andrés
authors.initials: A
authors.lastname: Santos
mesh_terms: D000465:Algorithms; D000818:Animals; D030801:Animals, Genetically Modified; D017173:Caenorhabditis elegans; D002460:Cell Line; D019070:Cell Lineage; D002467:Cell Nucleus / Q000378:metabolism; D049109:Cell Proliferation; D004331:Drosophila melanogaster; D004625:Embryo, Nonmammalian; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional; D013997:Time Factors