title: Deciphering tissue morphodynamics using bioimage informatics.
abstract: In recent years developmental biology has greatly benefited from the latest advances in fluorescence microscopy techniques. Consequently, quantitative and automated analysis of this data is becoming a vital first step in the quest for novel insights into the various aspects of development. Here we present an introductory overview of the various image analysis methods proposed for developmental biology images, with particular attention to openly available software packages. These tools, as well as others to come, are rapidly paving the way towards standardized and reproducible bioimaging studies at the whole-tissue level. Reflecting on these achievements, we discuss the remaining challenges and the future endeavours lying ahead in the post-image analysis era.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'.
authors.affiliation: Institut Pasteur, Bioimage Analysis Unit, 25-28 rue du Docteur Roux, Paris, France adufour@pasteur.fr.|CNRS, UMR 3691, 25-28 rue du Docteur Roux, Paris, France.
authors.forename: Alexandre C
authors.identifier: http://orcid.org/0000-0002-9417-7389
authors.initials: AC
authors.lastname: Dufour
authors.affiliation: INSERM US14, 96 rue Didot, Paris, France.
authors.forename: Anneliene H
authors.identifier: http://orcid.org/0000-0001-5883-7610
authors.initials: AH
authors.lastname: Jonker
authors.affiliation: Institut Pasteur, Bioimage Analysis Unit, 25-28 rue du Docteur Roux, Paris, France jcolivo@pasteur.fr.|CNRS, UMR 3691, 25-28 rue du Docteur Roux, Paris, France.
authors.forename: Jean-Christophe
authors.identifier: http://orcid.org/0000-0001-6796-0696
authors.initials: JC
authors.lastname: Olivo-Marin
mesh_terms: D015509:Developmental Biology / Q000295:instrumentation / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods; D009024:Morphogenesis; D063245:Plant Development; D012984:Software
keywords: bioimage informatics; cell segmentation; cell tracking; reproducible research; software