title: Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks.
abstract: Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states.
authors: School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, U.K.
authors: Timothy
authors: T
authors: Grocott
authors: School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, U.K.
authors: Paul
authors: P
authors: Thomas
authors: School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, U.K.
authors: Andrea E
authors: AE
authors: Münsterberg
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D030161:Avian Proteins / Q000235:genetics* / Q000378:metabolism; D002642:Chick Embryo; D066264:Datasets as Topic; D048049:Extracellular Signal-Regulated MAP Kinases / Q000235:genetics / Q000378:metabolism; D005123:Eye / Q000196:embryology / Q000378:metabolism* / Q000648:ultrastructure; D005455:Fluorescent Antibody Technique; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional / Q000379:methods* / Q000706:statistics & numerical data; D038081:Organogenesis / Q000235:genetics*; D000071841:PAX6 Transcription Factor / Q000235:genetics / Q000378:metabolism; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D051785:Smad Proteins / Q000235:genetics / Q000378:metabolism; D051176:beta Catenin / Q000235:genetics / Q000378:metabolism
chemical_list: D030161:Avian Proteins; D000071841:PAX6 Transcription Factor; D010750:Phosphoproteins; D051785:Smad Proteins; D051176:beta Catenin; D048049:Extracellular Signal-Regulated MAP Kinases